[1] "ofn"       "-oTGBM-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/GBM-TP/15078636/GBM-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/GBM-TP/15096483/transformed.cor.cli.txt"

nPatients in clinical file=592, in cluster file=577, common to both=570
[1]  82 570
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               81               489 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               81               489 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               88               482 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               88               482 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               37               533 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               37               533 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               36               534 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               36               534 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               57               513 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               57               513 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               63               507 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               63               507 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               36               534 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               36               534 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               33               537 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               33               537 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               49               521 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               49               521 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               41               529 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               41               529 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               24               546 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               24               546 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               23               547 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               23               547 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              462               108 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              462               108 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              467               103 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              467               103 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               52               518 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               52               518 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               59               511 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               59               511 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               47               523 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               47               523 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               70               500 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               70               500 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                13                557 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                13                557 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 3                567 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 3                567 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                17                553 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                17                553 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                14                556 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                14                556 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                59                511 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                59                511 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                48                522 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                48                522 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                10                560 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                10                560 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                22                548 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                22                548 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                24                546 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                24                546 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                38                532 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                38                532 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                37                533 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                37                533 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                48                522 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                48                522 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                59                511 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                59                511 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                57                513 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                57                513 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                57                513 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                57                513 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
               222                348 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
               222                348 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
               196                374 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
               196                374 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               220                350 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               220                350 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               218                352 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               218                352 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                63                507 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                63                507 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                34                536 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                34                536 
[1] "XP GAIN MUTATION ANALYSIS"
[1] 3
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               15               555 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               15               555 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               16               554 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               16               554 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               15               555 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               15               555 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               14               556 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               14               556 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               31               539 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               31               539 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               31               539 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               31               539 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               40               530 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               40               530 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               34               536 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               34               536 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               53               517 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               53               517 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               54               516 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               54               516 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               42               528 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               42               528 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               43               527 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               43               527 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               86               484 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               86               484 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              124               446 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              124               446 
[1] "7P LOSS MUTATION ANALYSIS"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                8               562 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                8               562 
[1] "7Q LOSS MUTATION ANALYSIS"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                6               564 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                6               564 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               58               512 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               58               512 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               42               528 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               42               528 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              198               372 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              198               372 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               93               477 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               93               477 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               476                 94 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               476                 94 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               487                 83 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               487                 83 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                99                471 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                99                471 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                93                477 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                93                477 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                58                512 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                58                512 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                57                513 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                57                513 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               184                386 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               184                386 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               145                425 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               145                425 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               105                465 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               105                465 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                63                507 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                63                507 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                82                488 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                82                488 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                63                507 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                63                507 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                40                530 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                40                530 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                70                500 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                70                500 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                62                508 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                62                508 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                27                543 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                27                543 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                35                535 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                35                535 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                18                552 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                18                552 
[1] "20Q LOSS MUTATION ANALYSIS"
[1] 3
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                16                554 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                16                554 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                42                528 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                42                528 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               181                389 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               181                389 
[1] "XP LOSS MUTATION ANALYSIS"
[1] 3
  XP LOSS MUTATED XP LOSS WILD-TYPE 
              113               457 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
              113               457 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
              105               465 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
              105               465 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                        
 [2] "VITAL_STATUS"                          
 [3] "DAYS_TO_DEATH"                         
 [4] "DAYS_TO_LAST_FOLLOWUP"                 
 [5] "PRIMARY_SITE_OF_DISEASE"               
 [6] "DCC_UPLOAD_DATE"                       
 [7] "GENDER"                                
 [8] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"  
 [9] "RADIATION_THERAPY"                     
[10] "KARNOFSKY_PERFORMANCE_SCORE"           
[11] "HISTOLOGICAL_TYPE"                     
[12] "RADIATIONS_RADIATION_REGIMENINDICATION"
[13] "RACE"                                  
[14] "ETHNICITY"                             
[15] "BATCH_NUMBER"                          

Input Data has 15 rows and 570 columns.

[1] "Batch" "15"   
[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=72,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=372,	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=398,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'PRIMARY_SITE_OF_DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PRIMARY_SITE_OF_DISEASE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'DCC_UPLOAD_DATE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "DCC_UPLOAD_DATE excluded in the analysis because there is no case of (both >= 3) in the table below"
              17-7-2014 26-3-2015 6-11-2014
freq.values   "1"       "568"     "1"      
freq.contrast "569"     "2"       "569"    
both >= 3     "FALSE"   "FALSE"   "FALSE"  
Variable 7:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=25,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 9:'RADIATION_THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_THERAPY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 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:'RADIATIONS_RADIATION_REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'BATCH_NUMBER':	nDistinctValues=22,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] NA
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "****** SUMMARY ***** "
Output Data has 570 columns, 1 survival variables, and 7 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
[1] "YEARS_TO_BIRTH"                        
[2] "GENDER"                                
[3] "KARNOFSKY_PERFORMANCE_SCORE"           
[4] "HISTOLOGICAL_TYPE"                     
[5] "RADIATIONS_RADIATION_REGIMENINDICATION"
[6] "RACE"                                  
[7] "ETHNICITY"                             
YEARS_TO_BIRTH, nv=72, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY_PERFORMANCE_SCORE, nv=7, binary=FALSE, numeric=TRUE
HISTOLOGICAL_TYPE, nv=3, binary=FALSE, numeric=FALSE
RADIATIONS_RADIATION_REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
RACE, nv=3, 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    15  66
  1P GAIN WILD-TYPE  89 399
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               81               488 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               66               399 
$`1P GAIN MUTATED`
TCGA-02-0001 TCGA-02-0052 TCGA-02-0055 TCGA-02-0106 TCGA-02-0113 TCGA-02-0266 
       11.77        12.59         2.50        11.67        92.65        17.72 
TCGA-02-0330 TCGA-02-0332 TCGA-02-0451 TCGA-02-0456 TCGA-02-2483 TCGA-06-0128 
       15.91        25.71        16.21         3.35        15.32        22.72 
TCGA-06-0130 TCGA-06-0133 TCGA-06-0152 TCGA-06-0168 TCGA-06-0177 TCGA-06-0182 
       12.95        14.30        12.33        19.66         4.18         3.65 
TCGA-06-0188 TCGA-06-0192 TCGA-06-0195 TCGA-06-0206 TCGA-06-0209 TCGA-06-0216 
       44.58        38.96         7.40         7.66         7.63        24.16 
TCGA-06-0237 TCGA-06-0410 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 TCGA-06-0649 
       13.64         4.70        35.11        12.62         5.75         2.10 
TCGA-06-1084 TCGA-06-1087 TCGA-06-2557 TCGA-06-5856 TCGA-06-6698 TCGA-08-0349 
       23.93         4.04         1.08         3.75         4.77         9.80 
TCGA-08-0350 TCGA-08-0386 TCGA-08-0531 TCGA-12-0619 TCGA-12-0662 TCGA-12-0773 
       29.23        18.02         7.56        34.92        38.17        43.23 
TCGA-12-0826 TCGA-12-1090 TCGA-12-1098 TCGA-12-1099 TCGA-12-1598 TCGA-12-3653 
       27.78         7.59         3.98         4.14        15.65        14.53 
TCGA-14-0783 TCGA-14-0813 TCGA-14-0817 TCGA-14-0867 TCGA-14-1034 TCGA-14-1452 
        6.21         1.35         5.39         2.04        15.95         7.10 
TCGA-14-1454 TCGA-14-1794 TCGA-14-1823 TCGA-14-1827 TCGA-14-3477 TCGA-15-0742 
       30.18         0.99        17.85         5.88         3.78        13.78 
TCGA-15-1447 TCGA-15-1449 TCGA-19-0962 TCGA-19-1786 TCGA-19-1787 TCGA-19-2625 
       53.19        13.28         0.66         7.17        12.66         4.08 
TCGA-19-4065 TCGA-26-1440 TCGA-26-5132 TCGA-26-6173 TCGA-28-1752 TCGA-28-2509 
        7.04         9.73         9.40         7.92         8.48         4.77 
TCGA-28-5207 TCGA-28-5216 TCGA-32-1970 TCGA-32-1987 TCGA-32-2634 TCGA-32-4210 
       11.28        13.64        15.39        14.86        22.78         3.72 
TCGA-32-5222 TCGA-74-6584 TCGA-76-4934 
       19.23         7.50         2.53 

$`1P GAIN WILD-TYPE`
TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 TCGA-02-0011 
        4.73        18.35        23.18        10.59        35.41        20.71 
TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0024 
       82.59        20.61        87.06        77.65        20.12        53.10 
TCGA-02-0025 TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 
       42.74        24.59        12.16        90.58         2.83        14.14 
TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 
        3.62        10.72        10.52        18.31         6.87        14.73 
TCGA-02-0048 TCGA-02-0051 TCGA-02-0054 TCGA-02-0057 TCGA-02-0058 TCGA-02-0059 
        3.22        15.09         6.54        19.86         8.35         9.57 
TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 TCGA-02-0069 TCGA-02-0070 TCGA-02-0071 
        6.02        19.73        26.43        28.70        25.05         5.49 
TCGA-02-0074 TCGA-02-0075 TCGA-02-0079 TCGA-02-0080 TCGA-02-0083 TCGA-02-0084 
       10.19        20.84        27.25        89.72        22.72        12.62 
TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 
       51.32         8.81        57.76        16.96         3.48        27.02 
TCGA-02-0104 TCGA-02-0107 TCGA-02-0111 TCGA-02-0114 TCGA-02-0115 TCGA-02-0116 
       65.00        17.65        23.18        99.98        15.65        48.95 
TCGA-02-0258 TCGA-02-0260 TCGA-02-0269 TCGA-02-0271 TCGA-02-0281 TCGA-02-0285 
       16.54        16.93        10.75        14.47         3.98        13.87 
TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 
       14.20        15.95        12.23         9.90         7.73        10.62 
TCGA-02-0326 TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 
        7.33         4.37        25.12        10.59        12.39        14.50 
TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 TCGA-02-2466 TCGA-02-2470 
       10.55        47.11        11.34         9.27        16.80        12.92 
TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 
       15.45        20.32         2.70         6.15        20.38        47.61 
TCGA-06-0126 TCGA-06-0127 TCGA-06-0129 TCGA-06-0132 TCGA-06-0137 TCGA-06-0138 
        6.94         3.98        33.67        25.35        26.70        24.23 
TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 
       11.90         0.20        10.29         2.20        11.74         2.33 
TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 
       20.09        17.79        10.09         8.61        19.46        46.59 
TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 
       13.94        10.45         3.19        10.82         9.44        11.80 
TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0169 TCGA-06-0171 
        3.42        56.91        10.65         5.85         3.29        13.12 
TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0178 TCGA-06-0179 
        4.47         3.22         4.04        91.00        88.14        20.25 
TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0189 TCGA-06-0190 TCGA-06-0194 
       69.90        73.84        27.22        15.42        10.42         4.67 
TCGA-06-0197 TCGA-06-0201 TCGA-06-0208 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 
        5.56         0.39         8.42         7.40        11.84         0.53 
TCGA-06-0214 TCGA-06-0219 TCGA-06-0221 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 
       15.02         0.72        19.82        13.32        20.42        48.69 
TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0412 TCGA-06-0413 
       10.82         9.01         0.26        72.36         9.57         3.16 
TCGA-06-0646 TCGA-06-0648 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 
        5.75         9.80        23.57        14.20        26.40        46.88 
TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 
        7.86         2.70         2.70         0.92        43.46        46.19 
TCGA-06-0877 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 
        5.65         7.17        40.41        16.57        20.78        26.76 
TCGA-06-1086 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 
        6.84        26.79        11.84        15.32        13.61        33.90 
TCGA-06-1806 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 
       15.32        12.49         4.93        17.65        12.56        30.64 
TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 
        5.95        16.64         5.98         4.37         0.43        31.50 
TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 
       11.74         3.55         8.35         4.54         8.81         8.98 
TCGA-06-5415 TCGA-06-5416 TCGA-06-5418 TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 
        8.55         6.71         2.73         6.15         4.57         5.23 
TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 
        7.79         5.39         1.48       120.56         7.36         8.32 
TCGA-06-6697 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A5U1 
       12.85         1.55         4.77         4.96         4.70         1.87 
TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK TCGA-06-A7TL TCGA-08-0244 TCGA-08-0245 
        3.12         2.56         5.39         5.42        22.68        37.84 
TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 
        4.18       115.86         1.74         8.42        25.71        12.16 
TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 
       65.33         1.28         8.42        17.95        24.56        31.10 
TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0389 
       37.58        22.29         3.39        12.23        14.93        15.35 
TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 
       13.97         0.72        12.56         4.27        42.15        11.08 
TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 
       19.59        58.68        19.33        10.75         4.80         7.27 
TCGA-08-0525 TCGA-08-0529 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0620 
       15.98        18.41        15.35        14.73        12.99        10.45 
TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 
        7.59        94.78         0.10        25.97        26.66        12.13 
TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0775 
        3.65        20.38        28.41        15.06        53.85         7.63 
TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 
        9.73        14.93        14.86        91.76        24.79        18.48 
TCGA-12-0821 TCGA-12-0822 TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 
       10.62        23.51        38.76         8.94        20.58       127.59 
TCGA-12-1089 TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 
        5.82        33.21        21.73        15.98        12.23        15.85 
TCGA-12-1096 TCGA-12-1097 TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 
        9.11        14.53        25.68        14.73         6.77        59.77 
TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 
       44.02        26.93        15.22        10.95        12.69        34.92 
TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 
       14.93         3.22         2.04        15.12        11.97         0.95 
TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 TCGA-14-0812 TCGA-14-0862 
       23.05         2.24        11.24        13.78         3.25         2.89 
TCGA-14-0865 TCGA-14-0866 TCGA-14-0871 TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 
       16.50        26.33        28.93        19.30         0.79         1.38 
TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 TCGA-14-1453 
        1.12         3.75        32.05        58.78        23.11         1.15 
TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 TCGA-14-1795 TCGA-14-1821 
        0.92        40.96         6.67        12.43         1.97        17.79 
TCGA-14-1825 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-4157 TCGA-15-1444 
        7.63         7.17        17.49         7.96         3.42        50.53 
TCGA-15-1446 TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 
       19.10         3.91        17.59        26.07        16.37         4.31 
TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 
       29.03         4.57        10.29        14.01         9.14        21.24 
TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 TCGA-19-0963 
       13.97         6.41        11.77        21.90         8.61        14.27 
TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 TCGA-19-1388 TCGA-19-1389 
        3.39        10.75         9.07         5.95        12.95         4.64 
TCGA-19-1390 TCGA-19-1392 TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 
       25.38         3.65         3.25         0.13         9.67         4.87 
TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 TCGA-19-2629 TCGA-19-2631 TCGA-19-5947 
        1.08         7.53         0.16        24.23         7.00         6.64 
TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 
       17.19         8.02        18.90         4.73        12.10         1.78 
TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J4 
       22.49        14.07        16.80        14.96        17.79         3.98 
TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 
       28.54        10.03        13.87        31.33         7.13         9.37 
TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 TCGA-26-6174 
       14.86         5.49         8.88        18.97         1.58         2.33 
TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 
       19.33         5.06        16.60         9.86        24.23        40.54 
TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 
       21.30        30.05        14.04        11.51        24.76        10.39 
TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 
       10.39        16.08         7.59         2.86        14.40        15.78 
TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 TCGA-28-1753 
        0.20         2.53         9.21         8.35         7.63         1.22 
TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 TCGA-28-2502 TCGA-28-2506 TCGA-28-2513 
        1.55         2.83         0.13         0.66         6.74         7.30 
TCGA-28-2514 TCGA-28-5204 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 
        5.26        14.93        17.88        14.53        11.77        31.27 
TCGA-28-5214 TCGA-28-5215 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 
       23.44        11.01         5.16        22.68        12.76         5.42 
TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 TCGA-32-1980 
       21.07         0.49         0.10        15.85        19.50         1.18 
TCGA-32-1982 TCGA-32-1986 TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 
        4.67        12.69        16.93        12.23        20.78        15.02 
TCGA-32-2615 TCGA-32-2616 TCGA-32-2632 TCGA-32-2638 TCGA-32-4208 TCGA-32-4211 
       15.95         7.36         8.84        25.18        21.14        12.59 
TCGA-32-4213 TCGA-32-4719 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 
       19.86        10.85         0.85        13.35         8.94         9.53 
TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 
        0.99         4.44        11.84         0.20        15.12        12.46 
TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 
        4.14        14.76         3.45        20.91         4.34        14.33 
TCGA-74-6581 TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 
        8.22         4.80         4.54         3.09         3.65         9.17 
TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 
       10.78        16.70         3.29         2.70        11.38        17.06 
TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 
        8.35        20.98         4.83         5.03         0.23         9.27 
TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R 
        7.73         7.79         1.61        17.72        26.30         5.92 
TCGA-RR-A6KA TCGA-RR-A6KC 
        6.28        20.55 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             0.66              0.10 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            92.65            127.59 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
           11.670            11.935 
[1] "0.7 - 92.7 (11.7)"  "0.1 - 127.6 (11.9)"
[1] "hr=" "1.1"
D1V2, continuous
D1V3, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    34  47
  1P GAIN WILD-TYPE 190 299
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     34   47
  1P GAIN WILD-TYPE  190  299
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE              34               190
  MALE                47               299
[1] 2 2
[1] FALSE
D1V4, continuous
                   vv
clus                GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  1P GAIN MUTATED                               0                   1
  1P GAIN WILD-TYPE                            27                  17
                   vv
clus                UNTREATED PRIMARY (DE NOVO) GBM
  1P GAIN MUTATED                                80
  1P GAIN WILD-TYPE                             445
D1V5, multiclass
                                 clus
vv                                1P GAIN MUTATED 1P GAIN WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                 0                27
  TREATED PRIMARY GBM                           1                17
  UNTREATED PRIMARY (DE NOVO) GBM              80               445
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V6, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    59  22
  1P GAIN WILD-TYPE 323 166
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     59   22
  1P GAIN WILD-TYPE  323  166
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  NO               59               323
  YES              22               166
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1P GAIN MUTATED       2                         6    68
  1P GAIN WILD-TYPE    11                        43   417
D1V7, multiclass
                           clus
vv                          1P GAIN MUTATED 1P GAIN WILD-TYPE
  ASIAN                                   2                11
  BLACK OR AFRICAN AMERICAN               6                43
  WHITE                                  68               417
[1] 3 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     2  62
  1P GAIN WILD-TYPE  10 410
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      2   62
  1P GAIN WILD-TYPE   10  410
                        clus
vv                       1P GAIN MUTATED 1P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                10
  NOT HISPANIC OR LATINO              62               410
[1] 2 2
[1] FALSE

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                 0   1
  1Q GAIN MUTATED    18  70
  1Q GAIN WILD-TYPE  86 395
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               88               481 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               70               395 
$`1Q GAIN MUTATED`
TCGA-02-0001 TCGA-02-0024 TCGA-02-0052 TCGA-02-0055 TCGA-02-0106 TCGA-02-0113 
       11.77        53.10        12.59         2.50        11.67        92.65 
TCGA-02-0266 TCGA-02-0330 TCGA-02-0451 TCGA-02-0456 TCGA-02-2483 TCGA-06-0128 
       17.72        15.91        16.21         3.35        15.32        22.72 
TCGA-06-0130 TCGA-06-0133 TCGA-06-0152 TCGA-06-0168 TCGA-06-0177 TCGA-06-0182 
       12.95        14.30        12.33        19.66         4.18         3.65 
TCGA-06-0188 TCGA-06-0192 TCGA-06-0195 TCGA-06-0206 TCGA-06-0209 TCGA-06-0216 
       44.58        38.96         7.40         7.66         7.63        24.16 
TCGA-06-0237 TCGA-06-0409 TCGA-06-0410 TCGA-06-0414 TCGA-06-0645 TCGA-06-0649 
       13.64        72.36         4.70        35.11         5.75         2.10 
TCGA-06-1084 TCGA-06-1087 TCGA-06-2557 TCGA-06-2569 TCGA-06-5856 TCGA-06-6698 
       23.93         4.04         1.08         0.43         3.75         4.77 
TCGA-06-A5U0 TCGA-08-0349 TCGA-08-0350 TCGA-08-0386 TCGA-08-0524 TCGA-08-0531 
        4.70         9.80        29.23        18.02         7.27         7.56 
TCGA-12-0619 TCGA-12-0662 TCGA-12-0773 TCGA-12-0826 TCGA-12-0827 TCGA-12-1090 
       34.92        38.17        43.23        27.78        38.76         7.59 
TCGA-12-1098 TCGA-12-1099 TCGA-12-1598 TCGA-12-3653 TCGA-14-0783 TCGA-14-0813 
        3.98         4.14        15.65        14.53         6.21         1.35 
TCGA-14-0817 TCGA-14-0865 TCGA-14-0867 TCGA-14-0871 TCGA-14-1452 TCGA-14-1454 
        5.39        16.50         2.04        28.93         7.10        30.18 
TCGA-14-1794 TCGA-14-1823 TCGA-14-3477 TCGA-15-0742 TCGA-15-1447 TCGA-15-1449 
        0.99        17.85         3.78        13.78        53.19        13.28 
TCGA-19-0962 TCGA-19-1786 TCGA-19-1791 TCGA-19-2625 TCGA-19-4065 TCGA-26-1440 
        0.66         7.17         0.13         4.08         7.04         9.73 
TCGA-26-5132 TCGA-26-6173 TCGA-28-1752 TCGA-28-2509 TCGA-28-5207 TCGA-28-5216 
        9.40         7.92         8.48         4.77        11.28        13.64 
TCGA-28-5218 TCGA-32-1970 TCGA-32-1987 TCGA-32-2632 TCGA-32-2634 TCGA-32-4210 
        5.16        15.39        14.86         8.84        22.78         3.72 
TCGA-32-5222 TCGA-41-5651 TCGA-74-6584 TCGA-76-4934 
       19.23        15.12         7.50         2.53 

$`1Q GAIN WILD-TYPE`
TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 TCGA-02-0011 
        4.73        18.35        23.18        10.59        35.41        20.71 
TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0025 
       82.59        20.61        87.06        77.65        20.12        42.74 
TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 
       24.59        12.16        90.58         2.83        14.14         3.62 
TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 TCGA-02-0048 
       10.72        10.52        18.31         6.87        14.73         3.22 
TCGA-02-0051 TCGA-02-0054 TCGA-02-0057 TCGA-02-0058 TCGA-02-0059 TCGA-02-0060 
       15.09         6.54        19.86         8.35         9.57         6.02 
TCGA-02-0064 TCGA-02-0068 TCGA-02-0069 TCGA-02-0070 TCGA-02-0071 TCGA-02-0074 
       19.73        26.43        28.70        25.05         5.49        10.19 
TCGA-02-0075 TCGA-02-0079 TCGA-02-0080 TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 
       20.84        27.25        89.72        22.72        12.62        51.32 
TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 TCGA-02-0104 
        8.81        57.76        16.96         3.48        27.02        65.00 
TCGA-02-0107 TCGA-02-0111 TCGA-02-0114 TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 
       17.65        23.18        99.98        15.65        48.95        16.54 
TCGA-02-0260 TCGA-02-0269 TCGA-02-0271 TCGA-02-0281 TCGA-02-0285 TCGA-02-0289 
       16.93        10.75        14.47         3.98        13.87        14.20 
TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 
       15.95        12.23         9.90         7.73        10.62         7.33 
TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 
       25.71         4.37        25.12        10.59        12.39        14.50 
TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 TCGA-02-2466 TCGA-02-2470 
       10.55        47.11        11.34         9.27        16.80        12.92 
TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 
       15.45        20.32         2.70         6.15        20.38        47.61 
TCGA-06-0126 TCGA-06-0127 TCGA-06-0129 TCGA-06-0132 TCGA-06-0137 TCGA-06-0138 
        6.94         3.98        33.67        25.35        26.70        24.23 
TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 
       11.90         0.20        10.29         2.20        11.74         2.33 
TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 
       20.09        17.79        10.09         8.61        19.46        46.59 
TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 
       13.94        10.45         3.19        10.82         9.44        11.80 
TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0169 TCGA-06-0171 
        3.42        56.91        10.65         5.85         3.29        13.12 
TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0178 TCGA-06-0179 
        4.47         3.22         4.04        91.00        88.14        20.25 
TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0189 TCGA-06-0190 TCGA-06-0194 
       69.90        73.84        27.22        15.42        10.42         4.67 
TCGA-06-0197 TCGA-06-0201 TCGA-06-0208 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 
        5.56         0.39         8.42         7.40        11.84         0.53 
TCGA-06-0214 TCGA-06-0219 TCGA-06-0221 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 
       15.02         0.72        19.82        13.32        20.42        48.69 
TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0412 TCGA-06-0413 TCGA-06-0644 
       10.82         9.01         0.26         9.57         3.16        12.62 
TCGA-06-0646 TCGA-06-0648 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 
        5.75         9.80        23.57        14.20        26.40        46.88 
TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 
        7.86         2.70         2.70         0.92        43.46        46.19 
TCGA-06-0877 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 
        5.65         7.17        40.41        16.57        20.78        26.76 
TCGA-06-1086 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 
        6.84        26.79        11.84        15.32        13.61        33.90 
TCGA-06-1806 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 
       15.32        12.49         4.93        17.65        12.56        30.64 
TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2570 TCGA-06-5408 
        5.95        16.64         5.98         4.37        31.50        11.74 
TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 
        3.55         8.35         4.54         8.81         8.98         8.55 
TCGA-06-5416 TCGA-06-5418 TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 TCGA-06-6389 
        6.71         2.73         6.15         4.57         5.23         7.79 
TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 
        5.39         1.48       120.56         7.36         8.32        12.85 
TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 
        1.55         4.77         4.96         1.87         3.12         2.56 
TCGA-06-A7TK TCGA-06-A7TL TCGA-08-0244 TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 
        5.39         5.42        22.68        37.84         4.18       115.86 
TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0351 TCGA-08-0352 
        1.74         8.42        25.71        12.16        65.33         1.28 
TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 
        8.42        17.95        24.56        31.10        37.58        22.29 
TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 
        3.39        12.23        14.93        15.35        13.97         0.72 
TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 
       12.56         4.27        42.15        11.08        19.59        58.68 
TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0525 TCGA-08-0529 TCGA-12-0615 
       19.33        10.75         4.80        15.98        18.41        15.35 
TCGA-12-0616 TCGA-12-0618 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 
       14.73        12.99        10.45         7.59        94.78         0.10 
TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 
       25.97        26.66        12.13         3.65        20.38        28.41 
TCGA-12-0769 TCGA-12-0772 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 
       15.06        53.85         7.63         9.73        14.93        14.86 
TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 TCGA-12-0828 
       91.76        24.79        18.48        10.62        23.51         8.94 
TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 
       20.58       127.59         5.82        33.21        21.73        15.98 
TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1599 TCGA-12-1600 
       12.23        15.85         9.11        14.53        25.68        14.73 
TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 
        6.77        59.77        44.02        26.93        15.22        10.95 
TCGA-12-3651 TCGA-12-3652 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 
       12.69        34.92        14.93         3.22         2.04        15.12 
TCGA-14-0740 TCGA-14-0781 TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 
       11.97         0.95        23.05         2.24        11.24        13.78 
TCGA-14-0812 TCGA-14-0862 TCGA-14-0866 TCGA-14-1034 TCGA-14-1037 TCGA-14-1043 
        3.25         2.89        26.33        15.95        19.30         0.79 
TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 
        1.38         1.12         3.75        32.05        58.78        23.11 
TCGA-14-1453 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 TCGA-14-1795 
        1.15         0.92        40.96         6.67        12.43         1.97 
TCGA-14-1821 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 
       17.79         7.63         5.88         7.17        17.49         7.96 
TCGA-14-4157 TCGA-15-1444 TCGA-15-1446 TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 
        3.42        50.53        19.10         3.91        17.59        26.07 
TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 
       16.37         4.31        29.03         4.57        10.29        14.01 
TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 
        9.14        21.24        13.97         6.41        11.77        21.90 
TCGA-19-0960 TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 
        8.61        14.27         3.39        10.75         9.07         5.95 
TCGA-19-1388 TCGA-19-1389 TCGA-19-1390 TCGA-19-1392 TCGA-19-1787 TCGA-19-1789 
       12.95         4.64        25.38         3.65        12.66         3.25 
TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 TCGA-19-2629 
        9.67         4.87         1.08         7.53         0.16        24.23 
TCGA-19-2631 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 
        7.00         6.64        17.19         8.02        18.90         4.73 
TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 
       12.10         1.78        22.49        14.07        16.80        14.96 
TCGA-19-A60I TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1442 
       17.79         3.98        28.54        10.03        13.87        31.33 
TCGA-26-1443 TCGA-26-1799 TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 
        7.13         9.37        14.86         5.49         8.88        18.97 
TCGA-26-5139 TCGA-26-6174 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 
        1.58         2.33        19.33         5.06        16.60         9.86 
TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 
       24.23        40.54        21.30        30.05        14.04        11.51 
TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 
       24.76        10.39        10.39        16.08         7.59         2.86 
TCGA-27-2527 TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 
       14.40        15.78         0.20         2.53         9.21         8.35 
TCGA-28-1751 TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 TCGA-28-2502 
        7.63         1.22         1.55         2.83         0.13         0.66 
TCGA-28-2506 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5208 TCGA-28-5209 
        6.74         7.30         5.26        14.93        17.88        14.53 
TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5219 TCGA-28-5220 
       11.77        31.27        23.44        11.01        22.68        12.76 
TCGA-28-6450 TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 
        5.42        21.07         0.49         0.10        15.85        19.50 
TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 
        1.18         4.67        12.69        16.93        12.23        20.78 
TCGA-32-2495 TCGA-32-2615 TCGA-32-2616 TCGA-32-2638 TCGA-32-4208 TCGA-32-4211 
       15.02        15.95         7.36        25.18        21.14        12.59 
TCGA-32-4213 TCGA-32-4719 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 
       19.86        10.85         0.85        13.35         8.94         9.53 
TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-41-6646 TCGA-4W-AA9S 
        0.99         4.44        11.84         0.20        12.46         4.14 
TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 
       14.76         3.45        20.91         4.34        14.33         8.22 
TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-4935 
        4.80         4.54         3.09         3.65         9.17        10.78 
TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 
       16.70         3.29         2.70        11.38        17.06         8.35 
TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 
       20.98         4.83         5.03         0.23         9.27         7.73 
TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R TCGA-RR-A6KA 
        7.79         1.61        17.72        26.30         5.92         6.28 
TCGA-RR-A6KC 
       20.55 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             0.13              0.10 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            92.65            127.59 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            10.54             12.10 
[1] "0.1 - 92.7 (10.5)"  "0.1 - 127.6 (12.1)"
[1] "hr=" "1"  
D2V2, continuous
D2V3, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    39  49
  1Q GAIN WILD-TYPE 185 297
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     39   49
  1Q GAIN WILD-TYPE  185  297
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE              39               185
  MALE                49               297
[1] 2 2
[1] FALSE
D2V4, continuous
                   vv
clus                GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  1Q GAIN MUTATED                               1                   2
  1Q GAIN WILD-TYPE                            26                  16
                   vv
clus                UNTREATED PRIMARY (DE NOVO) GBM
  1Q GAIN MUTATED                                85
  1Q GAIN WILD-TYPE                             440
D2V5, multiclass
                                 clus
vv                                1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                 1                26
  TREATED PRIMARY GBM                           2                16
  UNTREATED PRIMARY (DE NOVO) GBM              85               440
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V6, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    63  25
  1Q GAIN WILD-TYPE 319 163
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     63   25
  1Q GAIN WILD-TYPE  319  163
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  NO               63               319
  YES              25               163
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1Q GAIN MUTATED       2                         9    73
  1Q GAIN WILD-TYPE    11                        40   412
D2V7, multiclass
                           clus
vv                          1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  ASIAN                                   2                11
  BLACK OR AFRICAN AMERICAN               9                40
  WHITE                                  73               412
[1] 3 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     2  68
  1Q GAIN WILD-TYPE  10 404
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      2   68
  1Q GAIN WILD-TYPE   10  404
                        clus
vv                       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                10
  NOT HISPANIC OR LATINO              68               404
[1] 2 2
[1] FALSE

Clustering(3) Variable = 2P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                 0   1
  2P GAIN MUTATED     5  32
  2P GAIN WILD-TYPE  99 433
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               37               532 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               32               433 
$`2P GAIN MUTATED`
TCGA-02-0001 TCGA-02-0106 TCGA-02-0113 TCGA-02-0281 TCGA-06-0133 TCGA-06-0151 
       11.77        11.67        92.65         3.98        14.30        46.59 
TCGA-06-0192 TCGA-06-0216 TCGA-06-0649 TCGA-06-0877 TCGA-06-1086 TCGA-06-1802 
       38.96        24.16         2.10         5.65         6.84        15.32 
TCGA-06-2557 TCGA-06-2569 TCGA-06-6391 TCGA-08-0346 TCGA-08-0386 TCGA-08-0510 
        1.08         0.43         1.48         8.42        18.02         4.27 
TCGA-08-0517 TCGA-08-0524 TCGA-12-0778 TCGA-12-1099 TCGA-12-3653 TCGA-14-0817 
       58.68         7.27        14.93         4.14        14.53         5.39 
TCGA-14-0871 TCGA-14-1453 TCGA-14-1823 TCGA-14-3477 TCGA-16-0846 TCGA-19-0957 
       28.93         1.15        17.85         3.78         3.91        21.90 
TCGA-19-1786 TCGA-19-2629 TCGA-26-1439 TCGA-27-1834 TCGA-28-5218 TCGA-32-4210 
        7.17        24.23        13.87        40.54         5.16         3.72 
TCGA-74-6584 
        7.50 

$`2P GAIN WILD-TYPE`
TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 TCGA-02-0011 
        4.73        18.35        23.18        10.59        35.41        20.71 
TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0024 
       82.59        20.61        87.06        77.65        20.12        53.10 
TCGA-02-0025 TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 
       42.74        24.59        12.16        90.58         2.83        14.14 
TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 
        3.62        10.72        10.52        18.31         6.87        14.73 
TCGA-02-0048 TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 TCGA-02-0055 TCGA-02-0057 
        3.22        15.09        12.59         6.54         2.50        19.86 
TCGA-02-0058 TCGA-02-0059 TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 TCGA-02-0069 
        8.35         9.57         6.02        19.73        26.43        28.70 
TCGA-02-0070 TCGA-02-0071 TCGA-02-0074 TCGA-02-0075 TCGA-02-0079 TCGA-02-0080 
       25.05         5.49        10.19        20.84        27.25        89.72 
TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 
       22.72        12.62        51.32         8.81        57.76        16.96 
TCGA-02-0099 TCGA-02-0102 TCGA-02-0104 TCGA-02-0107 TCGA-02-0111 TCGA-02-0114 
        3.48        27.02        65.00        17.65        23.18        99.98 
TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 TCGA-02-0266 TCGA-02-0269 
       15.65        48.95        16.54        16.93        17.72        10.75 
TCGA-02-0271 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 
       14.47        13.87        14.20        15.95        12.23         9.90 
TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 TCGA-02-0333 
        7.73        10.62         7.33        15.91        25.71         4.37 
TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 
       25.12        10.59        12.39        14.50        10.55        47.11 
TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 TCGA-02-2466 TCGA-02-2470 
       11.34         9.27        16.21         3.35        16.80        12.92 
TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 
       15.32        15.45        20.32         2.70         6.15        20.38 
TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 
       47.61         6.94         3.98        22.72        33.67        12.95 
TCGA-06-0132 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 
       25.35        26.70        24.23        11.90         0.20        10.29 
TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 
        2.20        11.74         2.33        20.09        17.79        10.09 
TCGA-06-0149 TCGA-06-0150 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 
        8.61        19.46        12.33        13.94        10.45         3.19 
TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 
       10.82         9.44        11.80         3.42        56.91        10.65 
TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 
        5.85        19.66         3.29        13.12         4.47         3.22 
TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 
        4.04        91.00         4.18        88.14        20.25         3.65 
TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 
       69.90        73.84        27.22        44.58        15.42        10.42 
TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 
        4.67         7.40         5.56         0.39         7.66         8.42 
TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0219 
        7.63         7.40        11.84         0.53        15.02         0.72 
TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 
       19.82        13.64        13.32        20.42        48.69        10.82 
TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 
        9.01         0.26        72.36         4.70         9.57         3.16 
TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0650 
       35.11        12.62         5.75         5.75         9.80        23.57 
TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 
       14.20        26.40        46.88         7.86         2.70         2.70 
TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 
        0.92        43.46        46.19         7.17        40.41        16.57 
TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 
       20.78        26.76        23.93         4.04        26.79        11.84 
TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 
       13.61        33.90        15.32        12.49         4.93        17.65 
TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 
       12.56        30.64         5.95        16.64         5.98         4.37 
TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 
       31.50        11.74         3.55         8.35         4.54         8.81 
TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 
        8.98         8.55         6.71         2.73         3.75         6.15 
TCGA-06-5859 TCGA-06-6388 TCGA-06-6389 TCGA-06-6390 TCGA-06-6693 TCGA-06-6694 
        4.57         5.23         7.79         5.39       120.56         7.36 
TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 
        8.32        12.85         4.77         1.55         4.77         4.96 
TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK TCGA-06-A7TL 
        4.70         1.87         3.12         2.56         5.39         5.42 
TCGA-08-0244 TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0347 
       22.68        37.84         4.18       115.86         1.74        25.71 
TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 
       12.16         9.80        29.23        65.33         1.28         8.42 
TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 
       17.95        24.56        31.10        37.58        22.29         3.39 
TCGA-08-0375 TCGA-08-0380 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 
       12.23        14.93        15.35        13.97         0.72        12.56 
TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 
       42.15        11.08        19.59        19.33        10.75         4.80 
TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 
       15.98        18.41         7.56        15.35        14.73        12.99 
TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 
       34.92        10.45         7.59        94.78         0.10        38.17 
TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 
       25.97        26.66        12.13         3.65        20.38        28.41 
TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0780 
       15.06        53.85        43.23         7.63         9.73        14.86 
TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 TCGA-12-0826 
       91.76        24.79        18.48        10.62        23.51        27.78 
TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 
       38.76         8.94        20.58       127.59         5.82         7.59 
TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 
       33.21        21.73        15.98        12.23        15.85         9.11 
TCGA-12-1097 TCGA-12-1098 TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 
       14.53         3.98        15.65        25.68        14.73         6.77 
TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 
       59.77        44.02        26.93        15.22        10.95        12.69 
TCGA-12-3652 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 
       34.92        14.93         3.22         2.04        15.12        11.97 
TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 
        0.95         6.21        23.05         2.24        11.24        13.78 
TCGA-14-0812 TCGA-14-0813 TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 TCGA-14-0867 
        3.25         1.35         2.89        16.50        26.33         2.04 
TCGA-14-1034 TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 
       15.95        19.30         0.79         1.38         1.12         3.75 
TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 TCGA-14-1452 TCGA-14-1454 TCGA-14-1455 
       32.05        58.78        23.11         7.10        30.18         0.92 
TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 
       40.96         6.67        12.43         0.99         1.97        17.79 
TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-4157 
        7.63         5.88         7.17        17.49         7.96         3.42 
TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 TCGA-16-0848 
       13.78        50.53        19.10        53.19        13.28        17.59 
TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 
       26.07        16.37         4.31        29.03         4.57        10.29 
TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 
       14.01         9.14        21.24        13.97         6.41        11.77 
TCGA-19-0960 TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 
        8.61         0.66        14.27         3.39        10.75         9.07 
TCGA-19-1387 TCGA-19-1388 TCGA-19-1389 TCGA-19-1390 TCGA-19-1392 TCGA-19-1787 
        5.95        12.95         4.64        25.38         3.65        12.66 
TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 
        3.25         0.13         9.67         4.87         1.08         7.53 
TCGA-19-2624 TCGA-19-2625 TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 
        0.16         4.08         7.00         7.04         6.64        17.19 
TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 
        8.02        18.90         4.73        12.10         1.78        22.49 
TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J4 TCGA-19-A6J5 
       14.07        16.80        14.96        17.79         3.98        28.54 
TCGA-26-1438 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 
       10.03         9.73        31.33         7.13         9.37         9.40 
TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 
       14.86         5.49         8.88        18.97         1.58         7.92 
TCGA-26-6174 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 
        2.33        19.33         5.06        16.60         9.86        24.23 
TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 
       21.30        30.05        14.04        11.51        24.76        10.39 
TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 
       10.39        16.08         7.59         2.86        14.40        15.78 
TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 TCGA-28-1752 
        0.20         2.53         9.21         8.35         7.63         8.48 
TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 TCGA-28-2502 TCGA-28-2506 
        1.22         1.55         2.83         0.13         0.66         6.74 
TCGA-28-2509 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 
        4.77         7.30         5.26        14.93        11.28        17.88 
TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 
       14.53        11.77        31.27        23.44        11.01        13.64 
TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 
       22.68        12.76         5.42        15.39        21.07         0.49 
TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 
        0.10        15.85        19.50         1.18         4.67        12.69 
TCGA-32-1987 TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 
       14.86        16.93        12.23        20.78        15.02        15.95 
TCGA-32-2616 TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4211 
        7.36         8.84        22.78        25.18        21.14        12.59 
TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 
       19.86        10.85        19.23         0.85        13.35         8.94 
TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 
        9.53         0.99         4.44        11.84         0.20        15.12 
TCGA-41-6646 TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 
       12.46         4.14        14.76         3.45        20.91         4.34 
TCGA-74-6578 TCGA-74-6581 TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 
       14.33         8.22         4.80         4.54         3.09         3.65 
TCGA-76-4931 TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 
        9.17         2.53        10.78        16.70         3.29         2.70 
TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 
       11.38        17.06         8.35        20.98         4.83         5.03 
TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 
        0.23         9.27         7.73         7.79         1.61        17.72 
TCGA-87-5896 TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC 
       26.30         5.92         6.28        20.55 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             0.43              0.10 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            92.65            127.59 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            8.420            12.035 
[1] "0.4 - 92.7 (8.4)"   "0.1 - 127.6 (12.0)"
[1] "hr=" "1.1"
D3V2, continuous
D3V3, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    19  18
  2P GAIN WILD-TYPE 205 328
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     19   18
  2P GAIN WILD-TYPE  205  328
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE              19               205
  MALE                18               328
[1] 2 2
[1] FALSE
D3V4, continuous
                   vv
clus                GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  2P GAIN MUTATED                               1                   1
  2P GAIN WILD-TYPE                            26                  17
                   vv
clus                UNTREATED PRIMARY (DE NOVO) GBM
  2P GAIN MUTATED                                35
  2P GAIN WILD-TYPE                             490
D3V5, multiclass
                                 clus
vv                                2P GAIN MUTATED 2P GAIN WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                 1                26
  TREATED PRIMARY GBM                           1                17
  UNTREATED PRIMARY (DE NOVO) GBM              35               490
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V6, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    24  13
  2P GAIN WILD-TYPE 358 175
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     24   13
  2P GAIN WILD-TYPE  358  175
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  NO               24               358
  YES              13               175
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2P GAIN MUTATED       1                         5    29
  2P GAIN WILD-TYPE    12                        44   456
D3V7, multiclass
                           clus
vv                          2P GAIN MUTATED 2P GAIN WILD-TYPE
  ASIAN                                   1                12
  BLACK OR AFRICAN AMERICAN               5                44
  WHITE                                  29               456
[1] 3 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     0  30
  2P GAIN WILD-TYPE  12 442
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      0   30
  2P GAIN WILD-TYPE   12  442
                        clus
vv                       2P GAIN MUTATED 2P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                12
  NOT HISPANIC OR LATINO              30               442
[1] 2 2
[1] FALSE

Clustering(4) Variable = 2Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                 0   1
  2Q GAIN MUTATED     5  31
  2Q GAIN WILD-TYPE  99 434
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               36               533 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               31               434 
$`2Q GAIN MUTATED`
TCGA-02-0001 TCGA-02-0106 TCGA-02-0113 TCGA-02-0281 TCGA-06-0128 TCGA-06-0133 
       11.77        11.67        92.65         3.98        22.72        14.30 
TCGA-06-0151 TCGA-06-0192 TCGA-06-0216 TCGA-06-0649 TCGA-06-0877 TCGA-06-1086 
       46.59        38.96        24.16         2.10         5.65         6.84 
TCGA-06-1802 TCGA-06-2557 TCGA-06-2569 TCGA-08-0346 TCGA-08-0386 TCGA-08-0510 
       15.32         1.08         0.43         8.42        18.02         4.27 
TCGA-08-0524 TCGA-12-0778 TCGA-12-1099 TCGA-12-3653 TCGA-14-0740 TCGA-14-0817 
        7.27        14.93         4.14        14.53        11.97         5.39 
TCGA-14-0871 TCGA-14-1453 TCGA-14-1823 TCGA-14-3477 TCGA-16-0846 TCGA-19-0957 
       28.93         1.15        17.85         3.78         3.91        21.90 
TCGA-19-1786 TCGA-26-1439 TCGA-27-1834 TCGA-28-5218 TCGA-32-4210 TCGA-74-6584 
        7.17        13.87        40.54         5.16         3.72         7.50 

$`2Q GAIN WILD-TYPE`
TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 TCGA-02-0011 
        4.73        18.35        23.18        10.59        35.41        20.71 
TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0024 
       82.59        20.61        87.06        77.65        20.12        53.10 
TCGA-02-0025 TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 
       42.74        24.59        12.16        90.58         2.83        14.14 
TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 
        3.62        10.72        10.52        18.31         6.87        14.73 
TCGA-02-0048 TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 TCGA-02-0055 TCGA-02-0057 
        3.22        15.09        12.59         6.54         2.50        19.86 
TCGA-02-0058 TCGA-02-0059 TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 TCGA-02-0069 
        8.35         9.57         6.02        19.73        26.43        28.70 
TCGA-02-0070 TCGA-02-0071 TCGA-02-0074 TCGA-02-0075 TCGA-02-0079 TCGA-02-0080 
       25.05         5.49        10.19        20.84        27.25        89.72 
TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 
       22.72        12.62        51.32         8.81        57.76        16.96 
TCGA-02-0099 TCGA-02-0102 TCGA-02-0104 TCGA-02-0107 TCGA-02-0111 TCGA-02-0114 
        3.48        27.02        65.00        17.65        23.18        99.98 
TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 TCGA-02-0266 TCGA-02-0269 
       15.65        48.95        16.54        16.93        17.72        10.75 
TCGA-02-0271 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 
       14.47        13.87        14.20        15.95        12.23         9.90 
TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 TCGA-02-0333 
        7.73        10.62         7.33        15.91        25.71         4.37 
TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 
       25.12        10.59        12.39        14.50        10.55        47.11 
TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 TCGA-02-2466 TCGA-02-2470 
       11.34         9.27        16.21         3.35        16.80        12.92 
TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 
       15.32        15.45        20.32         2.70         6.15        20.38 
TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 
       47.61         6.94         3.98        33.67        12.95        25.35 
TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 
       26.70        24.23        11.90         0.20        10.29         2.20 
TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 
       11.74         2.33        20.09        17.79        10.09         8.61 
TCGA-06-0150 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 
       19.46        12.33        13.94        10.45         3.19        10.82 
TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 
        9.44        11.80         3.42        56.91        10.65         5.85 
TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 
       19.66         3.29        13.12         4.47         3.22         4.04 
TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 
       91.00         4.18        88.14        20.25         3.65        69.90 
TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0194 
       73.84        27.22        44.58        15.42        10.42         4.67 
TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 
        7.40         5.56         0.39         7.66         8.42         7.63 
TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0219 TCGA-06-0221 
        7.40        11.84         0.53        15.02         0.72        19.82 
TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 
       13.64        13.32        20.42        48.69        10.82         9.01 
TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 
        0.26        72.36         4.70         9.57         3.16        35.11 
TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0650 TCGA-06-0686 
       12.62         5.75         5.75         9.80        23.57        14.20 
TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 
       26.40        46.88         7.86         2.70         2.70         0.92 
TCGA-06-0875 TCGA-06-0876 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 
       43.46        46.19         7.17        40.41        16.57        20.78 
TCGA-06-0939 TCGA-06-1084 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1804 
       26.76        23.93         4.04        26.79        11.84        13.61 
TCGA-06-1805 TCGA-06-1806 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 
       33.90        15.32        12.49         4.93        17.65        12.56 
TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2570 
       30.64         5.95        16.64         5.98         4.37        31.50 
TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 
       11.74         3.55         8.35         4.54         8.81         8.98 
TCGA-06-5415 TCGA-06-5416 TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 TCGA-06-5859 
        8.55         6.71         2.73         3.75         6.15         4.57 
TCGA-06-6388 TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 
        5.23         7.79         5.39         1.48       120.56         7.36 
TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 
        8.32        12.85         4.77         1.55         4.77         4.96 
TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK TCGA-06-A7TL 
        4.70         1.87         3.12         2.56         5.39         5.42 
TCGA-08-0244 TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0347 
       22.68        37.84         4.18       115.86         1.74        25.71 
TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 
       12.16         9.80        29.23        65.33         1.28         8.42 
TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 
       17.95        24.56        31.10        37.58        22.29         3.39 
TCGA-08-0375 TCGA-08-0380 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 
       12.23        14.93        15.35        13.97         0.72        12.56 
TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 
       42.15        11.08        19.59        58.68        19.33        10.75 
TCGA-08-0521 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 
        4.80        15.98        18.41         7.56        15.35        14.73 
TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 
       12.99        34.92        10.45         7.59        94.78         0.10 
TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 
       38.17        25.97        26.66        12.13         3.65        20.38 
TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 
       28.41        15.06        53.85        43.23         7.63         9.73 
TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 
       14.86        91.76        24.79        18.48        10.62        23.51 
TCGA-12-0826 TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 
       27.78        38.76         8.94        20.58       127.59         5.82 
TCGA-12-1090 TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 
        7.59        33.21        21.73        15.98        12.23        15.85 
TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 
        9.11        14.53         3.98        15.65        25.68        14.73 
TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 
        6.77        59.77        44.02        26.93        15.22        10.95 
TCGA-12-3651 TCGA-12-3652 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 
       12.69        34.92        14.93         3.22         2.04        15.12 
TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 
        0.95         6.21        23.05         2.24        11.24        13.78 
TCGA-14-0812 TCGA-14-0813 TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 TCGA-14-0867 
        3.25         1.35         2.89        16.50        26.33         2.04 
TCGA-14-1034 TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 
       15.95        19.30         0.79         1.38         1.12         3.75 
TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 TCGA-14-1452 TCGA-14-1454 TCGA-14-1455 
       32.05        58.78        23.11         7.10        30.18         0.92 
TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 
       40.96         6.67        12.43         0.99         1.97        17.79 
TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-4157 
        7.63         5.88         7.17        17.49         7.96         3.42 
TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 TCGA-16-0848 
       13.78        50.53        19.10        53.19        13.28        17.59 
TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 
       26.07        16.37         4.31        29.03         4.57        10.29 
TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 
       14.01         9.14        21.24        13.97         6.41        11.77 
TCGA-19-0960 TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 
        8.61         0.66        14.27         3.39        10.75         9.07 
TCGA-19-1387 TCGA-19-1388 TCGA-19-1389 TCGA-19-1390 TCGA-19-1392 TCGA-19-1787 
        5.95        12.95         4.64        25.38         3.65        12.66 
TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 
        3.25         0.13         9.67         4.87         1.08         7.53 
TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 
        0.16         4.08        24.23         7.00         7.04         6.64 
TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 
       17.19         8.02        18.90         4.73        12.10         1.78 
TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J4 
       22.49        14.07        16.80        14.96        17.79         3.98 
TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 
       28.54        10.03         9.73        31.33         7.13         9.37 
TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 
        9.40        14.86         5.49         8.88        18.97         1.58 
TCGA-26-6173 TCGA-26-6174 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 
        7.92         2.33        19.33         5.06        16.60         9.86 
TCGA-27-1833 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 
       24.23        21.30        30.05        14.04        11.51        24.76 
TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 
       10.39        10.39        16.08         7.59         2.86        14.40 
TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 
       15.78         0.20         2.53         9.21         8.35         7.63 
TCGA-28-1752 TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 TCGA-28-2502 
        8.48         1.22         1.55         2.83         0.13         0.66 
TCGA-28-2506 TCGA-28-2509 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 
        6.74         4.77         7.30         5.26        14.93        11.28 
TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 
       17.88        14.53        11.77        31.27        23.44        11.01 
TCGA-28-5216 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 
       13.64        22.68        12.76         5.42        15.39        21.07 
TCGA-32-1976 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 
        0.49         0.10        15.85        19.50         1.18         4.67 
TCGA-32-1986 TCGA-32-1987 TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 
       12.69        14.86        16.93        12.23        20.78        15.02 
TCGA-32-2615 TCGA-32-2616 TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 
       15.95         7.36         8.84        22.78        25.18        21.14 
TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 
       12.59        19.86        10.85        19.23         0.85        13.35 
TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 
        8.94         9.53         0.99         4.44        11.84         0.20 
TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 
       15.12        12.46         4.14        14.76         3.45        20.91 
TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 
        4.34        14.33         8.22         4.80         4.54         3.09 
TCGA-76-4929 TCGA-76-4931 TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 
        3.65         9.17         2.53        10.78        16.70         3.29 
TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 
        2.70        11.38        17.06         8.35        20.98         4.83 
TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 
        5.03         0.23         9.27         7.73         7.79         1.61 
TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC 
       17.72        26.30         5.92         6.28        20.55 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             0.43              0.10 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            92.65            127.59 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
           10.045            12.100 
[1] "0.4 - 92.7 (10.0)"  "0.1 - 127.6 (12.1)"
[1] "hr=" "1.2"
D4V2, continuous
D4V3, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    17  19
  2Q GAIN WILD-TYPE 207 327
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     17   19
  2Q GAIN WILD-TYPE  207  327
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE              17               207
  MALE                19               327
[1] 2 2
[1] FALSE
D4V4, continuous
                   vv
clus                GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  2Q GAIN MUTATED                               1                   1
  2Q GAIN WILD-TYPE                            26                  17
                   vv
clus                UNTREATED PRIMARY (DE NOVO) GBM
  2Q GAIN MUTATED                                34
  2Q GAIN WILD-TYPE                             491
D4V5, multiclass
                                 clus
vv                                2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                 1                26
  TREATED PRIMARY GBM                           1                17
  UNTREATED PRIMARY (DE NOVO) GBM              34               491
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V6, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    24  12
  2Q GAIN WILD-TYPE 358 176
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     24   12
  2Q GAIN WILD-TYPE  358  176
     clus
vv    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  NO               24               358
  YES              12               176
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2Q GAIN MUTATED       1                         5    28
  2Q GAIN WILD-TYPE    12                        44   457
D4V7, multiclass
                           clus
vv                          2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  ASIAN                                   1                12
  BLACK OR AFRICAN AMERICAN               5                44
  WHITE                                  28               457
[1] 3 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     0  28
  2Q GAIN WILD-TYPE  12 444
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      0   28
  2Q GAIN WILD-TYPE   12  444
                        clus
vv                       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                12
  NOT HISPANIC OR LATINO              28               444
[1] 2 2
[1] FALSE

Clustering(5) Variable = 3P GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                 0   1
  3P GAIN MUTATED    10  47
  3P GAIN WILD-TYPE  94 418
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               57               512 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               47               418 
$`3P GAIN MUTATED`
TCGA-02-0001 TCGA-02-0028 TCGA-02-0069 TCGA-02-0074 TCGA-02-0281 TCGA-02-0324 
       11.77        90.58        28.70        10.19         3.98         7.73 
TCGA-02-0325 TCGA-02-0332 TCGA-06-0166 TCGA-06-0188 TCGA-06-0192 TCGA-06-0211 
       10.62        25.71         5.85        44.58        38.96        11.84 
TCGA-06-0237 TCGA-06-0410 TCGA-06-0413 TCGA-06-0414 TCGA-06-0648 TCGA-06-0649 
       13.64         4.70         3.16        35.11         9.80         2.10 
TCGA-06-0686 TCGA-06-0743 TCGA-06-1087 TCGA-06-2557 TCGA-06-A7TL TCGA-08-0345 
       14.20        26.40         4.04         1.08         5.42         1.74 
TCGA-08-0346 TCGA-08-0510 TCGA-12-0615 TCGA-12-0619 TCGA-12-0822 TCGA-12-0829 
        8.42         4.27        15.35        34.92        23.51        20.58 
TCGA-12-1088 TCGA-12-1099 TCGA-12-1598 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 
      127.59         4.14        15.65         6.77        59.77        44.02 
TCGA-14-0867 TCGA-14-1794 TCGA-14-1825 TCGA-19-2629 TCGA-19-4065 TCGA-26-1440 
        2.04         0.99         7.63        24.23         7.04         9.73 
TCGA-26-6174 TCGA-27-1834 TCGA-27-2521 TCGA-28-2506 TCGA-28-2509 TCGA-28-5207 
        2.33        40.54        10.39         6.74         4.77        11.28 
TCGA-28-5215 TCGA-28-5216 TCGA-28-5219 TCGA-28-6450 TCGA-32-2632 TCGA-41-3915 
       11.01        13.64        22.68         5.42         8.84        11.84 
TCGA-41-4097 TCGA-76-4934 TCGA-76-6285 
        0.20         2.53         8.35 

$`3P GAIN WILD-TYPE`
TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 TCGA-02-0011 
        4.73        18.35        23.18        10.59        35.41        20.71 
TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0024 
       82.59        20.61        87.06        77.65        20.12        53.10 
TCGA-02-0025 TCGA-02-0026 TCGA-02-0027 TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 
       42.74        24.59        12.16         2.83        14.14         3.62 
TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 TCGA-02-0048 
       10.72        10.52        18.31         6.87        14.73         3.22 
TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 TCGA-02-0055 TCGA-02-0057 TCGA-02-0058 
       15.09        12.59         6.54         2.50        19.86         8.35 
TCGA-02-0059 TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 TCGA-02-0070 TCGA-02-0071 
        9.57         6.02        19.73        26.43        25.05         5.49 
TCGA-02-0075 TCGA-02-0079 TCGA-02-0080 TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 
       20.84        27.25        89.72        22.72        12.62        51.32 
TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 TCGA-02-0104 
        8.81        57.76        16.96         3.48        27.02        65.00 
TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 TCGA-02-0113 TCGA-02-0114 TCGA-02-0115 
       11.67        17.65        23.18        92.65        99.98        15.65 
TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 TCGA-02-0266 TCGA-02-0269 TCGA-02-0271 
       48.95        16.54        16.93        17.72        10.75        14.47 
TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 TCGA-02-0326 
       13.87        14.20        15.95        12.23         9.90         7.33 
TCGA-02-0330 TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 
       15.91         4.37        25.12        10.59        12.39        14.50 
TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 
       10.55        47.11        11.34         9.27        16.21         3.35 
TCGA-02-2466 TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 
       16.80        12.92        15.32        15.45        20.32         2.70 
TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 
        6.15        20.38        47.61         6.94         3.98        22.72 
TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 
       33.67        12.95        25.35        14.30        26.70        24.23 
TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 
       11.90         0.20        10.29         2.20        11.74         2.33 
TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 
       20.09        17.79        10.09         8.61        19.46        46.59 
TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 
       12.33        13.94        10.45         3.19        10.82         9.44 
TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0168 TCGA-06-0169 
       11.80         3.42        56.91        10.65        19.66         3.29 
TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 
       13.12         4.47         3.22         4.04        91.00         4.18 
TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 
       88.14        20.25         3.65        69.90        73.84        27.22 
TCGA-06-0189 TCGA-06-0190 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 
       15.42        10.42         4.67         7.40         5.56         0.39 
TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0213 TCGA-06-0214 
        7.66         8.42         7.63         7.40         0.53        15.02 
TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 
       24.16         0.72        19.82        13.32        20.42        48.69 
TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0412 TCGA-06-0644 
       10.82         9.01         0.26        72.36         9.57        12.62 
TCGA-06-0645 TCGA-06-0646 TCGA-06-0650 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 
        5.75         5.75        23.57        46.88         7.86         2.70 
TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 
        2.70         0.92        43.46        46.19         5.65         7.17 
TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 
       40.41        16.57        20.78        26.76        23.93         6.84 
TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 
       26.79        11.84        15.32        13.61        33.90        15.32 
TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 
       12.49         4.93        17.65        12.56        30.64         5.95 
TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-5408 
       16.64         5.98         4.37         0.43        31.50        11.74 
TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 
        3.55         8.35         4.54         8.81         8.98         8.55 
TCGA-06-5416 TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 
        6.71         2.73         3.75         6.15         4.57         5.23 
TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 
        7.79         5.39         1.48       120.56         7.36         8.32 
TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 
       12.85         4.77         1.55         4.77         4.96         4.70 
TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK TCGA-08-0244 TCGA-08-0245 
        1.87         3.12         2.56         5.39        22.68        37.84 
TCGA-08-0246 TCGA-08-0344 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 
        4.18       115.86        25.71        12.16         9.80        29.23 
TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 
       65.33         1.28         8.42        17.95        24.56        31.10 
TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 
       37.58        22.29         3.39        12.23        14.93        18.02 
TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0512 TCGA-08-0514 
       15.35        13.97         0.72        12.56        42.15        11.08 
TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 
       19.59        58.68        19.33        10.75         4.80         7.27 
TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0616 TCGA-12-0618 TCGA-12-0620 
       15.98        18.41         7.56        14.73        12.99        10.45 
TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 
        7.59        94.78         0.10        38.17        25.97        26.66 
TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 
       12.13         3.65        20.38        28.41        15.06        53.85 
TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 
       43.23         7.63         9.73        14.93        14.86        91.76 
TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0826 TCGA-12-0827 TCGA-12-0828 
       24.79        18.48        10.62        27.78        38.76         8.94 
TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 
        5.82         7.59        33.21        21.73        15.98        12.23 
TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1599 TCGA-12-1600 
       15.85         9.11        14.53         3.98        25.68        14.73 
TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 
       26.93        15.22        10.95        12.69        34.92        14.53 
TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 
       14.93         3.22         2.04        15.12        11.97         0.95 
TCGA-14-0783 TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 TCGA-14-0812 
        6.21        23.05         2.24        11.24        13.78         3.25 
TCGA-14-0813 TCGA-14-0817 TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 TCGA-14-0871 
        1.35         5.39         2.89        16.50        26.33        28.93 
TCGA-14-1034 TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 
       15.95        19.30         0.79         1.38         1.12         3.75 
TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 TCGA-14-1452 TCGA-14-1453 TCGA-14-1454 
       32.05        58.78        23.11         7.10         1.15        30.18 
TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 TCGA-14-1795 TCGA-14-1821 
        0.92        40.96         6.67        12.43         1.97        17.79 
TCGA-14-1823 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-3477 
       17.85         5.88         7.17        17.49         7.96         3.78 
TCGA-14-4157 TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 
        3.42        13.78        50.53        19.10        53.19        13.28 
TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 
        3.91        17.59        26.07        16.37         4.31        29.03 
TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 
        4.57        10.29        14.01         9.14        21.24        13.97 
TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 TCGA-19-0962 TCGA-19-0963 
        6.41        11.77        21.90         8.61         0.66        14.27 
TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 TCGA-19-1388 TCGA-19-1389 
        3.39        10.75         9.07         5.95        12.95         4.64 
TCGA-19-1390 TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 
       25.38         3.65         7.17        12.66         3.25         0.13 
TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 
        9.67         4.87         1.08         7.53         0.16         4.08 
TCGA-19-2631 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 
        7.00         6.64        17.19         8.02        18.90         4.73 
TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 
       12.10         1.78        22.49        14.07        16.80        14.96 
TCGA-19-A60I TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1442 
       17.79         3.98        28.54        10.03        13.87        31.33 
TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 
        7.13         9.37         9.40        14.86         5.49         8.88 
TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 
       18.97         1.58         7.92        19.33         5.06        16.60 
TCGA-27-1832 TCGA-27-1833 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 
        9.86        24.23        21.30        30.05        14.04        11.51 
TCGA-27-2518 TCGA-27-2519 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 
       24.76        10.39        16.08         7.59         2.86        14.40 
TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 
       15.78         0.20         2.53         9.21         8.35         7.63 
TCGA-28-1752 TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 TCGA-28-2502 
        8.48         1.22         1.55         2.83         0.13         0.66 
TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 
        7.30         5.26        14.93        17.88        14.53        11.77 
TCGA-28-5213 TCGA-28-5214 TCGA-28-5218 TCGA-28-5220 TCGA-32-1970 TCGA-32-1973 
       31.27        23.44         5.16        12.76        15.39        21.07 
TCGA-32-1976 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 
        0.49         0.10        15.85        19.50         1.18         4.67 
TCGA-32-1986 TCGA-32-1987 TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 
       12.69        14.86        16.93        12.23        20.78        15.02 
TCGA-32-2615 TCGA-32-2616 TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4210 
       15.95         7.36        22.78        25.18        21.14         3.72 
TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 
       12.59        19.86        10.85        19.23         0.85        13.35 
TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-5651 TCGA-41-6646 
        8.94         9.53         0.99         4.44        15.12        12.46 
TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 
        4.14        14.76         3.45        20.91         4.34        14.33 
TCGA-74-6581 TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 
        8.22         7.50         4.80         4.54         3.09         3.65 
TCGA-76-4931 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 
        9.17        10.78        16.70         3.29         2.70        11.38 
TCGA-76-6282 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 
       17.06        20.98         4.83         5.03         0.23         9.27 
TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R 
        7.73         7.79         1.61        17.72        26.30         5.92 
TCGA-RR-A6KA TCGA-RR-A6KC 
        6.28        20.55 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
              0.2               0.1 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
           127.59            120.56 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            10.19             12.23 
[1] "0.2 - 127.6 (10.2)" "0.1 - 120.6 (12.2)"
[1] "hr=" "1"  
D5V2, continuous
D5V3, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    26  31
  3P GAIN WILD-TYPE 198 315
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     26   31
  3P GAIN WILD-TYPE  198  315
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE              26               198
  MALE                31               315
[1] 2 2
[1] FALSE
D5V4, continuous
                   vv
clus                GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  3P GAIN MUTATED                               1                   1
  3P GAIN WILD-TYPE                            26                  17
                   vv
clus                UNTREATED PRIMARY (DE NOVO) GBM
  3P GAIN MUTATED                                55
  3P GAIN WILD-TYPE                             470
D5V5, multiclass
                                 clus
vv                                3P GAIN MUTATED 3P GAIN WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                 1                26
  TREATED PRIMARY GBM                           1                17
  UNTREATED PRIMARY (DE NOVO) GBM              55               470
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V6, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    38  19
  3P GAIN WILD-TYPE 344 169
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     38   19
  3P GAIN WILD-TYPE  344  169
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  NO               38               344
  YES              19               169
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3P GAIN MUTATED       1                         4    48
  3P GAIN WILD-TYPE    12                        45   437
D5V7, multiclass
                           clus
vv                          3P GAIN MUTATED 3P GAIN WILD-TYPE
  ASIAN                                   1                12
  BLACK OR AFRICAN AMERICAN               4                45
  WHITE                                  48               437
[1] 3 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     1  45
  3P GAIN WILD-TYPE  11 427
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      1   45
  3P GAIN WILD-TYPE   11  427
                        clus
vv                       3P GAIN MUTATED 3P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                11
  NOT HISPANIC OR LATINO              45               427
[1] 2 2
[1] FALSE

Clustering(6) Variable = 3Q GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                 0   1
  3Q GAIN MUTATED    13  50
  3Q GAIN WILD-TYPE  91 415
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               63               506 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               50               415 
$`3Q GAIN MUTATED`
TCGA-02-0001 TCGA-02-0028 TCGA-02-0047 TCGA-02-0069 TCGA-02-0074 TCGA-02-0106 
       11.77        90.58        14.73        28.70        10.19        11.67 
TCGA-02-0281 TCGA-02-0324 TCGA-02-0325 TCGA-02-0332 TCGA-06-0166 TCGA-06-0188 
        3.98         7.73        10.62        25.71         5.85        44.58 
TCGA-06-0192 TCGA-06-0211 TCGA-06-0237 TCGA-06-0410 TCGA-06-0413 TCGA-06-0414 
       38.96        11.84        13.64         4.70         3.16        35.11 
TCGA-06-0648 TCGA-06-0649 TCGA-06-0686 TCGA-06-0743 TCGA-06-1087 TCGA-06-2557 
        9.80         2.10        14.20        26.40         4.04         1.08 
TCGA-06-5416 TCGA-06-A7TL TCGA-08-0345 TCGA-08-0346 TCGA-08-0510 TCGA-12-0615 
        6.71         5.42         1.74         8.42         4.27        15.35 
TCGA-12-0619 TCGA-12-0827 TCGA-12-0829 TCGA-12-1088 TCGA-12-1598 TCGA-12-1602 
       34.92        38.76        20.58       127.59        15.65         6.77 
TCGA-12-3644 TCGA-12-3646 TCGA-14-0867 TCGA-14-1794 TCGA-14-1825 TCGA-14-1829 
       59.77        44.02         2.04         0.99         7.63         7.17 
TCGA-14-3477 TCGA-19-2629 TCGA-19-4065 TCGA-26-1440 TCGA-26-6174 TCGA-27-1831 
        3.78        24.23         7.04         9.73         2.33        16.60 
TCGA-27-1834 TCGA-27-2521 TCGA-28-2506 TCGA-28-2509 TCGA-28-5207 TCGA-28-5215 
       40.54        10.39         6.74         4.77        11.28        11.01 
TCGA-28-5216 TCGA-28-5219 TCGA-28-6450 TCGA-32-1991 TCGA-32-2632 TCGA-41-3915 
       13.64        22.68         5.42        16.93         8.84        11.84 
TCGA-41-4097 TCGA-76-4934 TCGA-76-6285 
        0.20         2.53         8.35 

$`3Q GAIN WILD-TYPE`
TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 TCGA-02-0011 
        4.73        18.35        23.18        10.59        35.41        20.71 
TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0024 
       82.59        20.61        87.06        77.65        20.12        53.10 
TCGA-02-0025 TCGA-02-0026 TCGA-02-0027 TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 
       42.74        24.59        12.16         2.83        14.14         3.62 
TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0048 TCGA-02-0051 
       10.72        10.52        18.31         6.87         3.22        15.09 
TCGA-02-0052 TCGA-02-0054 TCGA-02-0055 TCGA-02-0057 TCGA-02-0058 TCGA-02-0059 
       12.59         6.54         2.50        19.86         8.35         9.57 
TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 TCGA-02-0070 TCGA-02-0071 TCGA-02-0075 
        6.02        19.73        26.43        25.05         5.49        20.84 
TCGA-02-0079 TCGA-02-0080 TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 TCGA-02-0086 
       27.25        89.72        22.72        12.62        51.32         8.81 
TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 TCGA-02-0104 TCGA-02-0107 
       57.76        16.96         3.48        27.02        65.00        17.65 
TCGA-02-0111 TCGA-02-0113 TCGA-02-0114 TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 
       23.18        92.65        99.98        15.65        48.95        16.54 
TCGA-02-0260 TCGA-02-0266 TCGA-02-0269 TCGA-02-0271 TCGA-02-0285 TCGA-02-0289 
       16.93        17.72        10.75        14.47        13.87        14.20 
TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 TCGA-02-0326 TCGA-02-0330 TCGA-02-0333 
       15.95        12.23         9.90         7.33        15.91         4.37 
TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 
       25.12        10.59        12.39        14.50        10.55        47.11 
TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 TCGA-02-2466 TCGA-02-2470 
       11.34         9.27        16.21         3.35        16.80        12.92 
TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 
       15.32        15.45        20.32         2.70         6.15        20.38 
TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 
       47.61         6.94         3.98        22.72        33.67        12.95 
TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 
       25.35        14.30        26.70        24.23        11.90         0.20 
TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 
       10.29         2.20        11.74         2.33        20.09        17.79 
TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 
       10.09         8.61        19.46        46.59        12.33        13.94 
TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 
       10.45         3.19        10.82         9.44        11.80         3.42 
TCGA-06-0164 TCGA-06-0165 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 
       56.91        10.65        19.66         3.29        13.12         4.47 
TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 
        3.22         4.04        91.00         4.18        88.14        20.25 
TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0189 TCGA-06-0190 
        3.65        69.90        73.84        27.22        15.42        10.42 
TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 
        4.67         7.40         5.56         0.39         7.66         8.42 
TCGA-06-0209 TCGA-06-0210 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 
        7.63         7.40         0.53        15.02        24.16         0.72 
TCGA-06-0221 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 
       19.82        13.32        20.42        48.69        10.82         9.01 
TCGA-06-0402 TCGA-06-0409 TCGA-06-0412 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 
        0.26        72.36         9.57        12.62         5.75         5.75 
TCGA-06-0650 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 
       23.57        46.88         7.86         2.70         2.70         0.92 
TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 
       43.46        46.19         5.65         7.17        40.41        16.57 
TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1800 TCGA-06-1801 
       20.78        26.76        23.93         6.84        26.79        11.84 
TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 TCGA-06-2558 TCGA-06-2559 
       15.32        13.61        33.90        15.32        12.49         4.93 
TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 
       17.65        12.56        30.64         5.95        16.64         5.98 
TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 
        4.37         0.43        31.50        11.74         3.55         8.35 
TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5418 TCGA-06-5856 
        4.54         8.81         8.98         8.55         2.73         3.75 
TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 
        6.15         4.57         5.23         7.79         5.39         1.48 
TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 
      120.56         7.36         8.32        12.85         4.77         1.55 
TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 
        4.77         4.96         4.70         1.87         3.12         2.56 
TCGA-06-A7TK TCGA-08-0244 TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 TCGA-08-0347 
        5.39        22.68        37.84         4.18       115.86        25.71 
TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 
       12.16         9.80        29.23        65.33         1.28         8.42 
TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 
       17.95        24.56        31.10        37.58        22.29         3.39 
TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 
       12.23        14.93        18.02        15.35        13.97         0.72 
TCGA-08-0509 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 
       12.56        42.15        11.08        19.59        58.68        19.33 
TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 
       10.75         4.80         7.27        15.98        18.41         7.56 
TCGA-12-0616 TCGA-12-0618 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 
       14.73        12.99        10.45         7.59        94.78         0.10 
TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 
       38.17        25.97        26.66        12.13         3.65        20.38 
TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 
       28.41        15.06        53.85        43.23         7.63         9.73 
TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 
       14.93        14.86        91.76        24.79        18.48        10.62 
TCGA-12-0822 TCGA-12-0826 TCGA-12-0828 TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 
       23.51        27.78         8.94         5.82         7.59        33.21 
TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 
       21.73        15.98        12.23        15.85         9.11        14.53 
TCGA-12-1098 TCGA-12-1099 TCGA-12-1599 TCGA-12-1600 TCGA-12-3648 TCGA-12-3649 
        3.98         4.14        25.68        14.73        26.93        15.22 
TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 
       10.95        12.69        34.92        14.53        14.93         3.22 
TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 
        2.04        15.12        11.97         0.95         6.21        23.05 
TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 TCGA-14-0812 TCGA-14-0813 TCGA-14-0817 
        2.24        11.24        13.78         3.25         1.35         5.39 
TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 TCGA-14-0871 TCGA-14-1034 TCGA-14-1037 
        2.89        16.50        26.33        28.93        15.95        19.30 
TCGA-14-1043 TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 
        0.79         1.38         1.12         3.75        32.05        58.78 
TCGA-14-1451 TCGA-14-1452 TCGA-14-1453 TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 
       23.11         7.10         1.15        30.18         0.92        40.96 
TCGA-14-1458 TCGA-14-1459 TCGA-14-1795 TCGA-14-1821 TCGA-14-1823 TCGA-14-1827 
        6.67        12.43         1.97        17.79        17.85         5.88 
TCGA-14-2554 TCGA-14-2555 TCGA-14-4157 TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 
       17.49         7.96         3.42        13.78        50.53        19.10 
TCGA-15-1447 TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 
       53.19        13.28         3.91        17.59        26.07        16.37 
TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 
        4.31        29.03         4.57        10.29        14.01         9.14 
TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 
       21.24        13.97         6.41        11.77        21.90         8.61 
TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 
        0.66        14.27         3.39        10.75         9.07         5.95 
TCGA-19-1388 TCGA-19-1389 TCGA-19-1390 TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 
       12.95         4.64        25.38         3.65         7.17        12.66 
TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 
        3.25         0.13         9.67         4.87         1.08         7.53 
TCGA-19-2624 TCGA-19-2625 TCGA-19-2631 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 
        0.16         4.08         7.00         6.64        17.19         8.02 
TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 
       18.90         4.73        12.10         1.78        22.49        14.07 
TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 
       16.80        14.96        17.79         3.98        28.54        10.03 
TCGA-26-1439 TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5133 
       13.87        31.33         7.13         9.37         9.40        14.86 
TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 TCGA-26-A7UX 
        5.49         8.88        18.97         1.58         7.92        19.33 
TCGA-27-1830 TCGA-27-1832 TCGA-27-1833 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 
        5.06         9.86        24.23        21.30        30.05        14.04 
TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 
       11.51        24.76        10.39        16.08         7.59         2.86 
TCGA-27-2527 TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 
       14.40        15.78         0.20         2.53         9.21         8.35 
TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 
        7.63         8.48         1.22         1.55         2.83         0.13 
TCGA-28-2502 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5208 TCGA-28-5209 
        0.66         7.30         5.26        14.93        17.88        14.53 
TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5218 TCGA-28-5220 TCGA-32-1970 
       11.77        31.27        23.44         5.16        12.76        15.39 
TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 TCGA-32-1980 
       21.07         0.49         0.10        15.85        19.50         1.18 
TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 
        4.67        12.69        14.86        12.23        20.78        15.02 
TCGA-32-2615 TCGA-32-2616 TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4210 
       15.95         7.36        22.78        25.18        21.14         3.72 
TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 
       12.59        19.86        10.85        19.23         0.85        13.35 
TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-5651 TCGA-41-6646 
        8.94         9.53         0.99         4.44        15.12        12.46 
TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 
        4.14        14.76         3.45        20.91         4.34        14.33 
TCGA-74-6581 TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 
        8.22         7.50         4.80         4.54         3.09         3.65 
TCGA-76-4931 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 
        9.17        10.78        16.70         3.29         2.70        11.38 
TCGA-76-6282 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 
       17.06        20.98         4.83         5.03         0.23         9.27 
TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R 
        7.73         7.79         1.61        17.72        26.30         5.92 
TCGA-RR-A6KA TCGA-RR-A6KC 
        6.28        20.55 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              0.2               0.1 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
           127.59            120.56 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            10.39             12.23 
[1] "0.2 - 127.6 (10.4)" "0.1 - 120.6 (12.2)"
[1] "hr=" "1.1"
D6V2, continuous
D6V3, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    28  35
  3Q GAIN WILD-TYPE 196 311
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     28   35
  3Q GAIN WILD-TYPE  196  311
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE              28               196
  MALE                35               311
[1] 2 2
[1] FALSE
D6V4, continuous
                   vv
clus                GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  3Q GAIN MUTATED                               1                   1
  3Q GAIN WILD-TYPE                            26                  17
                   vv
clus                UNTREATED PRIMARY (DE NOVO) GBM
  3Q GAIN MUTATED                                61
  3Q GAIN WILD-TYPE                             464
D6V5, multiclass
                                 clus
vv                                3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                 1                26
  TREATED PRIMARY GBM                           1                17
  UNTREATED PRIMARY (DE NOVO) GBM              61               464
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V6, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    44  19
  3Q GAIN WILD-TYPE 338 169
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     44   19
  3Q GAIN WILD-TYPE  338  169
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  NO               44               338
  YES              19               169
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3Q GAIN MUTATED       1                         6    52
  3Q GAIN WILD-TYPE    12                        43   433
D6V7, multiclass
                           clus
vv                          3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  ASIAN                                   1                12
  BLACK OR AFRICAN AMERICAN               6                43
  WHITE                                  52               433
[1] 3 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     1  50
  3Q GAIN WILD-TYPE  11 422
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      1   50
  3Q GAIN WILD-TYPE   11  422
                        clus
vv                       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                11
  NOT HISPANIC OR LATINO              50               422
[1] 2 2
[1] FALSE

Clustering(7) Variable = 4P GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                 0   1
  4P GAIN MUTATED     5  31
  4P GAIN WILD-TYPE  99 434
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               36               533 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               31               434 
$`4P GAIN MUTATED`
TCGA-02-0011 TCGA-02-0055 TCGA-02-0069 TCGA-02-0074 TCGA-02-0075 TCGA-02-0113 
       20.71         2.50        28.70        10.19        20.84        92.65 
TCGA-06-0130 TCGA-06-0174 TCGA-06-0192 TCGA-06-0195 TCGA-06-0409 TCGA-06-0410 
       12.95         3.22        38.96         7.40        72.36         4.70 
TCGA-06-0879 TCGA-06-5856 TCGA-06-6697 TCGA-08-0245 TCGA-08-0246 TCGA-08-0510 
       40.41         3.75        12.85        37.84         4.18         4.27 
TCGA-08-0514 TCGA-08-0516 TCGA-08-0531 TCGA-12-0616 TCGA-12-0691 TCGA-12-0826 
       11.08        19.59         7.56        14.73        12.13        27.78 
TCGA-14-1453 TCGA-14-1821 TCGA-14-3477 TCGA-16-0846 TCGA-19-A6J4 TCGA-26-1439 
        1.15        17.79         3.78         3.91         3.98        13.87 
TCGA-28-2506 TCGA-28-5215 TCGA-32-1991 TCGA-32-4210 TCGA-41-3915 TCGA-41-4097 
        6.74        11.01        16.93         3.72        11.84         0.20 

$`4P GAIN WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 
       11.77         4.73        18.35        23.18        10.59        35.41 
TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0024 
       82.59        20.61        87.06        77.65        20.12        53.10 
TCGA-02-0025 TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 
       42.74        24.59        12.16        90.58         2.83        14.14 
TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 
        3.62        10.72        10.52        18.31         6.87        14.73 
TCGA-02-0048 TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 TCGA-02-0057 TCGA-02-0058 
        3.22        15.09        12.59         6.54        19.86         8.35 
TCGA-02-0059 TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 TCGA-02-0070 TCGA-02-0071 
        9.57         6.02        19.73        26.43        25.05         5.49 
TCGA-02-0079 TCGA-02-0080 TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 TCGA-02-0086 
       27.25        89.72        22.72        12.62        51.32         8.81 
TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 TCGA-02-0104 TCGA-02-0106 
       57.76        16.96         3.48        27.02        65.00        11.67 
TCGA-02-0107 TCGA-02-0111 TCGA-02-0114 TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 
       17.65        23.18        99.98        15.65        48.95        16.54 
TCGA-02-0260 TCGA-02-0266 TCGA-02-0269 TCGA-02-0271 TCGA-02-0281 TCGA-02-0285 
       16.93        17.72        10.75        14.47         3.98        13.87 
TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 
       14.20        15.95        12.23         9.90         7.73        10.62 
TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 
        7.33        15.91        25.71         4.37        25.12        10.59 
TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 
       12.39        14.50        10.55        47.11        11.34         9.27 
TCGA-02-0451 TCGA-02-0456 TCGA-02-2466 TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 
       16.21         3.35        16.80        12.92        15.32        15.45 
TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 
       20.32         2.70         6.15        20.38        47.61         6.94 
TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 
        3.98        22.72        33.67        25.35        14.30        26.70 
TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 
       24.23        11.90         0.20        10.29         2.20        11.74 
TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 
        2.33        20.09        17.79        10.09         8.61        19.46 
TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 
       46.59        12.33        13.94        10.45         3.19        10.82 
TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 
        9.44        11.80         3.42        56.91        10.65         5.85 
TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0175 TCGA-06-0176 
       19.66         3.29        13.12         4.47         4.04        91.00 
TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 
        4.18        88.14        20.25         3.65        69.90        73.84 
TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0194 TCGA-06-0197 
       27.22        44.58        15.42        10.42         4.67         5.56 
TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 
        0.39         7.66         8.42         7.63         7.40        11.84 
TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 
        0.53        15.02        24.16         0.72        19.82        13.64 
TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 
       13.32        20.42        48.69        10.82         9.01         0.26 
TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 
        9.57         3.16        35.11        12.62         5.75         5.75 
TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 
        9.80         2.10        23.57        14.20        26.40        46.88 
TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 
        7.86         2.70         2.70         0.92        43.46        46.19 
TCGA-06-0877 TCGA-06-0878 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 
        5.65         7.17        16.57        20.78        26.76        23.93 
TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 
        6.84         4.04        26.79        11.84        15.32        13.61 
TCGA-06-1805 TCGA-06-1806 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 
       33.90        15.32         1.08        12.49         4.93        17.65 
TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 
       12.56        30.64         5.95        16.64         5.98         4.37 
TCGA-06-2569 TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 
        0.43        31.50        11.74         3.55         8.35         4.54 
TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 TCGA-06-5418 TCGA-06-5858 
        8.81         8.98         8.55         6.71         2.73         6.15 
TCGA-06-5859 TCGA-06-6388 TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 
        4.57         5.23         7.79         5.39         1.48       120.56 
TCGA-06-6694 TCGA-06-6695 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 
        7.36         8.32         4.77         1.55         4.77         4.96 
TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK TCGA-06-A7TL 
        4.70         1.87         3.12         2.56         5.39         5.42 
TCGA-08-0244 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 
       22.68       115.86         1.74         8.42        25.71        12.16 
TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 
        9.80        29.23        65.33         1.28         8.42        17.95 
TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 
       24.56        31.10        37.58        22.29         3.39        12.23 
TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 
       14.93        18.02        15.35        13.97         0.72        12.56 
TCGA-08-0512 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 
       42.15        58.68        19.33        10.75         4.80         7.27 
TCGA-08-0525 TCGA-08-0529 TCGA-12-0615 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 
       15.98        18.41        15.35        12.99        34.92        10.45 
TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 
        7.59        94.78         0.10        38.17        25.97        26.66 
TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 
        3.65        20.38        28.41        15.06        53.85        43.23 
TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 
        7.63         9.73        14.93        14.86        91.76        24.79 
TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 
       18.48        10.62        23.51        38.76         8.94        20.58 
TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 
      127.59         5.82         7.59        33.21        21.73        15.98 
TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 
       12.23        15.85         9.11        14.53         3.98         4.14 
TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 
       15.65        25.68        14.73         6.77        59.77        44.02 
TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 
       26.93        15.22        10.95        12.69        34.92        14.53 
TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 
       14.93         3.22         2.04        15.12        11.97         0.95 
TCGA-14-0783 TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 TCGA-14-0812 
        6.21        23.05         2.24        11.24        13.78         3.25 
TCGA-14-0813 TCGA-14-0817 TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 TCGA-14-0867 
        1.35         5.39         2.89        16.50        26.33         2.04 
TCGA-14-0871 TCGA-14-1034 TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 TCGA-14-1396 
       28.93        15.95        19.30         0.79         1.38         1.12 
TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 TCGA-14-1452 TCGA-14-1454 
        3.75        32.05        58.78        23.11         7.10        30.18 
TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 
        0.92        40.96         6.67        12.43         0.99         1.97 
TCGA-14-1823 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 
       17.85         7.63         5.88         7.17        17.49         7.96 
TCGA-14-4157 TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 
        3.42        13.78        50.53        19.10        53.19        13.28 
TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 
       17.59        26.07        16.37         4.31        29.03         4.57 
TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 
       10.29        14.01         9.14        21.24        13.97         6.41 
TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 
       11.77        21.90         8.61         0.66        14.27         3.39 
TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 TCGA-19-1388 TCGA-19-1389 TCGA-19-1390 
       10.75         9.07         5.95        12.95         4.64        25.38 
TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 
        3.65         7.17        12.66         3.25         0.13         9.67 
TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 
        4.87         1.08         7.53         0.16         4.08        24.23 
TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 
        7.00         7.04         6.64        17.19         8.02        18.90 
TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 
        4.73        12.10         1.78        22.49        14.07        16.80 
TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1440 TCGA-26-1442 
       14.96        17.79        28.54        10.03         9.73        31.33 
TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 
        7.13         9.37         9.40        14.86         5.49         8.88 
TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-26-A7UX TCGA-27-1830 
       18.97         1.58         7.92         2.33        19.33         5.06 
TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 
       16.60         9.86        24.23        40.54        21.30        30.05 
TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 
       14.04        11.51        24.76        10.39        10.39        16.08 
TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 
        7.59         2.86        14.40        15.78         0.20         2.53 
TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 TCGA-28-1755 
        9.21         8.35         7.63         8.48         1.22         1.55 
TCGA-28-1756 TCGA-28-1757 TCGA-28-2502 TCGA-28-2509 TCGA-28-2513 TCGA-28-2514 
        2.83         0.13         0.66         4.77         7.30         5.26 
TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 
       14.93        11.28        17.88        14.53        11.77        31.27 
TCGA-28-5214 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 
       23.44        13.64         5.16        22.68        12.76         5.42 
TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 
       15.39        21.07         0.49         0.10        15.85        19.50 
TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 TCGA-32-2491 TCGA-32-2494 
        1.18         4.67        12.69        14.86        12.23        20.78 
TCGA-32-2495 TCGA-32-2615 TCGA-32-2616 TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 
       15.02        15.95         7.36         8.84        22.78        25.18 
TCGA-32-4208 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 
       21.14        12.59        19.86        10.85        19.23         0.85 
TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-5651 
       13.35         8.94         9.53         0.99         4.44        15.12 
TCGA-41-6646 TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 
       12.46         4.14        14.76         3.45        20.91         4.34 
TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 
       14.33         8.22         7.50         4.80         4.54         3.09 
TCGA-76-4929 TCGA-76-4931 TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 
        3.65         9.17         2.53        10.78        16.70         3.29 
TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 
        2.70        11.38        17.06         8.35        20.98         4.83 
TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 
        5.03         0.23         9.27         7.73         7.79         1.61 
TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC 
       17.72        26.30         5.92         6.28        20.55 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
              0.2               0.1 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            92.65            127.59 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            11.46             11.90 
[1] "0.2 - 92.7 (11.5)"  "0.1 - 127.6 (11.9)"
[1] "hr=" "1"  
D7V2, continuous
D7V3, binary
                   cls
clus                  0   1
  4P GAIN MUTATED    15  21
  4P GAIN WILD-TYPE 209 325
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     15   21
  4P GAIN WILD-TYPE  209  325
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE              15               209
  MALE                21               325
[1] 2 2
[1] FALSE
D7V4, continuous
                   vv
clus                GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  4P GAIN MUTATED                               1                   1
  4P GAIN WILD-TYPE                            26                  17
                   vv
clus                UNTREATED PRIMARY (DE NOVO) GBM
  4P GAIN MUTATED                                34
  4P GAIN WILD-TYPE                             491
D7V5, multiclass
                                 clus
vv                                4P GAIN MUTATED 4P GAIN WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                 1                26
  TREATED PRIMARY GBM                           1                17
  UNTREATED PRIMARY (DE NOVO) GBM              34               491
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V6, binary
                   cls
clus                  0   1
  4P GAIN MUTATED    26  10
  4P GAIN WILD-TYPE 356 178
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     26   10
  4P GAIN WILD-TYPE  356  178
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  NO               26               356
  YES              10               178
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4P GAIN MUTATED       1                         4    31
  4P GAIN WILD-TYPE    12                        45   454
D7V7, multiclass
                           clus
vv                          4P GAIN MUTATED 4P GAIN WILD-TYPE
  ASIAN                                   1                12
  BLACK OR AFRICAN AMERICAN               4                45
  WHITE                                  31               454
[1] 3 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     1  32
  4P GAIN WILD-TYPE  11 440
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      1   32
  4P GAIN WILD-TYPE   11  440
                        clus
vv                       4P GAIN MUTATED 4P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                11
  NOT HISPANIC OR LATINO              32               440
[1] 2 2
[1] FALSE

Clustering(8) Variable = 4Q GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                 0   1
  4Q GAIN MUTATED     5  28
  4Q GAIN WILD-TYPE  99 437
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               33               536 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               28               437 
$`4Q GAIN MUTATED`
TCGA-02-0055 TCGA-02-0069 TCGA-02-0074 TCGA-02-0075 TCGA-02-0113 TCGA-06-0130 
        2.50        28.70        10.19        20.84        92.65        12.95 
TCGA-06-0174 TCGA-06-0192 TCGA-06-0195 TCGA-06-0409 TCGA-06-0410 TCGA-06-0879 
        3.22        38.96         7.40        72.36         4.70        40.41 
TCGA-06-5856 TCGA-06-6697 TCGA-08-0245 TCGA-08-0246 TCGA-08-0510 TCGA-08-0514 
        3.75        12.85        37.84         4.18         4.27        11.08 
TCGA-08-0516 TCGA-08-0531 TCGA-12-0616 TCGA-12-0826 TCGA-14-1821 TCGA-14-3477 
       19.59         7.56        14.73        27.78        17.79         3.78 
TCGA-16-0846 TCGA-19-5956 TCGA-19-A6J4 TCGA-26-1439 TCGA-28-2506 TCGA-28-5215 
        3.91        22.49         3.98        13.87         6.74        11.01 
TCGA-32-1991 TCGA-32-4210 TCGA-41-4097 
       16.93         3.72         0.20 

$`4Q GAIN WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 
       11.77         4.73        18.35        23.18        10.59        35.41 
TCGA-02-0011 TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 
       20.71        82.59        20.61        87.06        77.65        20.12 
TCGA-02-0024 TCGA-02-0025 TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 
       53.10        42.74        24.59        12.16        90.58         2.83 
TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 
       14.14         3.62        10.72        10.52        18.31         6.87 
TCGA-02-0047 TCGA-02-0048 TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 TCGA-02-0057 
       14.73         3.22        15.09        12.59         6.54        19.86 
TCGA-02-0058 TCGA-02-0059 TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 TCGA-02-0070 
        8.35         9.57         6.02        19.73        26.43        25.05 
TCGA-02-0071 TCGA-02-0079 TCGA-02-0080 TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 
        5.49        27.25        89.72        22.72        12.62        51.32 
TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 TCGA-02-0104 
        8.81        57.76        16.96         3.48        27.02        65.00 
TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 TCGA-02-0114 TCGA-02-0115 TCGA-02-0116 
       11.67        17.65        23.18        99.98        15.65        48.95 
TCGA-02-0258 TCGA-02-0260 TCGA-02-0266 TCGA-02-0269 TCGA-02-0271 TCGA-02-0281 
       16.54        16.93        17.72        10.75        14.47         3.98 
TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 
       13.87        14.20        15.95        12.23         9.90         7.73 
TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 
       10.62         7.33        15.91        25.71         4.37        25.12 
TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 
       10.59        12.39        14.50        10.55        47.11        11.34 
TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 TCGA-02-2466 TCGA-02-2470 TCGA-02-2483 
        9.27        16.21         3.35        16.80        12.92        15.32 
TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 
       15.45        20.32         2.70         6.15        20.38        47.61 
TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0132 TCGA-06-0133 
        6.94         3.98        22.72        33.67        25.35        14.30 
TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 
       26.70        24.23        11.90         0.20        10.29         2.20 
TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 
       11.74         2.33        20.09        17.79        10.09         8.61 
TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 
       19.46        46.59        12.33        13.94        10.45         3.19 
TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 
       10.82         9.44        11.80         3.42        56.91        10.65 
TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0175 
        5.85        19.66         3.29        13.12         4.47         4.04 
TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 
       91.00         4.18        88.14        20.25         3.65        69.90 
TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0194 
       73.84        27.22        44.58        15.42        10.42         4.67 
TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 
        5.56         0.39         7.66         8.42         7.63         7.40 
TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 
       11.84         0.53        15.02        24.16         0.72        19.82 
TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 
       13.64        13.32        20.42        48.69        10.82         9.01 
TCGA-06-0402 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 
        0.26         9.57         3.16        35.11        12.62         5.75 
TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 
        5.75         9.80         2.10        23.57        14.20        26.40 
TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 
       46.88         7.86         2.70         2.70         0.92        43.46 
TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 
       46.19         5.65         7.17        16.57        20.78        26.76 
TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 
       23.93         6.84         4.04        26.79        11.84        15.32 
TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 
       13.61        33.90        15.32         1.08        12.49         4.93 
TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 
       17.65        12.56        30.64         5.95        16.64         5.98 
TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 
        4.37         0.43        31.50        11.74         3.55         8.35 
TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 TCGA-06-5418 
        4.54         8.81         8.98         8.55         6.71         2.73 
TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 
        6.15         4.57         5.23         7.79         5.39         1.48 
TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 
      120.56         7.36         8.32         4.77         1.55         4.77 
TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK 
        4.96         4.70         1.87         3.12         2.56         5.39 
TCGA-06-A7TL TCGA-08-0244 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 
        5.42        22.68       115.86         1.74         8.42        25.71 
TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 
       12.16         9.80        29.23        65.33         1.28         8.42 
TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 
       17.95        24.56        31.10        37.58        22.29         3.39 
TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 
       12.23        14.93        18.02        15.35        13.97         0.72 
TCGA-08-0509 TCGA-08-0512 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 
       12.56        42.15        58.68        19.33        10.75         4.80 
TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-12-0615 TCGA-12-0618 TCGA-12-0619 
        7.27        15.98        18.41        15.35        12.99        34.92 
TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 
       10.45         7.59        94.78         0.10        38.17        25.97 
TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 
       26.66        12.13         3.65        20.38        28.41        15.06 
TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 
       53.85        43.23         7.63         9.73        14.93        14.86 
TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 TCGA-12-0827 
       91.76        24.79        18.48        10.62        23.51        38.76 
TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 
        8.94        20.58       127.59         5.82         7.59        33.21 
TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 
       21.73        15.98        12.23        15.85         9.11        14.53 
TCGA-12-1098 TCGA-12-1099 TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 
        3.98         4.14        15.65        25.68        14.73         6.77 
TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 
       59.77        44.02        26.93        15.22        10.95        12.69 
TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 
       34.92        14.53        14.93         3.22         2.04        15.12 
TCGA-14-0740 TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 
       11.97         0.95         6.21        23.05         2.24        11.24 
TCGA-14-0790 TCGA-14-0812 TCGA-14-0813 TCGA-14-0817 TCGA-14-0862 TCGA-14-0865 
       13.78         3.25         1.35         5.39         2.89        16.50 
TCGA-14-0866 TCGA-14-0867 TCGA-14-0871 TCGA-14-1034 TCGA-14-1037 TCGA-14-1043 
       26.33         2.04        28.93        15.95        19.30         0.79 
TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 
        1.38         1.12         3.75        32.05        58.78        23.11 
TCGA-14-1452 TCGA-14-1453 TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 
        7.10         1.15        30.18         0.92        40.96         6.67 
TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1823 TCGA-14-1825 TCGA-14-1827 
       12.43         0.99         1.97        17.85         7.63         5.88 
TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-4157 TCGA-15-0742 TCGA-15-1444 
        7.17        17.49         7.96         3.42        13.78        50.53 
TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 
       19.10        53.19        13.28        17.59        26.07        16.37 
TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 
        4.31        29.03         4.57        10.29        14.01         9.14 
TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 
       21.24        13.97         6.41        11.77        21.90         8.61 
TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 
        0.66        14.27         3.39        10.75         9.07         5.95 
TCGA-19-1388 TCGA-19-1389 TCGA-19-1390 TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 
       12.95         4.64        25.38         3.65         7.17        12.66 
TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 
        3.25         0.13         9.67         4.87         1.08         7.53 
TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 
        0.16         4.08        24.23         7.00         7.04         6.64 
TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 
       17.19         8.02        18.90         4.73        12.10         1.78 
TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J5 TCGA-26-1438 
       14.07        16.80        14.96        17.79        28.54        10.03 
TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5133 
        9.73        31.33         7.13         9.37         9.40        14.86 
TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 
        5.49         8.88        18.97         1.58         7.92         2.33 
TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 
       19.33         5.06        16.60         9.86        24.23        40.54 
TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 
       21.30        30.05        14.04        11.51        24.76        10.39 
TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 
       10.39        16.08         7.59         2.86        14.40        15.78 
TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 TCGA-28-1752 
        0.20         2.53         9.21         8.35         7.63         8.48 
TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 TCGA-28-2502 TCGA-28-2509 
        1.22         1.55         2.83         0.13         0.66         4.77 
TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 
        7.30         5.26        14.93        11.28        17.88        14.53 
TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 
       11.77        31.27        23.44        13.64         5.16        22.68 
TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 
       12.76         5.42        15.39        21.07         0.49         0.10 
TCGA-32-1978 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 
       15.85        19.50         1.18         4.67        12.69        14.86 
TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 TCGA-32-2616 TCGA-32-2632 
       12.23        20.78        15.02        15.95         7.36         8.84 
TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 
       22.78        25.18        21.14        12.59        19.86        10.85 
TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 
       19.23         0.85        13.35         8.94         9.53         0.99 
TCGA-41-3393 TCGA-41-3915 TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9S TCGA-4W-AA9T 
        4.44        11.84        15.12        12.46         4.14        14.76 
TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 
        3.45        20.91         4.34        14.33         8.22         7.50 
TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-4934 
        4.80         4.54         3.09         3.65         9.17         2.53 
TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 
       10.78        16.70         3.29         2.70        11.38        17.06 
TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 
        8.35        20.98         4.83         5.03         0.23         9.27 
TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R 
        7.73         7.79         1.61        17.72        26.30         5.92 
TCGA-RR-A6KA TCGA-RR-A6KC 
        6.28        20.55 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
              0.2               0.1 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            92.65            127.59 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            11.08             11.87 
[1] "0.2 - 92.7 (11.1)"  "0.1 - 127.6 (11.9)"
[1] "hr=" "1"  
D8V2, continuous
D8V3, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED    15  18
  4Q GAIN WILD-TYPE 209 328
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     15   18
  4Q GAIN WILD-TYPE  209  328
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE              15               209
  MALE                18               328
[1] 2 2
[1] FALSE
D8V4, continuous
                   vv
clus                GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  4Q GAIN MUTATED                               1                   1
  4Q GAIN WILD-TYPE                            26                  17
                   vv
clus                UNTREATED PRIMARY (DE NOVO) GBM
  4Q GAIN MUTATED                                31
  4Q GAIN WILD-TYPE                             494
D8V5, multiclass
                                 clus
vv                                4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                 1                26
  TREATED PRIMARY GBM                           1                17
  UNTREATED PRIMARY (DE NOVO) GBM              31               494
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V6, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED    25   8
  4Q GAIN WILD-TYPE 357 180
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     25    8
  4Q GAIN WILD-TYPE  357  180
     clus
vv    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  NO               25               357
  YES               8               180
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4Q GAIN MUTATED       1                         4    28
  4Q GAIN WILD-TYPE    12                        45   457
D8V7, multiclass
                           clus
vv                          4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  ASIAN                                   1                12
  BLACK OR AFRICAN AMERICAN               4                45
  WHITE                                  28               457
[1] 3 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  31
  4Q GAIN WILD-TYPE  12 441
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      0   31
  4Q GAIN WILD-TYPE   12  441
                        clus
vv                       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                12
  NOT HISPANIC OR LATINO              31               441
[1] 2 2
[1] FALSE

Clustering(9) Variable = 5P GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                 0   1
  5P GAIN MUTATED     6  43
  5P GAIN WILD-TYPE  98 422
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               49               520 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               43               422 
$`5P GAIN MUTATED`
TCGA-02-0024 TCGA-02-0028 TCGA-02-0051 TCGA-02-0054 TCGA-02-0075 TCGA-02-0086 
       53.10        90.58        15.09         6.54        20.84         8.81 
TCGA-02-0106 TCGA-02-0113 TCGA-02-0324 TCGA-02-0456 TCGA-06-0151 TCGA-06-0195 
       11.67        92.65         7.73         3.35        46.59         7.40 
TCGA-06-0209 TCGA-06-0237 TCGA-06-0397 TCGA-06-0409 TCGA-06-0410 TCGA-06-0645 
        7.63        13.64         9.01        72.36         4.70         5.75 
TCGA-06-0649 TCGA-06-1806 TCGA-06-2557 TCGA-06-5856 TCGA-08-0350 TCGA-08-0510 
        2.10        15.32         1.08         3.75        29.23         4.27 
TCGA-08-0518 TCGA-08-0524 TCGA-12-0691 TCGA-12-0778 TCGA-12-0826 TCGA-12-1096 
       19.33         7.27        12.13        14.93        27.78         9.11 
TCGA-12-1098 TCGA-12-1602 TCGA-12-3646 TCGA-14-1396 TCGA-14-1823 TCGA-15-1447 
        3.98         6.77        44.02         1.12        17.85        53.19 
TCGA-19-0955 TCGA-19-1388 TCGA-19-1787 TCGA-19-A6J4 TCGA-28-2506 TCGA-28-2509 
       11.77        12.95        12.66         3.98         6.74         4.77 
TCGA-28-5216 TCGA-32-1973 TCGA-32-2495 TCGA-32-2616 TCGA-32-2632 TCGA-32-4210 
       13.64        21.07        15.02         7.36         8.84         3.72 
TCGA-76-4934 
        2.53 

$`5P GAIN WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 
       11.77         4.73        18.35        23.18        10.59        35.41 
TCGA-02-0011 TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 
       20.71        82.59        20.61        87.06        77.65        20.12 
TCGA-02-0025 TCGA-02-0026 TCGA-02-0027 TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 
       42.74        24.59        12.16         2.83        14.14         3.62 
TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 TCGA-02-0048 
       10.72        10.52        18.31         6.87        14.73         3.22 
TCGA-02-0052 TCGA-02-0055 TCGA-02-0057 TCGA-02-0058 TCGA-02-0059 TCGA-02-0060 
       12.59         2.50        19.86         8.35         9.57         6.02 
TCGA-02-0064 TCGA-02-0068 TCGA-02-0069 TCGA-02-0070 TCGA-02-0071 TCGA-02-0074 
       19.73        26.43        28.70        25.05         5.49        10.19 
TCGA-02-0079 TCGA-02-0080 TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 TCGA-02-0087 
       27.25        89.72        22.72        12.62        51.32        57.76 
TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 TCGA-02-0104 TCGA-02-0107 TCGA-02-0111 
       16.96         3.48        27.02        65.00        17.65        23.18 
TCGA-02-0114 TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 TCGA-02-0266 
       99.98        15.65        48.95        16.54        16.93        17.72 
TCGA-02-0269 TCGA-02-0271 TCGA-02-0281 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 
       10.75        14.47         3.98        13.87        14.20        15.95 
TCGA-02-0317 TCGA-02-0321 TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 
       12.23         9.90        10.62         7.33        15.91        25.71 
TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 
        4.37        25.12        10.59        12.39        14.50        10.55 
TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 TCGA-02-2466 TCGA-02-2470 
       47.11        11.34         9.27        16.21        16.80        12.92 
TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 
       15.32        15.45        20.32         2.70         6.15        20.38 
TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 
       47.61         6.94         3.98        22.72        33.67        12.95 
TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 
       25.35        14.30        26.70        24.23        11.90         0.20 
TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 
       10.29         2.20        11.74         2.33        20.09        17.79 
TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 
       10.09         8.61        19.46        12.33        13.94        10.45 
TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 
        3.19        10.82         9.44        11.80         3.42        56.91 
TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 
       10.65         5.85        19.66         3.29        13.12         4.47 
TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 
        3.22         4.04        91.00         4.18        88.14        20.25 
TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 
        3.65        69.90        73.84        27.22        44.58        15.42 
TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 
       10.42        38.96         4.67         5.56         0.39         7.66 
TCGA-06-0208 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 
        8.42         7.40        11.84         0.53        15.02        24.16 
TCGA-06-0219 TCGA-06-0221 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 
        0.72        19.82        13.32        20.42        48.69        10.82 
TCGA-06-0402 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0646 
        0.26         9.57         3.16        35.11        12.62         5.75 
TCGA-06-0648 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 
        9.80        23.57        14.20        26.40        46.88         7.86 
TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 
        2.70         2.70         0.92        43.46        46.19         5.65 
TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 
        7.17        40.41        16.57        20.78        26.76        23.93 
TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 
        6.84         4.04        26.79        11.84        15.32        13.61 
TCGA-06-1805 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 
       33.90        12.49         4.93        17.65        12.56        30.64 
TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 
        5.95        16.64         5.98         4.37         0.43        31.50 
TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 
       11.74         3.55         8.35         4.54         8.81         8.98 
TCGA-06-5415 TCGA-06-5416 TCGA-06-5418 TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 
        8.55         6.71         2.73         6.15         4.57         5.23 
TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 
        7.79         5.39         1.48       120.56         7.36         8.32 
TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 
       12.85         4.77         1.55         4.77         4.96         4.70 
TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK TCGA-06-A7TL TCGA-08-0244 
        1.87         3.12         2.56         5.39         5.42        22.68 
TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 
       37.84         4.18       115.86         1.74         8.42        25.71 
TCGA-08-0348 TCGA-08-0349 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 
       12.16         9.80        65.33         1.28         8.42        17.95 
TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 
       24.56        31.10        37.58        22.29         3.39        12.23 
TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 
       14.93        18.02        15.35        13.97         0.72        12.56 
TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0520 TCGA-08-0521 
       42.15        11.08        19.59        58.68        10.75         4.80 
TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 
       15.98        18.41         7.56        15.35        14.73        12.99 
TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 
       34.92        10.45         7.59        94.78         0.10        38.17 
TCGA-12-0670 TCGA-12-0688 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 
       25.97        26.66         3.65        20.38        28.41        15.06 
TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0780 TCGA-12-0818 
       53.85        43.23         7.63         9.73        14.86        91.76 
TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 TCGA-12-0827 TCGA-12-0828 
       24.79        18.48        10.62        23.51        38.76         8.94 
TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 TCGA-12-1092 
       20.58       127.59         5.82         7.59        33.21        21.73 
TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1097 TCGA-12-1099 TCGA-12-1598 
       15.98        12.23        15.85        14.53         4.14        15.65 
TCGA-12-1599 TCGA-12-1600 TCGA-12-3644 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 
       25.68        14.73        59.77        26.93        15.22        10.95 
TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 
       12.69        34.92        14.53        14.93         3.22         2.04 
TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 TCGA-14-0787 
       15.12        11.97         0.95         6.21        23.05         2.24 
TCGA-14-0789 TCGA-14-0790 TCGA-14-0812 TCGA-14-0813 TCGA-14-0817 TCGA-14-0862 
       11.24        13.78         3.25         1.35         5.39         2.89 
TCGA-14-0865 TCGA-14-0866 TCGA-14-0867 TCGA-14-0871 TCGA-14-1034 TCGA-14-1037 
       16.50        26.33         2.04        28.93        15.95        19.30 
TCGA-14-1043 TCGA-14-1395 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 
        0.79         1.38         3.75        32.05        58.78        23.11 
TCGA-14-1452 TCGA-14-1453 TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 
        7.10         1.15        30.18         0.92        40.96         6.67 
TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 TCGA-14-1825 TCGA-14-1827 
       12.43         0.99         1.97        17.79         7.63         5.88 
TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-3477 TCGA-14-4157 TCGA-15-0742 
        7.17        17.49         7.96         3.78         3.42        13.78 
TCGA-15-1444 TCGA-15-1446 TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 
       50.53        19.10        13.28         3.91        17.59        26.07 
TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 
       16.37         4.31        29.03         4.57        10.29        14.01 
TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0957 TCGA-19-0960 
        9.14        21.24        13.97         6.41        21.90         8.61 
TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 
        0.66        14.27         3.39        10.75         9.07         5.95 
TCGA-19-1389 TCGA-19-1390 TCGA-19-1392 TCGA-19-1786 TCGA-19-1789 TCGA-19-1791 
        4.64        25.38         3.65         7.17         3.25         0.13 
TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 
        9.67         4.87         1.08         7.53         0.16         4.08 
TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 
       24.23         7.00         7.04         6.64        17.19         8.02 
TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 
       18.90         4.73        12.10         1.78        22.49        14.07 
TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 
       16.80        14.96        17.79        28.54        10.03        13.87 
TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5133 
        9.73        31.33         7.13         9.37         9.40        14.86 
TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 
        5.49         8.88        18.97         1.58         7.92         2.33 
TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 
       19.33         5.06        16.60         9.86        24.23        40.54 
TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 
       21.30        30.05        14.04        11.51        24.76        10.39 
TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 
       10.39        16.08         7.59         2.86        14.40        15.78 
TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 TCGA-28-1752 
        0.20         2.53         9.21         8.35         7.63         8.48 
TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 TCGA-28-2502 TCGA-28-2513 
        1.22         1.55         2.83         0.13         0.66         7.30 
TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 
        5.26        14.93        11.28        17.88        14.53        11.77 
TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 
       31.27        23.44        11.01         5.16        22.68        12.76 
TCGA-28-6450 TCGA-32-1970 TCGA-32-1976 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 
        5.42        15.39         0.49         0.10        15.85        19.50 
TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 TCGA-32-1991 TCGA-32-2491 
        1.18         4.67        12.69        14.86        16.93        12.23 
TCGA-32-2494 TCGA-32-2615 TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4211 
       20.78        15.95        22.78        25.18        21.14        12.59 
TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 
       19.86        10.85        19.23         0.85        13.35         8.94 
TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 
        9.53         0.99         4.44        11.84         0.20        15.12 
TCGA-41-6646 TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 
       12.46         4.14        14.76         3.45        20.91         4.34 
TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 
       14.33         8.22         7.50         4.80         4.54         3.09 
TCGA-76-4929 TCGA-76-4931 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 
        3.65         9.17        10.78        16.70         3.29         2.70 
TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 
       11.38        17.06         8.35        20.98         4.83         5.03 
TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 
        0.23         9.27         7.73         7.79         1.61        17.72 
TCGA-87-5896 TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC 
       26.30         5.92         6.28        20.55 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             1.08              0.10 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            92.65            127.59 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            9.110            12.035 
[1] "1.1 - 92.7 (9.1)"   "0.1 - 127.6 (12.0)"
[1] "hr=" "1.1"
D9V2, continuous
D9V3, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    24  25
  5P GAIN WILD-TYPE 200 321
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     24   25
  5P GAIN WILD-TYPE  200  321
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE              24               200
  MALE                25               321
[1] 2 2
[1] FALSE
D9V4, continuous
                   vv
clus                GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  5P GAIN MUTATED                               3                   4
  5P GAIN WILD-TYPE                            24                  14
                   vv
clus                UNTREATED PRIMARY (DE NOVO) GBM
  5P GAIN MUTATED                                42
  5P GAIN WILD-TYPE                             483
D9V5, multiclass
                                 clus
vv                                5P GAIN MUTATED 5P GAIN WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                 3                24
  TREATED PRIMARY GBM                           4                14
  UNTREATED PRIMARY (DE NOVO) GBM              42               483
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V6, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    32  17
  5P GAIN WILD-TYPE 350 171
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     32   17
  5P GAIN WILD-TYPE  350  171
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  NO               32               350
  YES              17               171
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5P GAIN MUTATED       1                         4    43
  5P GAIN WILD-TYPE    12                        45   442
D9V7, multiclass
                           clus
vv                          5P GAIN MUTATED 5P GAIN WILD-TYPE
  ASIAN                                   1                12
  BLACK OR AFRICAN AMERICAN               4                45
  WHITE                                  43               442
[1] 3 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     2  42
  5P GAIN WILD-TYPE  10 430
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      2   42
  5P GAIN WILD-TYPE   10  430
                        clus
vv                       5P GAIN MUTATED 5P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                10
  NOT HISPANIC OR LATINO              42               430
[1] 2 2
[1] FALSE

Clustering(10) Variable = 5Q GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                 0   1
  5Q GAIN MUTATED     6  35
  5Q GAIN WILD-TYPE  98 430
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               41               528 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               35               430 
$`5Q GAIN MUTATED`
TCGA-02-0028 TCGA-02-0054 TCGA-02-0075 TCGA-02-0086 TCGA-02-0106 TCGA-02-0113 
       90.58         6.54        20.84         8.81        11.67        92.65 
TCGA-02-0324 TCGA-02-0456 TCGA-06-0151 TCGA-06-0195 TCGA-06-0209 TCGA-06-0397 
        7.73         3.35        46.59         7.40         7.63         9.01 
TCGA-06-0409 TCGA-06-0410 TCGA-06-0645 TCGA-06-0649 TCGA-06-1806 TCGA-06-2557 
       72.36         4.70         5.75         2.10        15.32         1.08 
TCGA-06-5416 TCGA-06-5856 TCGA-08-0510 TCGA-08-0518 TCGA-12-0778 TCGA-12-0826 
        6.71         3.75         4.27        19.33        14.93        27.78 
TCGA-12-1096 TCGA-12-1098 TCGA-12-1602 TCGA-12-3646 TCGA-14-1396 TCGA-14-1823 
        9.11         3.98         6.77        44.02         1.12        17.85 
TCGA-19-0955 TCGA-19-1388 TCGA-19-1787 TCGA-19-A6J4 TCGA-28-2506 TCGA-28-2509 
       11.77        12.95        12.66         3.98         6.74         4.77 
TCGA-28-5216 TCGA-32-2495 TCGA-32-2632 TCGA-32-4210 TCGA-76-4934 
       13.64        15.02         8.84         3.72         2.53 

$`5Q GAIN WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 
       11.77         4.73        18.35        23.18        10.59        35.41 
TCGA-02-0011 TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 
       20.71        82.59        20.61        87.06        77.65        20.12 
TCGA-02-0024 TCGA-02-0025 TCGA-02-0026 TCGA-02-0027 TCGA-02-0033 TCGA-02-0034 
       53.10        42.74        24.59        12.16         2.83        14.14 
TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 
        3.62        10.72        10.52        18.31         6.87        14.73 
TCGA-02-0048 TCGA-02-0051 TCGA-02-0052 TCGA-02-0055 TCGA-02-0057 TCGA-02-0058 
        3.22        15.09        12.59         2.50        19.86         8.35 
TCGA-02-0059 TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 TCGA-02-0069 TCGA-02-0070 
        9.57         6.02        19.73        26.43        28.70        25.05 
TCGA-02-0071 TCGA-02-0074 TCGA-02-0079 TCGA-02-0080 TCGA-02-0083 TCGA-02-0084 
        5.49        10.19        27.25        89.72        22.72        12.62 
TCGA-02-0085 TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 TCGA-02-0104 
       51.32        57.76        16.96         3.48        27.02        65.00 
TCGA-02-0107 TCGA-02-0111 TCGA-02-0114 TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 
       17.65        23.18        99.98        15.65        48.95        16.54 
TCGA-02-0260 TCGA-02-0266 TCGA-02-0269 TCGA-02-0271 TCGA-02-0281 TCGA-02-0285 
       16.93        17.72        10.75        14.47         3.98        13.87 
TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 TCGA-02-0325 TCGA-02-0326 
       14.20        15.95        12.23         9.90        10.62         7.33 
TCGA-02-0330 TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 
       15.91        25.71         4.37        25.12        10.59        12.39 
TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 
       14.50        10.55        47.11        11.34         9.27        16.21 
TCGA-02-2466 TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 
       16.80        12.92        15.32        15.45        20.32         2.70 
TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 
        6.15        20.38        47.61         6.94         3.98        22.72 
TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 
       33.67        12.95        25.35        14.30        26.70        24.23 
TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 
       11.90         0.20        10.29         2.20        11.74         2.33 
TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0152 
       20.09        17.79        10.09         8.61        19.46        12.33 
TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 
       13.94        10.45         3.19        10.82         9.44        11.80 
TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 
        3.42        56.91        10.65         5.85        19.66         3.29 
TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 
       13.12         4.47         3.22         4.04        91.00         4.18 
TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 
       88.14        20.25         3.65        69.90        73.84        27.22 
TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0197 
       44.58        15.42        10.42        38.96         4.67         5.56 
TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 
        0.39         7.66         8.42         7.40        11.84         0.53 
TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 
       15.02        24.16         0.72        19.82        13.64        13.32 
TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0402 TCGA-06-0412 TCGA-06-0413 
       20.42        48.69        10.82         0.26         9.57         3.16 
TCGA-06-0414 TCGA-06-0644 TCGA-06-0646 TCGA-06-0648 TCGA-06-0650 TCGA-06-0686 
       35.11        12.62         5.75         9.80        23.57        14.20 
TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 
       26.40        46.88         7.86         2.70         2.70         0.92 
TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 
       43.46        46.19         5.65         7.17        40.41        16.57 
TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 
       20.78        26.76        23.93         6.84         4.04        26.79 
TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-2558 TCGA-06-2559 
       11.84        15.32        13.61        33.90        12.49         4.93 
TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 
       17.65        12.56        30.64         5.95        16.64         5.98 
TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 
        4.37         0.43        31.50        11.74         3.55         8.35 
TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5418 TCGA-06-5858 
        4.54         8.81         8.98         8.55         2.73         6.15 
TCGA-06-5859 TCGA-06-6388 TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 
        4.57         5.23         7.79         5.39         1.48       120.56 
TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 
        7.36         8.32        12.85         4.77         1.55         4.77 
TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK 
        4.96         4.70         1.87         3.12         2.56         5.39 
TCGA-06-A7TL TCGA-08-0244 TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 
        5.42        22.68        37.84         4.18       115.86         1.74 
TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 
        8.42        25.71        12.16         9.80        29.23        65.33 
TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 
        1.28         8.42        17.95        24.56        31.10        37.58 
TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 
       22.29         3.39        12.23        14.93        18.02        15.35 
TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 
       13.97         0.72        12.56        42.15        11.08        19.59 
TCGA-08-0517 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 
       58.68        10.75         4.80         7.27        15.98        18.41 
TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 
        7.56        15.35        14.73        12.99        34.92        10.45 
TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 
        7.59        94.78         0.10        38.17        25.97        26.66 
TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 
       12.13         3.65        20.38        28.41        15.06        53.85 
TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 
       43.23         7.63         9.73        14.86        91.76        24.79 
TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 
       18.48        10.62        23.51        38.76         8.94        20.58 
TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 
      127.59         5.82         7.59        33.21        21.73        15.98 
TCGA-12-1094 TCGA-12-1095 TCGA-12-1097 TCGA-12-1099 TCGA-12-1598 TCGA-12-1599 
       12.23        15.85        14.53         4.14        15.65        25.68 
TCGA-12-1600 TCGA-12-3644 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 
       14.73        59.77        26.93        15.22        10.95        12.69 
TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 
       34.92        14.53        14.93         3.22         2.04        15.12 
TCGA-14-0740 TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 
       11.97         0.95         6.21        23.05         2.24        11.24 
TCGA-14-0790 TCGA-14-0812 TCGA-14-0813 TCGA-14-0817 TCGA-14-0862 TCGA-14-0865 
       13.78         3.25         1.35         5.39         2.89        16.50 
TCGA-14-0866 TCGA-14-0867 TCGA-14-0871 TCGA-14-1034 TCGA-14-1037 TCGA-14-1043 
       26.33         2.04        28.93        15.95        19.30         0.79 
TCGA-14-1395 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 TCGA-14-1452 
        1.38         3.75        32.05        58.78        23.11         7.10 
TCGA-14-1453 TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 
        1.15        30.18         0.92        40.96         6.67        12.43 
TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 
        0.99         1.97        17.79         7.63         5.88         7.17 
TCGA-14-2554 TCGA-14-2555 TCGA-14-3477 TCGA-14-4157 TCGA-15-0742 TCGA-15-1444 
       17.49         7.96         3.78         3.42        13.78        50.53 
TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 
       19.10        53.19        13.28         3.91        17.59        26.07 
TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 
       16.37         4.31        29.03         4.57        10.29        14.01 
TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0957 TCGA-19-0960 
        9.14        21.24        13.97         6.41        21.90         8.61 
TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 
        0.66        14.27         3.39        10.75         9.07         5.95 
TCGA-19-1389 TCGA-19-1390 TCGA-19-1392 TCGA-19-1786 TCGA-19-1789 TCGA-19-1791 
        4.64        25.38         3.65         7.17         3.25         0.13 
TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 
        9.67         4.87         1.08         7.53         0.16         4.08 
TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 
       24.23         7.00         7.04         6.64        17.19         8.02 
TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 
       18.90         4.73        12.10         1.78        22.49        14.07 
TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 
       16.80        14.96        17.79        28.54        10.03        13.87 
TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5133 
        9.73        31.33         7.13         9.37         9.40        14.86 
TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 
        5.49         8.88        18.97         1.58         7.92         2.33 
TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 
       19.33         5.06        16.60         9.86        24.23        40.54 
TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 
       21.30        30.05        14.04        11.51        24.76        10.39 
TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 
       10.39        16.08         7.59         2.86        14.40        15.78 
TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 TCGA-28-1752 
        0.20         2.53         9.21         8.35         7.63         8.48 
TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 TCGA-28-2502 TCGA-28-2513 
        1.22         1.55         2.83         0.13         0.66         7.30 
TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 
        5.26        14.93        11.28        17.88        14.53        11.77 
TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 
       31.27        23.44        11.01         5.16        22.68        12.76 
TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 TCGA-32-1978 
        5.42        15.39        21.07         0.49         0.10        15.85 
TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 TCGA-32-1991 
       19.50         1.18         4.67        12.69        14.86        16.93 
TCGA-32-2491 TCGA-32-2494 TCGA-32-2615 TCGA-32-2616 TCGA-32-2634 TCGA-32-2638 
       12.23        20.78        15.95         7.36        22.78        25.18 
TCGA-32-4208 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 
       21.14        12.59        19.86        10.85        19.23         0.85 
TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 
       13.35         8.94         9.53         0.99         4.44        11.84 
TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 
        0.20        15.12        12.46         4.14        14.76         3.45 
TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 TCGA-76-4925 
       20.91         4.34        14.33         8.22         7.50         4.80 
TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-4935 TCGA-76-6191 
        4.54         3.09         3.65         9.17        10.78        16.70 
TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 
        3.29         2.70        11.38        17.06         8.35        20.98 
TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 
        4.83         5.03         0.23         9.27         7.73         7.79 
TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC 
        1.61        17.72        26.30         5.92         6.28        20.55 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             1.08              0.10 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            92.65            127.59 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             8.81             12.16 
[1] "1.1 - 92.7 (8.8)"   "0.1 - 127.6 (12.2)"
[1] "hr=" "1.2"
D10V2, continuous
D10V3, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    21  20
  5Q GAIN WILD-TYPE 203 326
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     21   20
  5Q GAIN WILD-TYPE  203  326
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE              21               203
  MALE                20               326
[1] 2 2
[1] FALSE
D10V4, continuous
                   vv
clus                GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  5Q GAIN MUTATED                               3                   3
  5Q GAIN WILD-TYPE                            24                  15
                   vv
clus                UNTREATED PRIMARY (DE NOVO) GBM
  5Q GAIN MUTATED                                35
  5Q GAIN WILD-TYPE                             490
D10V5, multiclass
                                 clus
vv                                5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                 3                24
  TREATED PRIMARY GBM                           3                15
  UNTREATED PRIMARY (DE NOVO) GBM              35               490
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V6, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    26  15
  5Q GAIN WILD-TYPE 356 173
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     26   15
  5Q GAIN WILD-TYPE  356  173
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  NO               26               356
  YES              15               173
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5Q GAIN MUTATED       1                         4    35
  5Q GAIN WILD-TYPE    12                        45   450
D10V7, multiclass
                           clus
vv                          5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  ASIAN                                   1                12
  BLACK OR AFRICAN AMERICAN               4                45
  WHITE                                  35               450
[1] 3 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  37
  5Q GAIN WILD-TYPE  12 435
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      0   37
  5Q GAIN WILD-TYPE   12  435
                        clus
vv                       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                12
  NOT HISPANIC OR LATINO              37               435
[1] 2 2
[1] FALSE

Clustering(11) Variable = 6P GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                 0   1
  6P GAIN MUTATED     5  19
  6P GAIN WILD-TYPE  99 446
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               24               545 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               19               446 
$`6P GAIN MUTATED`
TCGA-02-0052 TCGA-02-0069 TCGA-06-0177 TCGA-06-0237 TCGA-06-0410 TCGA-06-0414 
       12.59        28.70         4.18        13.64         4.70        35.11 
TCGA-06-A5U0 TCGA-08-0386 TCGA-08-0516 TCGA-12-0619 TCGA-12-0662 TCGA-12-0776 
        4.70        18.02        19.59        34.92        38.17         9.73 
TCGA-12-1092 TCGA-12-1598 TCGA-14-1454 TCGA-14-1794 TCGA-15-1447 TCGA-15-1449 
       21.73        15.65        30.18         0.99        53.19        13.28 
TCGA-19-1388 TCGA-27-1831 TCGA-28-5216 TCGA-76-4934 TCGA-76-6280 TCGA-81-5911 
       12.95        16.60        13.64         2.53        11.38        17.72 

$`6P GAIN WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 
       11.77         4.73        18.35        23.18        10.59        35.41 
TCGA-02-0011 TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 
       20.71        82.59        20.61        87.06        77.65        20.12 
TCGA-02-0024 TCGA-02-0025 TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 
       53.10        42.74        24.59        12.16        90.58         2.83 
TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 
       14.14         3.62        10.72        10.52        18.31         6.87 
TCGA-02-0047 TCGA-02-0048 TCGA-02-0051 TCGA-02-0054 TCGA-02-0055 TCGA-02-0057 
       14.73         3.22        15.09         6.54         2.50        19.86 
TCGA-02-0058 TCGA-02-0059 TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 TCGA-02-0070 
        8.35         9.57         6.02        19.73        26.43        25.05 
TCGA-02-0071 TCGA-02-0074 TCGA-02-0075 TCGA-02-0079 TCGA-02-0080 TCGA-02-0083 
        5.49        10.19        20.84        27.25        89.72        22.72 
TCGA-02-0084 TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 
       12.62        51.32         8.81        57.76        16.96         3.48 
TCGA-02-0102 TCGA-02-0104 TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 TCGA-02-0113 
       27.02        65.00        11.67        17.65        23.18        92.65 
TCGA-02-0114 TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 TCGA-02-0266 
       99.98        15.65        48.95        16.54        16.93        17.72 
TCGA-02-0269 TCGA-02-0271 TCGA-02-0281 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 
       10.75        14.47         3.98        13.87        14.20        15.95 
TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 
       12.23         9.90         7.73        10.62         7.33        15.91 
TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 
       25.71         4.37        25.12        10.59        12.39        14.50 
TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 
       10.55        47.11        11.34         9.27        16.21         3.35 
TCGA-02-2466 TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 
       16.80        12.92        15.32        15.45        20.32         2.70 
TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 
        6.15        20.38        47.61         6.94         3.98        22.72 
TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 
       33.67        12.95        25.35        14.30        26.70        24.23 
TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 
       11.90         0.20        10.29         2.20        11.74         2.33 
TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 
       20.09        17.79        10.09         8.61        19.46        46.59 
TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 
       12.33        13.94        10.45         3.19        10.82         9.44 
TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 
       11.80         3.42        56.91        10.65         5.85        19.66 
TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 
        3.29        13.12         4.47         3.22         4.04        91.00 
TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 
       88.14        20.25         3.65        69.90        73.84        27.22 
TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 
       44.58        15.42        10.42        38.96         4.67         7.40 
TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 
        5.56         0.39         7.66         8.42         7.63         7.40 
TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 
       11.84         0.53        15.02        24.16         0.72        19.82 
TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 
       13.32        20.42        48.69        10.82         9.01         0.26 
TCGA-06-0409 TCGA-06-0412 TCGA-06-0413 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 
       72.36         9.57         3.16        12.62         5.75         5.75 
TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 
        9.80         2.10        23.57        14.20        26.40        46.88 
TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 
        7.86         2.70         2.70         0.92        43.46        46.19 
TCGA-06-0877 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 
        5.65         7.17        40.41        16.57        20.78        26.76 
TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 
       23.93         6.84         4.04        26.79        11.84        15.32 
TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 
       13.61        33.90        15.32         1.08        12.49         4.93 
TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 
       17.65        12.56        30.64         5.95        16.64         5.98 
TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 
        4.37         0.43        31.50        11.74         3.55         8.35 
TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 TCGA-06-5418 
        4.54         8.81         8.98         8.55         6.71         2.73 
TCGA-06-5856 TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 TCGA-06-6389 TCGA-06-6390 
        3.75         6.15         4.57         5.23         7.79         5.39 
TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 
        1.48       120.56         7.36         8.32        12.85         4.77 
TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 
        1.55         4.77         4.96         1.87         3.12         2.56 
TCGA-06-A7TK TCGA-06-A7TL TCGA-08-0244 TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 
        5.39         5.42        22.68        37.84         4.18       115.86 
TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 
        1.74         8.42        25.71        12.16         9.80        29.23 
TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 
       65.33         1.28         8.42        17.95        24.56        31.10 
TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0389 
       37.58        22.29         3.39        12.23        14.93        15.35 
TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 
       13.97         0.72        12.56         4.27        42.15        11.08 
TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 
       58.68        19.33        10.75         4.80         7.27        15.98 
TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0620 
       18.41         7.56        15.35        14.73        12.99        10.45 
TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 
        7.59        94.78         0.10        25.97        26.66        12.13 
TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 
        3.65        20.38        28.41        15.06        53.85        43.23 
TCGA-12-0775 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 
        7.63        14.93        14.86        91.76        24.79        18.48 
TCGA-12-0821 TCGA-12-0822 TCGA-12-0826 TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 
       10.62        23.51        27.78        38.76         8.94        20.58 
TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 TCGA-12-1093 TCGA-12-1094 
      127.59         5.82         7.59        33.21        15.98        12.23 
TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 TCGA-12-1599 
       15.85         9.11        14.53         3.98         4.14        25.68 
TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 
       14.73         6.77        59.77        44.02        26.93        15.22 
TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 
       10.95        12.69        34.92        14.53        14.93         3.22 
TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 
        2.04        15.12        11.97         0.95         6.21        23.05 
TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 TCGA-14-0812 TCGA-14-0813 TCGA-14-0817 
        2.24        11.24        13.78         3.25         1.35         5.39 
TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 TCGA-14-0867 TCGA-14-0871 TCGA-14-1034 
        2.89        16.50        26.33         2.04        28.93        15.95 
TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 
       19.30         0.79         1.38         1.12         3.75        32.05 
TCGA-14-1450 TCGA-14-1451 TCGA-14-1452 TCGA-14-1453 TCGA-14-1455 TCGA-14-1456 
       58.78        23.11         7.10         1.15         0.92        40.96 
TCGA-14-1458 TCGA-14-1459 TCGA-14-1795 TCGA-14-1821 TCGA-14-1823 TCGA-14-1825 
        6.67        12.43         1.97        17.79        17.85         7.63 
TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-3477 TCGA-14-4157 
        5.88         7.17        17.49         7.96         3.78         3.42 
TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 
       13.78        50.53        19.10         3.91        17.59        26.07 
TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 
       16.37         4.31        29.03         4.57        10.29        14.01 
TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 
        9.14        21.24        13.97         6.41        11.77        21.90 
TCGA-19-0960 TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 
        8.61         0.66        14.27         3.39        10.75         9.07 
TCGA-19-1387 TCGA-19-1389 TCGA-19-1390 TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 
        5.95         4.64        25.38         3.65         7.17        12.66 
TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 
        3.25         0.13         9.67         4.87         1.08         7.53 
TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 
        0.16         4.08        24.23         7.00         7.04         6.64 
TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 
       17.19         8.02        18.90         4.73        12.10         1.78 
TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J4 
       22.49        14.07        16.80        14.96        17.79         3.98 
TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 
       28.54        10.03        13.87         9.73        31.33         7.13 
TCGA-26-1799 TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 
        9.37         9.40        14.86         5.49         8.88        18.97 
TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1832 
        1.58         7.92         2.33        19.33         5.06         9.86 
TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 
       24.23        40.54        21.30        30.05        14.04        11.51 
TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 
       24.76        10.39        10.39        16.08         7.59         2.86 
TCGA-27-2527 TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 
       14.40        15.78         0.20         2.53         9.21         8.35 
TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 
        7.63         8.48         1.22         1.55         2.83         0.13 
TCGA-28-2502 TCGA-28-2506 TCGA-28-2509 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 
        0.66         6.74         4.77         7.30         5.26        14.93 
TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 
       11.28        17.88        14.53        11.77        31.27        23.44 
TCGA-28-5215 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 
       11.01         5.16        22.68        12.76         5.42        15.39 
TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 TCGA-32-1980 
       21.07         0.49         0.10        15.85        19.50         1.18 
TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 
        4.67        12.69        14.86        16.93        12.23        20.78 
TCGA-32-2495 TCGA-32-2615 TCGA-32-2616 TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 
       15.02        15.95         7.36         8.84        22.78        25.18 
TCGA-32-4208 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 
       21.14         3.72        12.59        19.86        10.85        19.23 
TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 
        0.85        13.35         8.94         9.53         0.99         4.44 
TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9S TCGA-4W-AA9T 
       11.84         0.20        15.12        12.46         4.14        14.76 
TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 
        3.45        20.91         4.34        14.33         8.22         7.50 
TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-4935 
        4.80         4.54         3.09         3.65         9.17        10.78 
TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 
       16.70         3.29         2.70        17.06         8.35        20.98 
TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 
        4.83         5.03         0.23         9.27         7.73         7.79 
TCGA-81-5910 TCGA-87-5896 TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC 
        1.61        26.30         5.92         6.28        20.55 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             0.99              0.10 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            53.19            127.59 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           14.645            11.770 
[1] "1.0 - 53.2 (14.6)"  "0.1 - 127.6 (11.8)"
[1] "hr=" "1.2"
D11V2, continuous
D11V3, binary
                   cls
clus                  0   1
  6P GAIN MUTATED     8  16
  6P GAIN WILD-TYPE 216 330
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      8   16
  6P GAIN WILD-TYPE  216  330
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE               8               216
  MALE                16               330
[1] 2 2
[1] FALSE
D11V4, continuous
                   vv
clus                GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  6P GAIN MUTATED                               1                   0
  6P GAIN WILD-TYPE                            26                  18
                   vv
clus                UNTREATED PRIMARY (DE NOVO) GBM
  6P GAIN MUTATED                                23
  6P GAIN WILD-TYPE                             502
D11V5, multiclass
                                 clus
vv                                6P GAIN MUTATED 6P GAIN WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                 1                26
  TREATED PRIMARY GBM                           0                18
  UNTREATED PRIMARY (DE NOVO) GBM              23               502
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V6, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    19   5
  6P GAIN WILD-TYPE 363 183
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     19    5
  6P GAIN WILD-TYPE  363  183
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  NO               19               363
  YES               5               183
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6P GAIN MUTATED       1                         1    21
  6P GAIN WILD-TYPE    12                        48   464
D11V7, multiclass
                           clus
vv                          6P GAIN MUTATED 6P GAIN WILD-TYPE
  ASIAN                                   1                12
  BLACK OR AFRICAN AMERICAN               1                48
  WHITE                                  21               464
[1] 3 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  17
  6P GAIN WILD-TYPE  12 455
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      0   17
  6P GAIN WILD-TYPE   12  455
                        clus
vv                       6P GAIN MUTATED 6P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                12
  NOT HISPANIC OR LATINO              17               455
[1] 2 2
[1] FALSE

Clustering(12) Variable = 6Q GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                 0   1
  6Q GAIN MUTATED     6  17
  6Q GAIN WILD-TYPE  98 448
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               23               546 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               17               448 
$`6Q GAIN MUTATED`
TCGA-02-0052 TCGA-02-0069 TCGA-06-0177 TCGA-06-0237 TCGA-06-0410 TCGA-06-0414 
       12.59        28.70         4.18        13.64         4.70        35.11 
TCGA-06-2569 TCGA-06-A5U0 TCGA-08-0386 TCGA-08-0516 TCGA-12-0619 TCGA-12-0662 
        0.43         4.70        18.02        19.59        34.92        38.17 
TCGA-12-0776 TCGA-12-1092 TCGA-12-1598 TCGA-14-1454 TCGA-14-1794 TCGA-15-1447 
        9.73        21.73        15.65        30.18         0.99        53.19 
TCGA-15-1449 TCGA-19-1388 TCGA-28-5216 TCGA-76-4934 TCGA-81-5911 
       13.28        12.95        13.64         2.53        17.72 

$`6Q GAIN WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 
       11.77         4.73        18.35        23.18        10.59        35.41 
TCGA-02-0011 TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 
       20.71        82.59        20.61        87.06        77.65        20.12 
TCGA-02-0024 TCGA-02-0025 TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 
       53.10        42.74        24.59        12.16        90.58         2.83 
TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 
       14.14         3.62        10.72        10.52        18.31         6.87 
TCGA-02-0047 TCGA-02-0048 TCGA-02-0051 TCGA-02-0054 TCGA-02-0055 TCGA-02-0057 
       14.73         3.22        15.09         6.54         2.50        19.86 
TCGA-02-0058 TCGA-02-0059 TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 TCGA-02-0070 
        8.35         9.57         6.02        19.73        26.43        25.05 
TCGA-02-0071 TCGA-02-0074 TCGA-02-0075 TCGA-02-0079 TCGA-02-0080 TCGA-02-0083 
        5.49        10.19        20.84        27.25        89.72        22.72 
TCGA-02-0084 TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 
       12.62        51.32         8.81        57.76        16.96         3.48 
TCGA-02-0102 TCGA-02-0104 TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 TCGA-02-0113 
       27.02        65.00        11.67        17.65        23.18        92.65 
TCGA-02-0114 TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 TCGA-02-0266 
       99.98        15.65        48.95        16.54        16.93        17.72 
TCGA-02-0269 TCGA-02-0271 TCGA-02-0281 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 
       10.75        14.47         3.98        13.87        14.20        15.95 
TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 
       12.23         9.90         7.73        10.62         7.33        15.91 
TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 
       25.71         4.37        25.12        10.59        12.39        14.50 
TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 
       10.55        47.11        11.34         9.27        16.21         3.35 
TCGA-02-2466 TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 
       16.80        12.92        15.32        15.45        20.32         2.70 
TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 
        6.15        20.38        47.61         6.94         3.98        22.72 
TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 
       33.67        12.95        25.35        14.30        26.70        24.23 
TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 
       11.90         0.20        10.29         2.20        11.74         2.33 
TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 
       20.09        17.79        10.09         8.61        19.46        46.59 
TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 
       12.33        13.94        10.45         3.19        10.82         9.44 
TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 
       11.80         3.42        56.91        10.65         5.85        19.66 
TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 
        3.29        13.12         4.47         3.22         4.04        91.00 
TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 
       88.14        20.25         3.65        69.90        73.84        27.22 
TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 
       44.58        15.42        10.42        38.96         4.67         7.40 
TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 
        5.56         0.39         7.66         8.42         7.63         7.40 
TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 
       11.84         0.53        15.02        24.16         0.72        19.82 
TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 
       13.32        20.42        48.69        10.82         9.01         0.26 
TCGA-06-0409 TCGA-06-0412 TCGA-06-0413 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 
       72.36         9.57         3.16        12.62         5.75         5.75 
TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 
        9.80         2.10        23.57        14.20        26.40        46.88 
TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 
        7.86         2.70         2.70         0.92        43.46        46.19 
TCGA-06-0877 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 
        5.65         7.17        40.41        16.57        20.78        26.76 
TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 
       23.93         6.84         4.04        26.79        11.84        15.32 
TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 
       13.61        33.90        15.32         1.08        12.49         4.93 
TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 
       17.65        12.56        30.64         5.95        16.64         5.98 
TCGA-06-2567 TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 
        4.37        31.50        11.74         3.55         8.35         4.54 
TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 TCGA-06-5418 TCGA-06-5856 
        8.81         8.98         8.55         6.71         2.73         3.75 
TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 
        6.15         4.57         5.23         7.79         5.39         1.48 
TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 
      120.56         7.36         8.32        12.85         4.77         1.55 
TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK 
        4.77         4.96         1.87         3.12         2.56         5.39 
TCGA-06-A7TL TCGA-08-0244 TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 
        5.42        22.68        37.84         4.18       115.86         1.74 
TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 
        8.42        25.71        12.16         9.80        29.23        65.33 
TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 
        1.28         8.42        17.95        24.56        31.10        37.58 
TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0389 TCGA-08-0390 
       22.29         3.39        12.23        14.93        15.35        13.97 
TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 TCGA-08-0517 
        0.72        12.56         4.27        42.15        11.08        58.68 
TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 
       19.33        10.75         4.80         7.27        15.98        18.41 
TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0620 TCGA-12-0654 
        7.56        15.35        14.73        12.99        10.45         7.59 
TCGA-12-0656 TCGA-12-0657 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 
       94.78         0.10        25.97        26.66        12.13         3.65 
TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 
       20.38        28.41        15.06        53.85        43.23         7.63 
TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 
       14.93        14.86        91.76        24.79        18.48        10.62 
TCGA-12-0822 TCGA-12-0826 TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 
       23.51        27.78        38.76         8.94        20.58       127.59 
TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 
        5.82         7.59        33.21        15.98        12.23        15.85 
TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 TCGA-12-1599 TCGA-12-1600 
        9.11        14.53         3.98         4.14        25.68        14.73 
TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 
        6.77        59.77        44.02        26.93        15.22        10.95 
TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 
       12.69        34.92        14.53        14.93         3.22         2.04 
TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 TCGA-14-0787 
       15.12        11.97         0.95         6.21        23.05         2.24 
TCGA-14-0789 TCGA-14-0790 TCGA-14-0812 TCGA-14-0813 TCGA-14-0817 TCGA-14-0862 
       11.24        13.78         3.25         1.35         5.39         2.89 
TCGA-14-0865 TCGA-14-0866 TCGA-14-0867 TCGA-14-0871 TCGA-14-1034 TCGA-14-1037 
       16.50        26.33         2.04        28.93        15.95        19.30 
TCGA-14-1043 TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 
        0.79         1.38         1.12         3.75        32.05        58.78 
TCGA-14-1451 TCGA-14-1452 TCGA-14-1453 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 
       23.11         7.10         1.15         0.92        40.96         6.67 
TCGA-14-1459 TCGA-14-1795 TCGA-14-1821 TCGA-14-1823 TCGA-14-1825 TCGA-14-1827 
       12.43         1.97        17.79        17.85         7.63         5.88 
TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-3477 TCGA-14-4157 TCGA-15-0742 
        7.17        17.49         7.96         3.78         3.42        13.78 
TCGA-15-1444 TCGA-15-1446 TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 
       50.53        19.10         3.91        17.59        26.07        16.37 
TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 
        4.31        29.03         4.57        10.29        14.01         9.14 
TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 
       21.24        13.97         6.41        11.77        21.90         8.61 
TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 
        0.66        14.27         3.39        10.75         9.07         5.95 
TCGA-19-1389 TCGA-19-1390 TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 
        4.64        25.38         3.65         7.17        12.66         3.25 
TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 
        0.13         9.67         4.87         1.08         7.53         0.16 
TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 
        4.08        24.23         7.00         7.04         6.64        17.19 
TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 
        8.02        18.90         4.73        12.10         1.78        22.49 
TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J4 TCGA-19-A6J5 
       14.07        16.80        14.96        17.79         3.98        28.54 
TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 
       10.03        13.87         9.73        31.33         7.13         9.37 
TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 
        9.40        14.86         5.49         8.88        18.97         1.58 
TCGA-26-6173 TCGA-26-6174 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 
        7.92         2.33        19.33         5.06        16.60         9.86 
TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 
       24.23        40.54        21.30        30.05        14.04        11.51 
TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 
       24.76        10.39        10.39        16.08         7.59         2.86 
TCGA-27-2527 TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 
       14.40        15.78         0.20         2.53         9.21         8.35 
TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 
        7.63         8.48         1.22         1.55         2.83         0.13 
TCGA-28-2502 TCGA-28-2506 TCGA-28-2509 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 
        0.66         6.74         4.77         7.30         5.26        14.93 
TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 
       11.28        17.88        14.53        11.77        31.27        23.44 
TCGA-28-5215 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 
       11.01         5.16        22.68        12.76         5.42        15.39 
TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 TCGA-32-1980 
       21.07         0.49         0.10        15.85        19.50         1.18 
TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 
        4.67        12.69        14.86        16.93        12.23        20.78 
TCGA-32-2495 TCGA-32-2615 TCGA-32-2616 TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 
       15.02        15.95         7.36         8.84        22.78        25.18 
TCGA-32-4208 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 
       21.14         3.72        12.59        19.86        10.85        19.23 
TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 
        0.85        13.35         8.94         9.53         0.99         4.44 
TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9S TCGA-4W-AA9T 
       11.84         0.20        15.12        12.46         4.14        14.76 
TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 
        3.45        20.91         4.34        14.33         8.22         7.50 
TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-4935 
        4.80         4.54         3.09         3.65         9.17        10.78 
TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 
       16.70         3.29         2.70        11.38        17.06         8.35 
TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 
       20.98         4.83         5.03         0.23         9.27         7.73 
TCGA-76-6664 TCGA-81-5910 TCGA-87-5896 TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC 
        7.79         1.61        26.30         5.92         6.28        20.55 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
             0.43              0.10 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            53.19            127.59 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            13.64             11.77 
[1] "0.4 - 53.2 (13.6)"  "0.1 - 127.6 (11.8)"
[1] "hr=" "1.3"
D12V2, continuous
D12V3, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     9  14
  6Q GAIN WILD-TYPE 215 332
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      9   14
  6Q GAIN WILD-TYPE  215  332
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE               9               215
  MALE                14               332
[1] 2 2
[1] FALSE
D12V4, continuous
                   vv
clus                GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  6Q GAIN MUTATED                               1                   0
  6Q GAIN WILD-TYPE                            26                  18
                   vv
clus                UNTREATED PRIMARY (DE NOVO) GBM
  6Q GAIN MUTATED                                22
  6Q GAIN WILD-TYPE                             503
D12V5, multiclass
                                 clus
vv                                6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                 1                26
  TREATED PRIMARY GBM                           0                18
  UNTREATED PRIMARY (DE NOVO) GBM              22               503
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V6, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    17   6
  6Q GAIN WILD-TYPE 365 182
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     17    6
  6Q GAIN WILD-TYPE  365  182
     clus
vv    6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  NO               17               365
  YES               6               182
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6Q GAIN MUTATED       1                         2    19
  6Q GAIN WILD-TYPE    12                        47   466
D12V7, multiclass
                           clus
vv                          6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  ASIAN                                   1                12
  BLACK OR AFRICAN AMERICAN               2                47
  WHITE                                  19               466
[1] 3 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
  6Q GAIN MUTATED     0  16
  6Q GAIN WILD-TYPE  12 456
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      0   16
  6Q GAIN WILD-TYPE   12  456
                        clus
vv                       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                12
  NOT HISPANIC OR LATINO              16               456
[1] 2 2
[1] FALSE

Clustering(13) Variable = 7P GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                 0   1
  7P GAIN MUTATED    76 385
  7P GAIN WILD-TYPE  28  80
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              461               108 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              385                80 
$`7P GAIN MUTATED`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0016 
       11.77         4.73        18.35        23.18        10.59        87.06 
TCGA-02-0021 TCGA-02-0023 TCGA-02-0025 TCGA-02-0027 TCGA-02-0033 TCGA-02-0034 
       77.65        20.12        42.74        12.16         2.83        14.14 
TCGA-02-0037 TCGA-02-0038 TCGA-02-0043 TCGA-02-0046 TCGA-02-0051 TCGA-02-0052 
        3.62        10.72        18.31         6.87        15.09        12.59 
TCGA-02-0054 TCGA-02-0055 TCGA-02-0057 TCGA-02-0059 TCGA-02-0064 TCGA-02-0070 
        6.54         2.50        19.86         9.57        19.73        25.05 
TCGA-02-0071 TCGA-02-0074 TCGA-02-0075 TCGA-02-0079 TCGA-02-0085 TCGA-02-0086 
        5.49        10.19        20.84        27.25        51.32         8.81 
TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 TCGA-02-0106 TCGA-02-0107 
       57.76        16.96         3.48        27.02        11.67        17.65 
TCGA-02-0111 TCGA-02-0113 TCGA-02-0115 TCGA-02-0116 TCGA-02-0260 TCGA-02-0266 
       23.18        92.65        15.65        48.95        16.93        17.72 
TCGA-02-0269 TCGA-02-0271 TCGA-02-0281 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 
       10.75        14.47         3.98        13.87        14.20        15.95 
TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 
       12.23         9.90         7.73        10.62         7.33        15.91 
TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 TCGA-02-0430 TCGA-02-0440 TCGA-02-0446 
       25.71         4.37        25.12        10.55        11.34         9.27 
TCGA-02-0451 TCGA-02-0456 TCGA-02-2466 TCGA-02-2470 TCGA-02-2485 TCGA-02-2486 
       16.21         3.35        16.80        12.92        15.45        20.32 
TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0128 
        2.70         6.15        20.38        47.61         6.94        22.72 
TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 
       12.95        25.35        14.30        26.70        24.23        11.90 
TCGA-06-0140 TCGA-06-0141 TCGA-06-0143 TCGA-06-0145 TCGA-06-0147 TCGA-06-0148 
        0.20        10.29        11.74         2.33        17.79        10.09 
TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 
        8.61        19.46        46.59        12.33        13.94        10.45 
TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0164 TCGA-06-0166 TCGA-06-0168 
        3.19        10.82         9.44        56.91         5.85        19.66 
TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 
        3.29        13.12         4.47         3.22         4.04        91.00 
TCGA-06-0177 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0188 
        4.18        20.25         3.65        69.90        73.84        44.58 
TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 
       15.42        10.42        38.96         4.67         7.40         5.56 
TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 
        0.39         7.66         8.42         7.63         7.40        11.84 
TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0237 TCGA-06-0238 TCGA-06-0241 
        0.53        15.02        24.16        13.64        13.32        48.69 
TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0412 TCGA-06-0413 
       10.82         9.01         0.26        72.36         9.57         3.16 
TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 
       35.11        12.62         5.75         5.75         9.80         2.10 
TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0749 
       23.57        14.20        26.40        46.88         7.86         2.70 
TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 TCGA-06-0879 
        0.92        43.46        46.19         5.65         7.17        40.41 
TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 
       16.57        20.78        26.76        23.93         6.84         4.04 
TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1806 TCGA-06-2557 
       26.79        11.84        15.32        13.61        15.32         1.08 
TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 
       12.49         4.93        17.65        12.56        30.64         5.95 
TCGA-06-2567 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 
        4.37        11.74         3.55         8.35         4.54         8.81 
TCGA-06-5414 TCGA-06-5415 TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 TCGA-06-5859 
        8.98         8.55         2.73         3.75         6.15         4.57 
TCGA-06-6388 TCGA-06-6390 TCGA-06-6391 TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 
        5.23         5.39         1.48         7.36         8.32        12.85 
TCGA-06-6698 TCGA-06-6699 TCGA-06-A5U1 TCGA-06-A6S1 TCGA-06-A7TK TCGA-08-0244 
        4.77         1.55         1.87         2.56         5.39        22.68 
TCGA-08-0245 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 
       37.84         1.74         8.42        25.71        12.16         9.80 
TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 
        1.28         8.42        17.95        24.56        31.10        37.58 
TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 
       22.29         3.39        12.23        14.93        18.02        15.35 
TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 TCGA-08-0518 TCGA-08-0520 
       13.97         0.72        12.56         4.27        19.33        10.75 
TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 
       15.98        18.41         7.56        14.73        12.99        34.92 
TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 
       10.45         7.59        94.78         0.10        38.17        25.97 
TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 
       26.66        12.13         3.65        20.38        28.41        15.06 
TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 
       53.85        43.23         7.63         9.73        14.93        14.86 
TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 TCGA-12-0826 TCGA-12-0827 
       24.79        18.48        10.62        23.51        27.78        38.76 
TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 
        8.94        20.58       127.59         5.82         7.59        33.21 
TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 
       21.73        15.98        12.23        15.85         9.11        14.53 
TCGA-12-1098 TCGA-12-1099 TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 
        3.98         4.14        15.65        25.68        14.73         6.77 
TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 
       59.77        44.02        26.93        15.22        10.95        12.69 
TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 
       34.92        14.53        14.93         3.22         2.04        15.12 
TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 
        0.95         6.21        23.05         2.24        11.24        13.78 
TCGA-14-0813 TCGA-14-0817 TCGA-14-0866 TCGA-14-0867 TCGA-14-0871 TCGA-14-1034 
        1.35         5.39        26.33         2.04        28.93        15.95 
TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 TCGA-14-1450 
       19.30         0.79         1.38         1.12         3.75        58.78 
TCGA-14-1451 TCGA-14-1452 TCGA-14-1453 TCGA-14-1454 TCGA-14-1455 TCGA-14-1458 
       23.11         7.10         1.15        30.18         0.92         6.67 
TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1823 TCGA-14-1825 TCGA-14-1827 
       12.43         0.99         1.97        17.85         7.63         5.88 
TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-4157 TCGA-15-0742 TCGA-15-1446 
        7.17        17.49         7.96         3.42        13.78        19.10 
TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 
       13.28         3.91        17.59         4.31        29.03         4.57 
TCGA-16-1055 TCGA-16-1056 TCGA-16-1062 TCGA-16-1063 TCGA-19-0955 TCGA-19-0957 
       10.29        14.01        21.24        13.97        11.77        21.90 
TCGA-19-0962 TCGA-19-0963 TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 TCGA-19-1388 
        0.66        14.27        10.75         9.07         5.95        12.95 
TCGA-19-1389 TCGA-19-1390 TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 TCGA-19-1791 
        4.64        25.38         3.65         7.17        12.66         0.13 
TCGA-19-2619 TCGA-19-2623 TCGA-19-2624 TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 
        9.67         7.53         0.16        24.23         7.00         7.04 
TCGA-19-5947 TCGA-19-5950 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 
        6.64        17.19        18.90         4.73        12.10         1.78 
TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J4 TCGA-19-A6J5 
       14.07        16.80        14.96        17.79         3.98        28.54 
TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 
       10.03        13.87         9.73         7.13         9.37         9.40 
TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-26-A7UX 
        8.88        18.97         1.58         7.92         2.33        19.33 
TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 
        5.06        16.60         9.86        24.23        40.54        21.30 
TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 
       11.51        24.76        10.39        16.08         7.59         2.86 
TCGA-27-2527 TCGA-28-1746 TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 TCGA-28-1752 
       14.40         0.20         9.21         8.35         7.63         8.48 
TCGA-28-1753 TCGA-28-1755 TCGA-28-1757 TCGA-28-2502 TCGA-28-2506 TCGA-28-2509 
        1.22         1.55         0.13         0.66         6.74         4.77 
TCGA-28-2513 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 
        7.30        14.93        11.28        17.88        14.53        11.77 
TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 
       31.27        23.44        11.01         5.16        22.68        12.76 
TCGA-28-6450 TCGA-32-1970 TCGA-32-1976 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 
        5.42        15.39         0.49         0.10        15.85        19.50 
TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 TCGA-32-2491 TCGA-32-2494 
        1.18         4.67        12.69        14.86        12.23        20.78 
TCGA-32-2616 TCGA-32-2632 TCGA-32-2638 TCGA-32-4210 TCGA-32-4211 TCGA-32-5222 
        7.36         8.84        25.18         3.72        12.59        19.23 
TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 
        0.85        13.35         8.94         9.53         0.99         4.44 
TCGA-41-3915 TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 
       11.84        15.12        12.46         4.14        14.76         3.45 
TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 TCGA-76-4925 
       20.91         4.34        14.33         8.22         7.50         4.80 
TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-4934 TCGA-76-4935 
        4.54         3.09         3.65         9.17         2.53        10.78 
TCGA-76-6191 TCGA-76-6192 TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 
       16.70         3.29        11.38        17.06         8.35        20.98 
TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 
        5.03         0.23         9.27         7.73         7.79         1.61 
TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC 
       17.72        26.30         5.92         6.28        20.55 

$`7P GAIN WILD-TYPE`
TCGA-02-0010 TCGA-02-0011 TCGA-02-0014 TCGA-02-0015 TCGA-02-0024 TCGA-02-0026 
       35.41        20.71        82.59        20.61        53.10        24.59 
TCGA-02-0028 TCGA-02-0039 TCGA-02-0047 TCGA-02-0048 TCGA-02-0058 TCGA-02-0060 
       90.58        10.52        14.73         3.22         8.35         6.02 
TCGA-02-0068 TCGA-02-0069 TCGA-02-0080 TCGA-02-0083 TCGA-02-0084 TCGA-02-0104 
       26.43        28.70        89.72        22.72        12.62        65.00 
TCGA-02-0114 TCGA-02-0258 TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 TCGA-02-0432 
       99.98        16.54        10.59        12.39        14.50        47.11 
TCGA-02-2483 TCGA-06-0127 TCGA-06-0129 TCGA-06-0142 TCGA-06-0146 TCGA-06-0160 
       15.32         3.98        33.67         2.20        20.09        11.80 
TCGA-06-0162 TCGA-06-0165 TCGA-06-0178 TCGA-06-0187 TCGA-06-0219 TCGA-06-0221 
        3.42        10.65        88.14        27.22         0.72        19.82 
TCGA-06-0240 TCGA-06-0410 TCGA-06-0747 TCGA-06-1805 TCGA-06-2565 TCGA-06-2566 
       20.42         4.70         2.70        33.90        16.64         5.98 
TCGA-06-2569 TCGA-06-2570 TCGA-06-5416 TCGA-06-6389 TCGA-06-6693 TCGA-06-6700 
        0.43        31.50         6.71         7.79       120.56         4.77 
TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A6S0 TCGA-06-A7TL TCGA-08-0246 TCGA-08-0344 
        4.96         4.70         3.12         5.42         4.18       115.86 
TCGA-08-0350 TCGA-08-0351 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 
       29.23        65.33        42.15        11.08        19.59        58.68 
TCGA-08-0521 TCGA-08-0524 TCGA-12-0615 TCGA-12-0818 TCGA-14-0740 TCGA-14-0812 
        4.80         7.27        15.35        91.76        11.97         3.25 
TCGA-14-0862 TCGA-14-0865 TCGA-14-1402 TCGA-14-1456 TCGA-14-1821 TCGA-14-3477 
        2.89        16.50        32.05        40.96        17.79         3.78 
TCGA-15-1444 TCGA-15-1447 TCGA-16-0849 TCGA-16-0850 TCGA-16-1060 TCGA-16-1460 
       50.53        53.19        26.07        16.37         9.14         6.41 
TCGA-19-0960 TCGA-19-0964 TCGA-19-1789 TCGA-19-2620 TCGA-19-2621 TCGA-19-2625 
        8.61         3.39         3.25         4.87         1.08         4.08 
TCGA-19-5951 TCGA-19-5956 TCGA-26-1442 TCGA-26-5133 TCGA-26-5134 TCGA-27-1836 
        8.02        22.49        31.33        14.86         5.49        30.05 
TCGA-27-1837 TCGA-27-2521 TCGA-27-2528 TCGA-28-1747 TCGA-28-1756 TCGA-28-2514 
       14.04        10.39        15.78         2.53         2.83         5.26 
TCGA-28-5216 TCGA-32-1973 TCGA-32-1991 TCGA-32-2495 TCGA-32-2615 TCGA-32-2634 
       13.64        21.07        16.93        15.02        15.95        22.78 
TCGA-32-4208 TCGA-32-4213 TCGA-32-4719 TCGA-41-4097 TCGA-76-6193 TCGA-76-6656 
       21.14        19.86        10.85         0.20         2.70         4.83 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              0.1               0.2 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           127.59            120.56 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           11.740            14.795 
[1] "0.1 - 127.6 (11.7)" "0.2 - 120.6 (14.8)"
[1] "hr=" "1.7"
D13V2, continuous
D13V3, binary
                   cls
clus                  0   1
  7P GAIN MUTATED   180 282
  7P GAIN WILD-TYPE  44  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED    180  282
  7P GAIN WILD-TYPE   44   64
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE             180                44
  MALE               282                64
[1] 2 2
[1] FALSE
D13V4, continuous
                   vv
clus                GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  7P GAIN MUTATED                              19                  11
  7P GAIN WILD-TYPE                             8                   7
                   vv
clus                UNTREATED PRIMARY (DE NOVO) GBM
  7P GAIN MUTATED                               432
  7P GAIN WILD-TYPE                              93
D13V5, multiclass
                                 clus
vv                                7P GAIN MUTATED 7P GAIN WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                19                 8
  TREATED PRIMARY GBM                          11                 7
  UNTREATED PRIMARY (DE NOVO) GBM             432                93
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V6, binary
                   cls
clus                  0   1
  7P GAIN MUTATED   303 159
  7P GAIN WILD-TYPE  79  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED    303  159
  7P GAIN WILD-TYPE   79   29
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  NO              303                79
  YES             159                29
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7P GAIN MUTATED       7                        41   393
  7P GAIN WILD-TYPE     6                         8    92
D13V7, multiclass
                           clus
vv                          7P GAIN MUTATED 7P GAIN WILD-TYPE
  ASIAN                                   7                 6
  BLACK OR AFRICAN AMERICAN              41                 8
  WHITE                                 393                92
[1] 3 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
  7P GAIN MUTATED     8 379
  7P GAIN WILD-TYPE   4  93
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      8  379
  7P GAIN WILD-TYPE    4   93
                        clus
vv                       7P GAIN MUTATED 7P GAIN WILD-TYPE
  HISPANIC OR LATINO                   8                 4
  NOT HISPANIC OR LATINO             379                93
[1] 2 2
[1] FALSE

Clustering(14) Variable = 7Q GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                 0   1
  7Q GAIN MUTATED    80 386
  7Q GAIN WILD-TYPE  24  79
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              466               103 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              386                79 
$`7Q GAIN MUTATED`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0009 TCGA-02-0016 TCGA-02-0021 
       11.77         4.73        18.35        10.59        87.06        77.65 
TCGA-02-0023 TCGA-02-0025 TCGA-02-0027 TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 
       20.12        42.74        12.16         2.83        14.14         3.62 
TCGA-02-0038 TCGA-02-0043 TCGA-02-0046 TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 
       10.72        18.31         6.87        15.09        12.59         6.54 
TCGA-02-0055 TCGA-02-0057 TCGA-02-0059 TCGA-02-0064 TCGA-02-0070 TCGA-02-0071 
        2.50        19.86         9.57        19.73        25.05         5.49 
TCGA-02-0074 TCGA-02-0075 TCGA-02-0079 TCGA-02-0080 TCGA-02-0085 TCGA-02-0086 
       10.19        20.84        27.25        89.72        51.32         8.81 
TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 TCGA-02-0106 TCGA-02-0107 
       57.76        16.96         3.48        27.02        11.67        17.65 
TCGA-02-0111 TCGA-02-0113 TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 
       23.18        92.65        15.65        48.95        16.54        16.93 
TCGA-02-0266 TCGA-02-0269 TCGA-02-0271 TCGA-02-0281 TCGA-02-0285 TCGA-02-0289 
       17.72        10.75        14.47         3.98        13.87        14.20 
TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 
       15.95        12.23         9.90         7.73        10.62         7.33 
TCGA-02-0330 TCGA-02-0332 TCGA-02-0337 TCGA-02-0422 TCGA-02-0430 TCGA-02-0440 
       15.91        25.71        25.12        14.50        10.55        11.34 
TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 TCGA-02-2466 TCGA-02-2470 TCGA-02-2485 
        9.27        16.21         3.35        16.80        12.92        15.45 
TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 
       20.32         2.70         6.15        20.38        47.61         6.94 
TCGA-06-0128 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 
       22.72        12.95        25.35        14.30        26.70        24.23 
TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0143 TCGA-06-0145 TCGA-06-0147 
       11.90         0.20        10.29        11.74         2.33        17.79 
TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 
       10.09         8.61        19.46        46.59        12.33        13.94 
TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0164 TCGA-06-0166 
       10.45         3.19        10.82         9.44        56.91         5.85 
TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 
       19.66         3.29        13.12         4.47         3.22         4.04 
TCGA-06-0176 TCGA-06-0177 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 
       91.00         4.18        20.25         3.65        69.90        73.84 
TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 
       27.22        44.58        15.42        10.42        38.96         4.67 
TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 
        7.40         5.56         0.39         7.66         8.42         7.63 
TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0237 
        7.40        11.84         0.53        15.02        24.16        13.64 
TCGA-06-0238 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 
       13.32        48.69        10.82         9.01         0.26        72.36 
TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 
        9.57         3.16        35.11        12.62         5.75         5.75 
TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 
        9.80         2.10        23.57        14.20        26.40        46.88 
TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 
        7.86         2.70         2.70         0.92        43.46        46.19 
TCGA-06-0877 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 
        5.65         7.17        40.41        16.57        20.78        26.76 
TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 
       23.93         6.84         4.04        26.79        11.84        15.32 
TCGA-06-1804 TCGA-06-1806 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 
       13.61        15.32         1.08        12.49         4.93        17.65 
TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2567 TCGA-06-5408 TCGA-06-5410 
       12.56        30.64         5.95         4.37        11.74         3.55 
TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5418 
        8.35         4.54         8.81         8.98         8.55         2.73 
TCGA-06-5856 TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 TCGA-06-6390 TCGA-06-6391 
        3.75         6.15         4.57         5.23         5.39         1.48 
TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 
        7.36         8.32        12.85         4.77         1.55         4.77 
TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK TCGA-08-0244 TCGA-08-0345 
        1.87         3.12         2.56         5.39        22.68         1.74 
TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0352 TCGA-08-0353 
        8.42        25.71        12.16         9.80         1.28         8.42 
TCGA-08-0354 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 
       17.95        31.10        37.58        22.29         3.39        12.23 
TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 
       14.93        18.02        15.35        13.97         0.72        12.56 
TCGA-08-0510 TCGA-08-0518 TCGA-08-0520 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 
        4.27        19.33        10.75        15.98        18.41         7.56 
TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 
       14.73        12.99        34.92        10.45         7.59        94.78 
TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 
        0.10        38.17        25.97        26.66        12.13         3.65 
TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 
       20.38        28.41        15.06        53.85        43.23         7.63 
TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 
        9.73        14.93        14.86        91.76        24.79        18.48 
TCGA-12-0821 TCGA-12-0822 TCGA-12-0826 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 
       10.62        23.51        27.78         8.94        20.58       127.59 
TCGA-12-1089 TCGA-12-1090 TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 
        5.82         7.59        21.73        15.98        12.23        15.85 
TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 TCGA-12-1598 TCGA-12-1599 
        9.11        14.53         3.98         4.14        15.65        25.68 
TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 
       14.73         6.77        59.77        44.02        26.93        15.22 
TCGA-12-3650 TCGA-12-3651 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 
       10.95        12.69        14.53        14.93         3.22         2.04 
TCGA-14-0736 TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 
       15.12         0.95         6.21        23.05         2.24        11.24 
TCGA-14-0790 TCGA-14-0813 TCGA-14-0817 TCGA-14-0866 TCGA-14-0867 TCGA-14-0871 
       13.78         1.35         5.39        26.33         2.04        28.93 
TCGA-14-1034 TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 
       15.95        19.30         0.79         1.38         1.12         3.75 
TCGA-14-1450 TCGA-14-1451 TCGA-14-1452 TCGA-14-1454 TCGA-14-1455 TCGA-14-1458 
       58.78        23.11         7.10        30.18         0.92         6.67 
TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1823 TCGA-14-1825 TCGA-14-1827 
       12.43         0.99         1.97        17.85         7.63         5.88 
TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-4157 TCGA-15-0742 TCGA-15-1446 
        7.17        17.49         7.96         3.42        13.78        19.10 
TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 
       13.28         3.91        17.59         4.31        29.03         4.57 
TCGA-16-1055 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 
       10.29        21.24        13.97         6.41        11.77        21.90 
TCGA-19-0962 TCGA-19-0963 TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 TCGA-19-1388 
        0.66        14.27        10.75         9.07         5.95        12.95 
TCGA-19-1389 TCGA-19-1390 TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 TCGA-19-1791 
        4.64        25.38         3.65         7.17        12.66         0.13 
TCGA-19-2619 TCGA-19-2623 TCGA-19-2624 TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 
        9.67         7.53         0.16        24.23         7.00         7.04 
TCGA-19-5947 TCGA-19-5950 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 
        6.64        17.19        18.90         4.73        12.10         1.78 
TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J4 TCGA-19-A6J5 
       14.07        16.80        14.96        17.79         3.98        28.54 
TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 
       10.03        13.87         9.73        31.33         7.13         9.37 
TCGA-26-5132 TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 
        9.40         8.88        18.97         1.58         7.92         2.33 
TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 
       19.33         5.06        16.60         9.86        24.23        40.54 
TCGA-27-1835 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 
       21.30        14.04        11.51        24.76        10.39        10.39 
TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 
       16.08         7.59         2.86         0.20         2.53         9.21 
TCGA-28-1750 TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 TCGA-28-1755 TCGA-28-1757 
        8.35         7.63         8.48         1.22         1.55         0.13 
TCGA-28-2502 TCGA-28-2506 TCGA-28-2509 TCGA-28-2513 TCGA-28-5204 TCGA-28-5207 
        0.66         6.74         4.77         7.30        14.93        11.28 
TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5218 
       14.53        11.77        31.27        23.44        11.01         5.16 
TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1976 TCGA-32-1977 
       22.68        12.76         5.42        15.39         0.49         0.10 
TCGA-32-1978 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 
       15.85        19.50         1.18         4.67        12.69        14.86 
TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2616 TCGA-32-2632 
       16.93        12.23        20.78        15.02         7.36         8.84 
TCGA-32-2638 TCGA-32-4210 TCGA-32-4211 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 
       25.18         3.72        12.59        19.23         0.85        13.35 
TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 TCGA-41-5651 
        8.94         9.53         0.99         4.44        11.84        15.12 
TCGA-41-6646 TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 
       12.46         4.14        14.76         3.45        20.91         4.34 
TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 
       14.33         8.22         7.50         4.80         4.54         3.09 
TCGA-76-4929 TCGA-76-4931 TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 
        3.65         9.17         2.53        10.78        16.70         3.29 
TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 
       11.38        17.06         8.35        20.98         4.83         5.03 
TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 
        0.23         9.27         7.73         7.79         1.61        17.72 
TCGA-87-5896 TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC 
       26.30         5.92         6.28        20.55 

$`7Q GAIN WILD-TYPE`
TCGA-02-0007 TCGA-02-0010 TCGA-02-0011 TCGA-02-0014 TCGA-02-0015 TCGA-02-0024 
       23.18        35.41        20.71        82.59        20.61        53.10 
TCGA-02-0026 TCGA-02-0028 TCGA-02-0039 TCGA-02-0047 TCGA-02-0048 TCGA-02-0058 
       24.59        90.58        10.52        14.73         3.22         8.35 
TCGA-02-0060 TCGA-02-0068 TCGA-02-0069 TCGA-02-0083 TCGA-02-0084 TCGA-02-0104 
        6.02        26.43        28.70        22.72        12.62        65.00 
TCGA-02-0114 TCGA-02-0333 TCGA-02-0338 TCGA-02-0339 TCGA-02-0432 TCGA-02-2483 
       99.98         4.37        10.59        12.39        47.11        15.32 
TCGA-06-0127 TCGA-06-0129 TCGA-06-0142 TCGA-06-0146 TCGA-06-0160 TCGA-06-0162 
        3.98        33.67         2.20        20.09        11.80         3.42 
TCGA-06-0165 TCGA-06-0178 TCGA-06-0219 TCGA-06-0221 TCGA-06-0240 TCGA-06-0410 
       10.65        88.14         0.72        19.82        20.42         4.70 
TCGA-06-1805 TCGA-06-2565 TCGA-06-2566 TCGA-06-2569 TCGA-06-2570 TCGA-06-5416 
       33.90        16.64         5.98         0.43        31.50         6.71 
TCGA-06-6389 TCGA-06-6693 TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A7TL TCGA-08-0245 
        7.79       120.56         4.96         4.70         5.42        37.84 
TCGA-08-0246 TCGA-08-0344 TCGA-08-0350 TCGA-08-0351 TCGA-08-0355 TCGA-08-0512 
        4.18       115.86        29.23        65.33        24.56        42.15 
TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0521 TCGA-08-0524 TCGA-12-0615 
       11.08        19.59        58.68         4.80         7.27        15.35 
TCGA-12-0827 TCGA-12-1091 TCGA-12-3652 TCGA-14-0740 TCGA-14-0812 TCGA-14-0862 
       38.76        33.21        34.92        11.97         3.25         2.89 
TCGA-14-0865 TCGA-14-1402 TCGA-14-1453 TCGA-14-1456 TCGA-14-1821 TCGA-14-3477 
       16.50        32.05         1.15        40.96        17.79         3.78 
TCGA-15-1444 TCGA-15-1447 TCGA-16-0849 TCGA-16-0850 TCGA-16-1056 TCGA-16-1060 
       50.53        53.19        26.07        16.37        14.01         9.14 
TCGA-19-0960 TCGA-19-0964 TCGA-19-1789 TCGA-19-2620 TCGA-19-2621 TCGA-19-2625 
        8.61         3.39         3.25         4.87         1.08         4.08 
TCGA-19-5951 TCGA-19-5956 TCGA-26-5133 TCGA-26-5134 TCGA-27-1836 TCGA-27-2527 
        8.02        22.49        14.86         5.49        30.05        14.40 
TCGA-27-2528 TCGA-28-1756 TCGA-28-2514 TCGA-28-5208 TCGA-28-5216 TCGA-32-1973 
       15.78         2.83         5.26        17.88        13.64        21.07 
TCGA-32-2615 TCGA-32-2634 TCGA-32-4208 TCGA-32-4213 TCGA-32-4719 TCGA-41-4097 
       15.95        22.78        21.14        19.86        10.85         0.20 
TCGA-76-6193 
        2.70 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              0.1               0.2 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           127.59            120.56 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           11.445            15.350 
[1] "0.1 - 127.6 (11.4)" "0.2 - 120.6 (15.3)"
[1] "hr=" "1.6"
D14V2, continuous
D14V3, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED   178 289
  7Q GAIN WILD-TYPE  46  57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED    178  289
  7Q GAIN WILD-TYPE   46   57
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE             178                46
  MALE               289                57
[1] 2 2
[1] FALSE
D14V4, continuous
                   vv
clus                GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  7Q GAIN MUTATED                              20                  11
  7Q GAIN WILD-TYPE                             7                   7
                   vv
clus                UNTREATED PRIMARY (DE NOVO) GBM
  7Q GAIN MUTATED                               436
  7Q GAIN WILD-TYPE                              89
D14V5, multiclass
                                 clus
vv                                7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                20                 7
  TREATED PRIMARY GBM                          11                 7
  UNTREATED PRIMARY (DE NOVO) GBM             436                89
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V6, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED   306 161
  7Q GAIN WILD-TYPE  76  27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED    306  161
  7Q GAIN WILD-TYPE   76   27
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  NO              306                76
  YES             161                27
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7Q GAIN MUTATED       7                        42   397
  7Q GAIN WILD-TYPE     6                         7    88
D14V7, multiclass
                           clus
vv                          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  ASIAN                                   7                 6
  BLACK OR AFRICAN AMERICAN              42                 7
  WHITE                                 397                88
[1] 3 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
  7Q GAIN MUTATED     8 386
  7Q GAIN WILD-TYPE   4  86
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      8  386
  7Q GAIN WILD-TYPE    4   86
                        clus
vv                       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   8                 4
  NOT HISPANIC OR LATINO             386                86
[1] 2 2
[1] FALSE

Clustering(15) Variable = 8P GAIN MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                 0   1
  8P GAIN MUTATED     7  45
  8P GAIN WILD-TYPE  97 420
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               52               517 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               45               420 
$`8P GAIN MUTATED`
TCGA-02-0010 TCGA-02-0024 TCGA-02-0055 TCGA-02-0074 TCGA-02-0075 TCGA-02-0084 
       35.41        53.10         2.50        10.19        20.84        12.62 
TCGA-02-0325 TCGA-06-0128 TCGA-06-0146 TCGA-06-0177 TCGA-06-0188 TCGA-06-0192 
       10.62        22.72        20.09         4.18        44.58        38.96 
TCGA-06-0209 TCGA-06-0211 TCGA-06-0409 TCGA-06-0414 TCGA-06-0686 TCGA-06-2557 
        7.63        11.84        72.36        35.11        14.20         1.08 
TCGA-06-2569 TCGA-06-5856 TCGA-06-6389 TCGA-06-6694 TCGA-08-0350 TCGA-08-0351 
        0.43         3.75         7.79         7.36        29.23        65.33 
TCGA-12-0616 TCGA-12-0819 TCGA-12-1099 TCGA-12-1602 TCGA-12-3646 TCGA-12-3653 
       14.73        24.79         4.14         6.77        44.02        14.53 
TCGA-14-0817 TCGA-14-0865 TCGA-14-0867 TCGA-14-0871 TCGA-14-1825 TCGA-14-3477 
        5.39        16.50         2.04        28.93         7.63         3.78 
TCGA-19-1388 TCGA-19-1392 TCGA-19-A6J4 TCGA-27-1834 TCGA-27-2521 TCGA-28-1746 
       12.95         3.65         3.98        40.54        10.39         0.20 
TCGA-28-5215 TCGA-28-5218 TCGA-28-5219 TCGA-32-1970 TCGA-32-1976 TCGA-32-1978 
       11.01         5.16        22.68        15.39         0.49        15.85 
TCGA-32-2632 TCGA-41-2573 TCGA-41-4097 TCGA-41-5651 
        8.84         8.94         0.20        15.12 

$`8P GAIN WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0011 
       11.77         4.73        18.35        23.18        10.59        20.71 
TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0025 
       82.59        20.61        87.06        77.65        20.12        42.74 
TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 
       24.59        12.16        90.58         2.83        14.14         3.62 
TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 TCGA-02-0048 
       10.72        10.52        18.31         6.87        14.73         3.22 
TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 TCGA-02-0057 TCGA-02-0058 TCGA-02-0059 
       15.09        12.59         6.54        19.86         8.35         9.57 
TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 TCGA-02-0069 TCGA-02-0070 TCGA-02-0071 
        6.02        19.73        26.43        28.70        25.05         5.49 
TCGA-02-0079 TCGA-02-0080 TCGA-02-0083 TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 
       27.25        89.72        22.72        51.32         8.81        57.76 
TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 TCGA-02-0104 TCGA-02-0106 TCGA-02-0107 
       16.96         3.48        27.02        65.00        11.67        17.65 
TCGA-02-0111 TCGA-02-0113 TCGA-02-0114 TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 
       23.18        92.65        99.98        15.65        48.95        16.54 
TCGA-02-0260 TCGA-02-0266 TCGA-02-0269 TCGA-02-0271 TCGA-02-0281 TCGA-02-0285 
       16.93        17.72        10.75        14.47         3.98        13.87 
TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 TCGA-02-0326 
       14.20        15.95        12.23         9.90         7.73         7.33 
TCGA-02-0330 TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 
       15.91        25.71         4.37        25.12        10.59        12.39 
TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 
       14.50        10.55        47.11        11.34         9.27        16.21 
TCGA-02-0456 TCGA-02-2466 TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 
        3.35        16.80        12.92        15.32        15.45        20.32 
TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 
        2.70         6.15        20.38        47.61         6.94         3.98 
TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 
       33.67        12.95        25.35        14.30        26.70        24.23 
TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 
       11.90         0.20        10.29         2.20        11.74         2.33 
TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 
       17.79        10.09         8.61        19.46        46.59        12.33 
TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 
       13.94        10.45         3.19        10.82         9.44        11.80 
TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 
        3.42        56.91        10.65         5.85        19.66         3.29 
TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0178 
       13.12         4.47         3.22         4.04        91.00        88.14 
TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0189 
       20.25         3.65        69.90        73.84        27.22        15.42 
TCGA-06-0190 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 
       10.42         4.67         7.40         5.56         0.39         7.66 
TCGA-06-0208 TCGA-06-0210 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 
        8.42         7.40         0.53        15.02        24.16         0.72 
TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 
       19.82        13.64        13.32        20.42        48.69        10.82 
TCGA-06-0397 TCGA-06-0402 TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0644 
        9.01         0.26         4.70         9.57         3.16        12.62 
TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0743 
        5.75         5.75         9.80         2.10        23.57        26.40 
TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 
       46.88         7.86         2.70         2.70         0.92        43.46 
TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 
       46.19         5.65         7.17        40.41        16.57        20.78 
TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 
       26.76        23.93         6.84         4.04        26.79        11.84 
TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 TCGA-06-2558 TCGA-06-2559 
       15.32        13.61        33.90        15.32        12.49         4.93 
TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 
       17.65        12.56        30.64         5.95        16.64         5.98 
TCGA-06-2567 TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 
        4.37        31.50        11.74         3.55         8.35         4.54 
TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 TCGA-06-5418 TCGA-06-5858 
        8.81         8.98         8.55         6.71         2.73         6.15 
TCGA-06-5859 TCGA-06-6388 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6695 
        4.57         5.23         5.39         1.48       120.56         8.32 
TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 
       12.85         4.77         1.55         4.77         4.96         4.70 
TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK TCGA-06-A7TL TCGA-08-0244 
        1.87         3.12         2.56         5.39         5.42        22.68 
TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 
       37.84         4.18       115.86         1.74         8.42        25.71 
TCGA-08-0348 TCGA-08-0349 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 
       12.16         9.80         1.28         8.42        17.95        24.56 
TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 
       31.10        37.58        22.29         3.39        12.23        14.93 
TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 
       18.02        15.35        13.97         0.72        12.56         4.27 
TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 
       42.15        11.08        19.59        58.68        19.33        10.75 
TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 
        4.80         7.27        15.98        18.41         7.56        15.35 
TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 
       12.99        34.92        10.45         7.59        94.78         0.10 
TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 
       38.17        25.97        26.66        12.13         3.65        20.38 
TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 
       28.41        15.06        53.85        43.23         7.63         9.73 
TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 
       14.93        14.86        91.76        18.48        10.62        23.51 
TCGA-12-0826 TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 
       27.78        38.76         8.94        20.58       127.59         5.82 
TCGA-12-1090 TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 
        7.59        33.21        21.73        15.98        12.23        15.85 
TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 
        9.11        14.53         3.98        15.65        25.68        14.73 
TCGA-12-3644 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 
       59.77        26.93        15.22        10.95        12.69        34.92 
TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 
       14.93         3.22         2.04        15.12        11.97         0.95 
TCGA-14-0783 TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 TCGA-14-0812 
        6.21        23.05         2.24        11.24        13.78         3.25 
TCGA-14-0813 TCGA-14-0862 TCGA-14-0866 TCGA-14-1034 TCGA-14-1037 TCGA-14-1043 
        1.35         2.89        26.33        15.95        19.30         0.79 
TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 
        1.38         1.12         3.75        32.05        58.78        23.11 
TCGA-14-1452 TCGA-14-1453 TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 
        7.10         1.15        30.18         0.92        40.96         6.67 
TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 TCGA-14-1823 TCGA-14-1827 
       12.43         0.99         1.97        17.79        17.85         5.88 
TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-4157 TCGA-15-0742 TCGA-15-1444 
        7.17        17.49         7.96         3.42        13.78        50.53 
TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 
       19.10        53.19        13.28         3.91        17.59        26.07 
TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 
       16.37         4.31        29.03         4.57        10.29        14.01 
TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 
        9.14        21.24        13.97         6.41        11.77        21.90 
TCGA-19-0960 TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 
        8.61         0.66        14.27         3.39        10.75         9.07 
TCGA-19-1387 TCGA-19-1389 TCGA-19-1390 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 
        5.95         4.64        25.38         7.17        12.66         3.25 
TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 
        0.13         9.67         4.87         1.08         7.53         0.16 
TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 
        4.08        24.23         7.00         7.04         6.64        17.19 
TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 
        8.02        18.90         4.73        12.10         1.78        22.49 
TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J5 TCGA-26-1438 
       14.07        16.80        14.96        17.79        28.54        10.03 
TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 
       13.87         9.73        31.33         7.13         9.37         9.40 
TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 
       14.86         5.49         8.88        18.97         1.58         7.92 
TCGA-26-6174 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 
        2.33        19.33         5.06        16.60         9.86        24.23 
TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 
       21.30        30.05        14.04        11.51        24.76        10.39 
TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1747 
       16.08         7.59         2.86        14.40        15.78         2.53 
TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 TCGA-28-1755 
        9.21         8.35         7.63         8.48         1.22         1.55 
TCGA-28-1756 TCGA-28-1757 TCGA-28-2502 TCGA-28-2506 TCGA-28-2509 TCGA-28-2513 
        2.83         0.13         0.66         6.74         4.77         7.30 
TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 
        5.26        14.93        11.28        17.88        14.53        11.77 
TCGA-28-5213 TCGA-28-5214 TCGA-28-5216 TCGA-28-5220 TCGA-28-6450 TCGA-32-1973 
       31.27        23.44        13.64        12.76         5.42        21.07 
TCGA-32-1977 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 
        0.10        19.50         1.18         4.67        12.69        14.86 
TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 TCGA-32-2616 
       16.93        12.23        20.78        15.02        15.95         7.36 
TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 
       22.78        25.18        21.14         3.72        12.59        19.86 
TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2575 TCGA-41-3392 
       10.85        19.23         0.85        13.35         9.53         0.99 
TCGA-41-3393 TCGA-41-3915 TCGA-41-6646 TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 
        4.44        11.84        12.46         4.14        14.76         3.45 
TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 TCGA-76-4925 
       20.91         4.34        14.33         8.22         7.50         4.80 
TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-4934 TCGA-76-4935 
        4.54         3.09         3.65         9.17         2.53        10.78 
TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 
       16.70         3.29         2.70        11.38        17.06         8.35 
TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 
       20.98         4.83         5.03         0.23         9.27         7.73 
TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R TCGA-RR-A6KA 
        7.79         1.61        17.72        26.30         5.92         6.28 
TCGA-RR-A6KC 
       20.55 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              0.2               0.1 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            72.36            127.59 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           11.425            11.900 
[1] "0.2 - 72.4 (11.4)"  "0.1 - 127.6 (11.9)"
[1] "hr=" "1"  
D15V2, continuous
D15V3, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    22  30
  8P GAIN WILD-TYPE 202 316
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     22   30
  8P GAIN WILD-TYPE  202  316
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE              22               202
  MALE                30               316
[1] 2 2
[1] FALSE
D15V4, continuous
                   vv
clus                GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  8P GAIN MUTATED                               1                   2
  8P GAIN WILD-TYPE                            26                  16
                   vv
clus                UNTREATED PRIMARY (DE NOVO) GBM
  8P GAIN MUTATED                                49
  8P GAIN WILD-TYPE                             476
D15V5, multiclass
                                 clus
vv                                8P GAIN MUTATED 8P GAIN WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                 1                26
  TREATED PRIMARY GBM                           2                16
  UNTREATED PRIMARY (DE NOVO) GBM              49               476
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V6, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    34  18
  8P GAIN WILD-TYPE 348 170
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     34   18
  8P GAIN WILD-TYPE  348  170
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  NO               34               348
  YES              18               170
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8P GAIN MUTATED       0                         7    45
  8P GAIN WILD-TYPE    13                        42   440
D15V7, multiclass
                           clus
vv                          8P GAIN MUTATED 8P GAIN WILD-TYPE
  ASIAN                                   0                13
  BLACK OR AFRICAN AMERICAN               7                42
  WHITE                                  45               440
[1] 3 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
  8P GAIN MUTATED     1  43
  8P GAIN WILD-TYPE  11 429
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      1   43
  8P GAIN WILD-TYPE   11  429
                        clus
vv                       8P GAIN MUTATED 8P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                11
  NOT HISPANIC OR LATINO              43               429
[1] 2 2
[1] FALSE

Clustering(16) Variable = 8Q GAIN MUTATION ANALYSIS
D16V1, survival
                   sevent
clus2                 0   1
  8Q GAIN MUTATED     9  50
  8Q GAIN WILD-TYPE  95 415
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               59               510 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               50               415 
$`8Q GAIN MUTATED`
TCGA-02-0010 TCGA-02-0037 TCGA-02-0055 TCGA-02-0074 TCGA-02-0075 TCGA-02-0084 
       35.41         3.62         2.50        10.19        20.84        12.62 
TCGA-02-0104 TCGA-02-0325 TCGA-02-2483 TCGA-06-0128 TCGA-06-0146 TCGA-06-0177 
       65.00        10.62        15.32        22.72        20.09         4.18 
TCGA-06-0188 TCGA-06-0192 TCGA-06-0209 TCGA-06-0211 TCGA-06-0409 TCGA-06-0414 
       44.58        38.96         7.63        11.84        72.36        35.11 
TCGA-06-0686 TCGA-06-2557 TCGA-06-2569 TCGA-06-5856 TCGA-06-6389 TCGA-06-6694 
       14.20         1.08         0.43         3.75         7.79         7.36 
TCGA-08-0350 TCGA-08-0351 TCGA-08-0516 TCGA-12-0616 TCGA-12-0818 TCGA-12-0819 
       29.23        65.33        19.59        14.73        91.76        24.79 
TCGA-12-0827 TCGA-12-1099 TCGA-12-1602 TCGA-12-3646 TCGA-12-3653 TCGA-14-0817 
       38.76         4.14         6.77        44.02        14.53         5.39 
TCGA-14-0865 TCGA-14-0867 TCGA-14-0871 TCGA-14-1456 TCGA-14-1825 TCGA-14-3477 
       16.50         2.04        28.93        40.96         7.63         3.78 
TCGA-19-1388 TCGA-19-1392 TCGA-19-A6J4 TCGA-27-1834 TCGA-27-2521 TCGA-28-1746 
       12.95         3.65         3.98        40.54        10.39         0.20 
TCGA-28-5204 TCGA-28-5215 TCGA-28-5218 TCGA-28-5219 TCGA-32-1970 TCGA-32-1976 
       14.93        11.01         5.16        22.68        15.39         0.49 
TCGA-32-1978 TCGA-32-2632 TCGA-41-2573 TCGA-41-4097 TCGA-41-5651 
       15.85         8.84         8.94         0.20        15.12 

$`8Q GAIN WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0011 
       11.77         4.73        18.35        23.18        10.59        20.71 
TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0024 
       82.59        20.61        87.06        77.65        20.12        53.10 
TCGA-02-0025 TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 
       42.74        24.59        12.16        90.58         2.83        14.14 
TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 TCGA-02-0048 
       10.72        10.52        18.31         6.87        14.73         3.22 
TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 TCGA-02-0057 TCGA-02-0058 TCGA-02-0059 
       15.09        12.59         6.54        19.86         8.35         9.57 
TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 TCGA-02-0069 TCGA-02-0070 TCGA-02-0071 
        6.02        19.73        26.43        28.70        25.05         5.49 
TCGA-02-0079 TCGA-02-0080 TCGA-02-0083 TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 
       27.25        89.72        22.72        51.32         8.81        57.76 
TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 
       16.96         3.48        27.02        11.67        17.65        23.18 
TCGA-02-0113 TCGA-02-0114 TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 
       92.65        99.98        15.65        48.95        16.54        16.93 
TCGA-02-0266 TCGA-02-0269 TCGA-02-0271 TCGA-02-0281 TCGA-02-0285 TCGA-02-0289 
       17.72        10.75        14.47         3.98        13.87        14.20 
TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 TCGA-02-0326 TCGA-02-0330 
       15.95        12.23         9.90         7.73         7.33        15.91 
TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 
       25.71         4.37        25.12        10.59        12.39        14.50 
TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 
       10.55        47.11        11.34         9.27        16.21         3.35 
TCGA-02-2466 TCGA-02-2470 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 
       16.80        12.92        15.45        20.32         2.70         6.15 
TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0129 TCGA-06-0130 
       20.38        47.61         6.94         3.98        33.67        12.95 
TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 
       25.35        14.30        26.70        24.23        11.90         0.20 
TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0147 TCGA-06-0148 
       10.29         2.20        11.74         2.33        17.79        10.09 
TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 
        8.61        19.46        46.59        12.33        13.94        10.45 
TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 
        3.19        10.82         9.44        11.80         3.42        56.91 
TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 
       10.65         5.85        19.66         3.29        13.12         4.47 
TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 
        3.22         4.04        91.00        88.14        20.25         3.65 
TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0189 TCGA-06-0190 TCGA-06-0194 
       69.90        73.84        27.22        15.42        10.42         4.67 
TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0210 
        7.40         5.56         0.39         7.66         8.42         7.40 
TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 
        0.53        15.02        24.16         0.72        19.82        13.64 
TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 
       13.32        20.42        48.69        10.82         9.01         0.26 
TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 
        4.70         9.57         3.16        12.62         5.75         5.75 
TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 
        9.80         2.10        23.57        26.40        46.88         7.86 
TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 
        2.70         2.70         0.92        43.46        46.19         5.65 
TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 
        7.17        40.41        16.57        20.78        26.76        23.93 
TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 
        6.84         4.04        26.79        11.84        15.32        13.61 
TCGA-06-1805 TCGA-06-1806 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 
       33.90        15.32        12.49         4.93        17.65        12.56 
TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2570 
       30.64         5.95        16.64         5.98         4.37        31.50 
TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 
       11.74         3.55         8.35         4.54         8.81         8.98 
TCGA-06-5415 TCGA-06-5416 TCGA-06-5418 TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 
        8.55         6.71         2.73         6.15         4.57         5.23 
TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 
        5.39         1.48       120.56         8.32        12.85         4.77 
TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S0 
        1.55         4.77         4.96         4.70         1.87         3.12 
TCGA-06-A6S1 TCGA-06-A7TK TCGA-06-A7TL TCGA-08-0244 TCGA-08-0245 TCGA-08-0246 
        2.56         5.39         5.42        22.68        37.84         4.18 
TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 
      115.86         1.74         8.42        25.71        12.16         9.80 
TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 
        1.28         8.42        17.95        24.56        31.10        37.58 
TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 
       22.29         3.39        12.23        14.93        18.02        15.35 
TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 
       13.97         0.72        12.56         4.27        42.15        11.08 
TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 
       58.68        19.33        10.75         4.80         7.27        15.98 
TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 
       18.41         7.56        15.35        12.99        34.92        10.45 
TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 
        7.59        94.78         0.10        38.17        25.97        26.66 
TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 
       12.13         3.65        20.38        28.41        15.06        53.85 
TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0820 
       43.23         7.63         9.73        14.93        14.86        18.48 
TCGA-12-0821 TCGA-12-0822 TCGA-12-0826 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 
       10.62        23.51        27.78         8.94        20.58       127.59 
TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 
        5.82         7.59        33.21        21.73        15.98        12.23 
TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1598 TCGA-12-1599 
       15.85         9.11        14.53         3.98        15.65        25.68 
TCGA-12-1600 TCGA-12-3644 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 
       14.73        59.77        26.93        15.22        10.95        12.69 
TCGA-12-3652 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 
       34.92        14.93         3.22         2.04        15.12        11.97 
TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 
        0.95         6.21        23.05         2.24        11.24        13.78 
TCGA-14-0812 TCGA-14-0813 TCGA-14-0862 TCGA-14-0866 TCGA-14-1034 TCGA-14-1037 
        3.25         1.35         2.89        26.33        15.95        19.30 
TCGA-14-1043 TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 
        0.79         1.38         1.12         3.75        32.05        58.78 
TCGA-14-1451 TCGA-14-1452 TCGA-14-1453 TCGA-14-1454 TCGA-14-1455 TCGA-14-1458 
       23.11         7.10         1.15        30.18         0.92         6.67 
TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 TCGA-14-1823 TCGA-14-1827 
       12.43         0.99         1.97        17.79        17.85         5.88 
TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-4157 TCGA-15-0742 TCGA-15-1444 
        7.17        17.49         7.96         3.42        13.78        50.53 
TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 
       19.10        53.19        13.28         3.91        17.59        26.07 
TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 
       16.37         4.31        29.03         4.57        10.29        14.01 
TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 
        9.14        21.24        13.97         6.41        11.77        21.90 
TCGA-19-0960 TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 
        8.61         0.66        14.27         3.39        10.75         9.07 
TCGA-19-1387 TCGA-19-1389 TCGA-19-1390 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 
        5.95         4.64        25.38         7.17        12.66         3.25 
TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 
        0.13         9.67         4.87         1.08         7.53         0.16 
TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 
        4.08        24.23         7.00         7.04         6.64        17.19 
TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 
        8.02        18.90         4.73        12.10         1.78        22.49 
TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J5 TCGA-26-1438 
       14.07        16.80        14.96        17.79        28.54        10.03 
TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 
       13.87         9.73        31.33         7.13         9.37         9.40 
TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 
       14.86         5.49         8.88        18.97         1.58         7.92 
TCGA-26-6174 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 
        2.33        19.33         5.06        16.60         9.86        24.23 
TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 
       21.30        30.05        14.04        11.51        24.76        10.39 
TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1747 
       16.08         7.59         2.86        14.40        15.78         2.53 
TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 TCGA-28-1755 
        9.21         8.35         7.63         8.48         1.22         1.55 
TCGA-28-1756 TCGA-28-1757 TCGA-28-2502 TCGA-28-2506 TCGA-28-2509 TCGA-28-2513 
        2.83         0.13         0.66         6.74         4.77         7.30 
TCGA-28-2514 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 
        5.26        11.28        17.88        14.53        11.77        31.27 
TCGA-28-5214 TCGA-28-5216 TCGA-28-5220 TCGA-28-6450 TCGA-32-1973 TCGA-32-1977 
       23.44        13.64        12.76         5.42        21.07         0.10 
TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 TCGA-32-1991 
       19.50         1.18         4.67        12.69        14.86        16.93 
TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 TCGA-32-2616 TCGA-32-2634 
       12.23        20.78        15.02        15.95         7.36        22.78 
TCGA-32-2638 TCGA-32-4208 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 
       25.18        21.14         3.72        12.59        19.86        10.85 
TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 
       19.23         0.85        13.35         9.53         0.99         4.44 
TCGA-41-3915 TCGA-41-6646 TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 
       11.84        12.46         4.14        14.76         3.45        20.91 
TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 
        4.34        14.33         8.22         7.50         4.80         4.54 
TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 
        3.09         3.65         9.17         2.53        10.78        16.70 
TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 
        3.29         2.70        11.38        17.06         8.35        20.98 
TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 
        4.83         5.03         0.23         9.27         7.73         7.79 
TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC 
        1.61        17.72        26.30         5.92         6.28        20.55 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              0.2               0.1 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            91.76            127.59 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            12.95             11.82 
[1] "0.2 - 91.8 (12.9)"  "0.1 - 127.6 (11.8)"
[1] "hr=" "1.1"
D16V2, continuous
D16V3, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED    26  33
  8Q GAIN WILD-TYPE 198 313
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     26   33
  8Q GAIN WILD-TYPE  198  313
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE              26               198
  MALE                33               313
[1] 2 2
[1] FALSE
D16V4, continuous
                   vv
clus                GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  8Q GAIN MUTATED                               1                   1
  8Q GAIN WILD-TYPE                            26                  17
                   vv
clus                UNTREATED PRIMARY (DE NOVO) GBM
  8Q GAIN MUTATED                                57
  8Q GAIN WILD-TYPE                             468
D16V5, multiclass
                                 clus
vv                                8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                 1                26
  TREATED PRIMARY GBM                           1                17
  UNTREATED PRIMARY (DE NOVO) GBM              57               468
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V6, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED    40  19
  8Q GAIN WILD-TYPE 342 169
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     40   19
  8Q GAIN WILD-TYPE  342  169
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  NO               40               342
  YES              19               169
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8Q GAIN MUTATED       1                         7    51
  8Q GAIN WILD-TYPE    12                        42   434
D16V7, multiclass
                           clus
vv                          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  ASIAN                                   1                12
  BLACK OR AFRICAN AMERICAN               7                42
  WHITE                                  51               434
[1] 3 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
  8Q GAIN MUTATED     1  48
  8Q GAIN WILD-TYPE  11 424
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      1   48
  8Q GAIN WILD-TYPE   11  424
                        clus
vv                       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                11
  NOT HISPANIC OR LATINO              48               424
[1] 2 2
[1] FALSE

Clustering(17) Variable = 9P GAIN MUTATION ANALYSIS
D17V1, survival
                   sevent
clus2                 0   1
  9P GAIN MUTATED     7  40
  9P GAIN WILD-TYPE  97 425
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               47               522 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               40               425 
$`9P GAIN MUTATED`
TCGA-02-0001 TCGA-02-0025 TCGA-02-0051 TCGA-02-0052 TCGA-02-0069 TCGA-02-0074 
       11.77        42.74        15.09        12.59        28.70        10.19 
TCGA-02-0266 TCGA-02-0281 TCGA-02-0325 TCGA-02-0332 TCGA-02-0456 TCGA-06-0129 
       17.72         3.98        10.62        25.71         3.35        33.67 
TCGA-06-0195 TCGA-06-0216 TCGA-06-0410 TCGA-06-0414 TCGA-06-0644 TCGA-06-1087 
        7.40        24.16         4.70        35.11        12.62         4.04 
TCGA-06-2569 TCGA-06-5408 TCGA-06-5416 TCGA-08-0386 TCGA-12-0691 TCGA-12-0773 
        0.43        11.74         6.71        18.02        12.13        43.23 
TCGA-12-1096 TCGA-12-3646 TCGA-14-0790 TCGA-14-0812 TCGA-14-0817 TCGA-14-0867 
        9.11        44.02        13.78         3.25         5.39         2.04 
TCGA-15-1449 TCGA-19-0962 TCGA-19-1392 TCGA-19-4065 TCGA-26-5136 TCGA-27-1834 
       13.28         0.66         3.65         7.04        18.97        40.54 
TCGA-27-1838 TCGA-28-1751 TCGA-28-2509 TCGA-28-5204 TCGA-28-5215 TCGA-28-5216 
       11.51         7.63         4.77        14.93        11.01        13.64 
TCGA-32-1979 TCGA-32-2615 TCGA-41-3915 TCGA-76-4934 TCGA-76-6280 
       19.50        15.95        11.84         2.53        11.38 

$`9P GAIN WILD-TYPE`
TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 TCGA-02-0011 
        4.73        18.35        23.18        10.59        35.41        20.71 
TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0024 
       82.59        20.61        87.06        77.65        20.12        53.10 
TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 
       24.59        12.16        90.58         2.83        14.14         3.62 
TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 TCGA-02-0048 
       10.72        10.52        18.31         6.87        14.73         3.22 
TCGA-02-0054 TCGA-02-0055 TCGA-02-0057 TCGA-02-0058 TCGA-02-0059 TCGA-02-0060 
        6.54         2.50        19.86         8.35         9.57         6.02 
TCGA-02-0064 TCGA-02-0068 TCGA-02-0070 TCGA-02-0071 TCGA-02-0075 TCGA-02-0079 
       19.73        26.43        25.05         5.49        20.84        27.25 
TCGA-02-0080 TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 
       89.72        22.72        12.62        51.32         8.81        57.76 
TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 TCGA-02-0104 TCGA-02-0106 TCGA-02-0107 
       16.96         3.48        27.02        65.00        11.67        17.65 
TCGA-02-0111 TCGA-02-0113 TCGA-02-0114 TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 
       23.18        92.65        99.98        15.65        48.95        16.54 
TCGA-02-0260 TCGA-02-0269 TCGA-02-0271 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 
       16.93        10.75        14.47        13.87        14.20        15.95 
TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 TCGA-02-0326 TCGA-02-0330 TCGA-02-0333 
       12.23         9.90         7.73         7.33        15.91         4.37 
TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 
       25.12        10.59        12.39        14.50        10.55        47.11 
TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 TCGA-02-2466 TCGA-02-2470 TCGA-02-2483 
       11.34         9.27        16.21        16.80        12.92        15.32 
TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 
       15.45        20.32         2.70         6.15        20.38        47.61 
TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 
        6.94         3.98        22.72        12.95        25.35        14.30 
TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 
       26.70        24.23        11.90         0.20        10.29         2.20 
TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 
       11.74         2.33        20.09        17.79        10.09         8.61 
TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 
       19.46        46.59        12.33        13.94        10.45         3.19 
TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 
       10.82         9.44        11.80         3.42        56.91        10.65 
TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 
        5.85        19.66         3.29        13.12         4.47         3.22 
TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 
        4.04        91.00         4.18        88.14        20.25         3.65 
TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 
       69.90        73.84        27.22        44.58        15.42        10.42 
TCGA-06-0192 TCGA-06-0194 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 
       38.96         4.67         5.56         0.39         7.66         8.42 
TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0219 
        7.63         7.40        11.84         0.53        15.02         0.72 
TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 
       19.82        13.64        13.32        20.42        48.69        10.82 
TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0412 TCGA-06-0413 TCGA-06-0645 
        9.01         0.26        72.36         9.57         3.16         5.75 
TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 
        5.75         9.80         2.10        23.57        14.20        26.40 
TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 
       46.88         7.86         2.70         2.70         0.92        43.46 
TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 
       46.19         5.65         7.17        40.41        16.57        20.78 
TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 
       26.76        23.93         6.84        26.79        11.84        15.32 
TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 
       13.61        33.90        15.32         1.08        12.49         4.93 
TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 
       17.65        12.56        30.64         5.95        16.64         5.98 
TCGA-06-2567 TCGA-06-2570 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 
        4.37        31.50         3.55         8.35         4.54         8.81 
TCGA-06-5414 TCGA-06-5415 TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 TCGA-06-5859 
        8.98         8.55         2.73         3.75         6.15         4.57 
TCGA-06-6388 TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 
        5.23         7.79         5.39         1.48       120.56         7.36 
TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 
        8.32        12.85         4.77         1.55         4.77         4.96 
TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK TCGA-06-A7TL 
        4.70         1.87         3.12         2.56         5.39         5.42 
TCGA-08-0244 TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 
       22.68        37.84         4.18       115.86         1.74         8.42 
TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 
       25.71        12.16         9.80        29.23        65.33         1.28 
TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 
        8.42        17.95        24.56        31.10        37.58        22.29 
TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 
        3.39        12.23        14.93        15.35        13.97         0.72 
TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 
       12.56         4.27        42.15        11.08        19.59        58.68 
TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 
       19.33        10.75         4.80         7.27        15.98        18.41 
TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 
        7.56        15.35        14.73        12.99        34.92        10.45 
TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 
        7.59        94.78         0.10        38.17        25.97        26.66 
TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0775 
        3.65        20.38        28.41        15.06        53.85         7.63 
TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 
        9.73        14.93        14.86        91.76        24.79        18.48 
TCGA-12-0821 TCGA-12-0822 TCGA-12-0826 TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 
       10.62        23.51        27.78        38.76         8.94        20.58 
TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 
      127.59         5.82         7.59        33.21        21.73        15.98 
TCGA-12-1094 TCGA-12-1095 TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 TCGA-12-1598 
       12.23        15.85        14.53         3.98         4.14        15.65 
TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 TCGA-12-3648 TCGA-12-3649 
       25.68        14.73         6.77        59.77        26.93        15.22 
TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 
       10.95        12.69        34.92        14.53        14.93         3.22 
TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 
        2.04        15.12        11.97         0.95         6.21        23.05 
TCGA-14-0787 TCGA-14-0789 TCGA-14-0813 TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 
        2.24        11.24         1.35         2.89        16.50        26.33 
TCGA-14-0871 TCGA-14-1034 TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 TCGA-14-1396 
       28.93        15.95        19.30         0.79         1.38         1.12 
TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 TCGA-14-1452 TCGA-14-1453 
        3.75        32.05        58.78        23.11         7.10         1.15 
TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 TCGA-14-1794 
       30.18         0.92        40.96         6.67        12.43         0.99 
TCGA-14-1795 TCGA-14-1821 TCGA-14-1823 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 
        1.97        17.79        17.85         7.63         5.88         7.17 
TCGA-14-2554 TCGA-14-2555 TCGA-14-3477 TCGA-14-4157 TCGA-15-0742 TCGA-15-1444 
       17.49         7.96         3.78         3.42        13.78        50.53 
TCGA-15-1446 TCGA-15-1447 TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 
       19.10        53.19         3.91        17.59        26.07        16.37 
TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 
        4.31        29.03         4.57        10.29        14.01         9.14 
TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 
       21.24        13.97         6.41        11.77        21.90         8.61 
TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 TCGA-19-1388 
       14.27         3.39        10.75         9.07         5.95        12.95 
TCGA-19-1389 TCGA-19-1390 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 
        4.64        25.38         7.17        12.66         3.25         0.13 
TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 
        9.67         4.87         1.08         7.53         0.16         4.08 
TCGA-19-2629 TCGA-19-2631 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 
       24.23         7.00         6.64        17.19         8.02        18.90 
TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 
        4.73        12.10         1.78        22.49        14.07        16.80 
TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 
       14.96        17.79         3.98        28.54        10.03        13.87 
TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5133 
        9.73        31.33         7.13         9.37         9.40        14.86 
TCGA-26-5134 TCGA-26-5135 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-26-A7UX 
        5.49         8.88         1.58         7.92         2.33        19.33 
TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1835 TCGA-27-1836 
        5.06        16.60         9.86        24.23        21.30        30.05 
TCGA-27-1837 TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 
       14.04        24.76        10.39        10.39        16.08         7.59 
TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 
        2.86        14.40        15.78         0.20         2.53         9.21 
TCGA-28-1750 TCGA-28-1752 TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 
        8.35         8.48         1.22         1.55         2.83         0.13 
TCGA-28-2502 TCGA-28-2506 TCGA-28-2513 TCGA-28-2514 TCGA-28-5207 TCGA-28-5208 
        0.66         6.74         7.30         5.26        11.28        17.88 
TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5218 TCGA-28-5219 
       14.53        11.77        31.27        23.44         5.16        22.68 
TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 
       12.76         5.42        15.39        21.07         0.49         0.10 
TCGA-32-1978 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 TCGA-32-1991 
       15.85         1.18         4.67        12.69        14.86        16.93 
TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2616 TCGA-32-2632 TCGA-32-2634 
       12.23        20.78        15.02         7.36         8.84        22.78 
TCGA-32-2638 TCGA-32-4208 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 
       25.18        21.14         3.72        12.59        19.86        10.85 
TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 
       19.23         0.85        13.35         8.94         9.53         0.99 
TCGA-41-3393 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9S TCGA-4W-AA9T 
        4.44         0.20        15.12        12.46         4.14        14.76 
TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 
        3.45        20.91         4.34        14.33         8.22         7.50 
TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-4935 
        4.80         4.54         3.09         3.65         9.17        10.78 
TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 
       16.70         3.29         2.70        17.06         8.35        20.98 
TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 
        4.83         5.03         0.23         9.27         7.73         7.79 
TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC 
        1.61        17.72        26.30         5.92         6.28        20.55 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
             0.43              0.10 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            44.02            127.59 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           11.770            11.935 
[1] "0.4 - 44.0 (11.8)"  "0.1 - 127.6 (11.9)"
[1] "hr=" "1.2"
D17V2, continuous
D17V3, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    23  24
  9P GAIN WILD-TYPE 201 322
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     23   24
  9P GAIN WILD-TYPE  201  322
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE              23               201
  MALE                24               322
[1] 2 2
[1] FALSE
D17V4, continuous
                   vv
clus                GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  9P GAIN MUTATED                               0                   0
  9P GAIN WILD-TYPE                            27                  18
                   vv
clus                UNTREATED PRIMARY (DE NOVO) GBM
  9P GAIN MUTATED                                47
  9P GAIN WILD-TYPE                             478
D17V5, multiclass
                                 clus
vv                                9P GAIN MUTATED 9P GAIN WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                 0                27
  TREATED PRIMARY GBM                           0                18
  UNTREATED PRIMARY (DE NOVO) GBM              47               478
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V6, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    31  16
  9P GAIN WILD-TYPE 351 172
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     31   16
  9P GAIN WILD-TYPE  351  172
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  NO               31               351
  YES              16               172
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9P GAIN MUTATED       2                         2    42
  9P GAIN WILD-TYPE    11                        47   443
D17V7, multiclass
                           clus
vv                          9P GAIN MUTATED 9P GAIN WILD-TYPE
  ASIAN                                   2                11
  BLACK OR AFRICAN AMERICAN               2                47
  WHITE                                  42               443
[1] 3 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
  9P GAIN MUTATED     2  36
  9P GAIN WILD-TYPE  10 436
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      2   36
  9P GAIN WILD-TYPE   10  436
                        clus
vv                       9P GAIN MUTATED 9P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                10
  NOT HISPANIC OR LATINO              36               436
[1] 2 2
[1] FALSE

Clustering(18) Variable = 9Q GAIN MUTATION ANALYSIS
D18V1, survival
                   sevent
clus2                 0   1
  9Q GAIN MUTATED    11  59
  9Q GAIN WILD-TYPE  93 406
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               70               499 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               59               406 
$`9Q GAIN MUTATED`
TCGA-02-0001 TCGA-02-0025 TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 TCGA-02-0069 
       11.77        42.74        15.09        12.59         6.54        28.70 
TCGA-02-0074 TCGA-02-0106 TCGA-02-0266 TCGA-02-0281 TCGA-02-0325 TCGA-02-0332 
       10.19        11.67        17.72         3.98        10.62        25.71 
TCGA-02-0456 TCGA-06-0129 TCGA-06-0166 TCGA-06-0175 TCGA-06-0185 TCGA-06-0195 
        3.35        33.67         5.85         4.04        73.84         7.40 
TCGA-06-0216 TCGA-06-0410 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-1087 
       24.16         4.70         3.16        35.11        12.62         4.04 
TCGA-06-2562 TCGA-06-2569 TCGA-06-5408 TCGA-08-0386 TCGA-12-0618 TCGA-12-0654 
       12.56         0.43        11.74        18.02        12.99         7.59 
TCGA-12-0691 TCGA-12-0773 TCGA-12-0776 TCGA-12-0818 TCGA-12-0827 TCGA-12-1088 
       12.13        43.23         9.73        91.76        38.76       127.59 
TCGA-12-1096 TCGA-12-1098 TCGA-12-3646 TCGA-12-5299 TCGA-14-0790 TCGA-14-0812 
        9.11         3.98        44.02         3.22        13.78         3.25 
TCGA-14-0813 TCGA-14-0817 TCGA-14-0867 TCGA-14-1821 TCGA-15-1449 TCGA-19-0962 
        1.35         5.39         2.04        17.79        13.28         0.66 
TCGA-19-1392 TCGA-19-4065 TCGA-19-A6J5 TCGA-26-5136 TCGA-26-6174 TCGA-27-1834 
        3.65         7.04        28.54        18.97         2.33        40.54 
TCGA-27-1838 TCGA-28-1751 TCGA-28-2509 TCGA-28-5204 TCGA-28-5215 TCGA-28-5216 
       11.51         7.63         4.77        14.93        11.01        13.64 
TCGA-32-1976 TCGA-32-1979 TCGA-32-1991 TCGA-32-2495 TCGA-32-2615 TCGA-41-2573 
        0.49        19.50        16.93        15.02        15.95         8.94 
TCGA-41-3915 TCGA-76-4934 TCGA-76-4935 TCGA-76-6280 
       11.84         2.53        10.78        11.38 

$`9Q GAIN WILD-TYPE`
TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 TCGA-02-0011 
        4.73        18.35        23.18        10.59        35.41        20.71 
TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0024 
       82.59        20.61        87.06        77.65        20.12        53.10 
TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 
       24.59        12.16        90.58         2.83        14.14         3.62 
TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 TCGA-02-0048 
       10.72        10.52        18.31         6.87        14.73         3.22 
TCGA-02-0055 TCGA-02-0057 TCGA-02-0058 TCGA-02-0059 TCGA-02-0060 TCGA-02-0064 
        2.50        19.86         8.35         9.57         6.02        19.73 
TCGA-02-0068 TCGA-02-0070 TCGA-02-0071 TCGA-02-0075 TCGA-02-0079 TCGA-02-0080 
       26.43        25.05         5.49        20.84        27.25        89.72 
TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 
       22.72        12.62        51.32         8.81        57.76        16.96 
TCGA-02-0099 TCGA-02-0102 TCGA-02-0104 TCGA-02-0107 TCGA-02-0111 TCGA-02-0113 
        3.48        27.02        65.00        17.65        23.18        92.65 
TCGA-02-0114 TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 TCGA-02-0269 
       99.98        15.65        48.95        16.54        16.93        10.75 
TCGA-02-0271 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 
       14.47        13.87        14.20        15.95        12.23         9.90 
TCGA-02-0324 TCGA-02-0326 TCGA-02-0330 TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 
        7.73         7.33        15.91         4.37        25.12        10.59 
TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 
       12.39        14.50        10.55        47.11        11.34         9.27 
TCGA-02-0451 TCGA-02-2466 TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 
       16.21        16.80        12.92        15.32        15.45        20.32 
TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 
        2.70         6.15        20.38        47.61         6.94         3.98 
TCGA-06-0128 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 
       22.72        12.95        25.35        14.30        26.70        24.23 
TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 
       11.90         0.20        10.29         2.20        11.74         2.33 
TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 
       20.09        17.79        10.09         8.61        19.46        46.59 
TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 
       12.33        13.94        10.45         3.19        10.82         9.44 
TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0168 TCGA-06-0169 
       11.80         3.42        56.91        10.65        19.66         3.29 
TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 
       13.12         4.47         3.22        91.00         4.18        88.14 
TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 
       20.25         3.65        69.90        27.22        44.58        15.42 
TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 
       10.42        38.96         4.67         5.56         0.39         7.66 
TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 
        8.42         7.63         7.40        11.84         0.53        15.02 
TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 
        0.72        19.82        13.64        13.32        20.42        48.69 
TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0412 TCGA-06-0645 
       10.82         9.01         0.26        72.36         9.57         5.75 
TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 
        5.75         9.80         2.10        23.57        14.20        26.40 
TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 
       46.88         7.86         2.70         2.70         0.92        43.46 
TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 
       46.19         5.65         7.17        40.41        16.57        20.78 
TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 
       26.76        23.93         6.84        26.79        11.84        15.32 
TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 
       13.61        33.90        15.32         1.08        12.49         4.93 
TCGA-06-2561 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 
       17.65        30.64         5.95        16.64         5.98         4.37 
TCGA-06-2570 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 
       31.50         3.55         8.35         4.54         8.81         8.98 
TCGA-06-5415 TCGA-06-5416 TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 TCGA-06-5859 
        8.55         6.71         2.73         3.75         6.15         4.57 
TCGA-06-6388 TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 
        5.23         7.79         5.39         1.48       120.56         7.36 
TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 
        8.32        12.85         4.77         1.55         4.77         4.96 
TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK TCGA-06-A7TL 
        4.70         1.87         3.12         2.56         5.39         5.42 
TCGA-08-0244 TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 
       22.68        37.84         4.18       115.86         1.74         8.42 
TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 
       25.71        12.16         9.80        29.23        65.33         1.28 
TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 
        8.42        17.95        24.56        31.10        37.58        22.29 
TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 
        3.39        12.23        14.93        15.35        13.97         0.72 
TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 
       12.56         4.27        42.15        11.08        19.59        58.68 
TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 
       19.33        10.75         4.80         7.27        15.98        18.41 
TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0619 TCGA-12-0620 TCGA-12-0656 
        7.56        15.35        14.73        34.92        10.45        94.78 
TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0692 TCGA-12-0703 
        0.10        38.17        25.97        26.66         3.65        20.38 
TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0775 TCGA-12-0778 TCGA-12-0780 
       28.41        15.06        53.85         7.63        14.93        14.86 
TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 TCGA-12-0826 TCGA-12-0828 
       24.79        18.48        10.62        23.51        27.78         8.94 
TCGA-12-0829 TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 
       20.58         5.82         7.59        33.21        21.73        15.98 
TCGA-12-1094 TCGA-12-1095 TCGA-12-1097 TCGA-12-1099 TCGA-12-1598 TCGA-12-1599 
       12.23        15.85        14.53         4.14        15.65        25.68 
TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 
       14.73         6.77        59.77        26.93        15.22        10.95 
TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5301 TCGA-14-0736 
       12.69        34.92        14.53        14.93         2.04        15.12 
TCGA-14-0740 TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 
       11.97         0.95         6.21        23.05         2.24        11.24 
TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 TCGA-14-0871 TCGA-14-1034 TCGA-14-1037 
        2.89        16.50        26.33        28.93        15.95        19.30 
TCGA-14-1043 TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 
        0.79         1.38         1.12         3.75        32.05        58.78 
TCGA-14-1451 TCGA-14-1452 TCGA-14-1453 TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 
       23.11         7.10         1.15        30.18         0.92        40.96 
TCGA-14-1458 TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1823 TCGA-14-1825 
        6.67        12.43         0.99         1.97        17.85         7.63 
TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-3477 TCGA-14-4157 
        5.88         7.17        17.49         7.96         3.78         3.42 
TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 TCGA-16-0846 TCGA-16-0848 
       13.78        50.53        19.10        53.19         3.91        17.59 
TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 
       26.07        16.37         4.31        29.03         4.57        10.29 
TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 
       14.01         9.14        21.24        13.97         6.41        11.77 
TCGA-19-0957 TCGA-19-0960 TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 
       21.90         8.61        14.27         3.39        10.75         9.07 
TCGA-19-1387 TCGA-19-1388 TCGA-19-1389 TCGA-19-1390 TCGA-19-1786 TCGA-19-1787 
        5.95        12.95         4.64        25.38         7.17        12.66 
TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 
        3.25         0.13         9.67         4.87         1.08         7.53 
TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-5947 TCGA-19-5950 
        0.16         4.08        24.23         7.00         6.64        17.19 
TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 
        8.02        18.90         4.73        12.10         1.78        22.49 
TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J4 TCGA-26-1438 
       14.07        16.80        14.96        17.79         3.98        10.03 
TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 
       13.87         9.73        31.33         7.13         9.37         9.40 
TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 TCGA-26-5139 TCGA-26-6173 TCGA-26-A7UX 
       14.86         5.49         8.88         1.58         7.92        19.33 
TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1835 TCGA-27-1836 
        5.06        16.60         9.86        24.23        21.30        30.05 
TCGA-27-1837 TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 
       14.04        24.76        10.39        10.39        16.08         7.59 
TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 
        2.86        14.40        15.78         0.20         2.53         9.21 
TCGA-28-1750 TCGA-28-1752 TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 
        8.35         8.48         1.22         1.55         2.83         0.13 
TCGA-28-2502 TCGA-28-2506 TCGA-28-2513 TCGA-28-2514 TCGA-28-5207 TCGA-28-5208 
        0.66         6.74         7.30         5.26        11.28        17.88 
TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5218 TCGA-28-5219 
       14.53        11.77        31.27        23.44         5.16        22.68 
TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 TCGA-32-1977 TCGA-32-1978 
       12.76         5.42        15.39        21.07         0.10        15.85 
TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 TCGA-32-2491 TCGA-32-2494 
        1.18         4.67        12.69        14.86        12.23        20.78 
TCGA-32-2616 TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4210 
        7.36         8.84        22.78        25.18        21.14         3.72 
TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 
       12.59        19.86        10.85        19.23         0.85        13.35 
TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 
        9.53         0.99         4.44         0.20        15.12        12.46 
TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 
        4.14        14.76         3.45        20.91         4.34        14.33 
TCGA-74-6581 TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 
        8.22         7.50         4.80         4.54         3.09         3.65 
TCGA-76-4931 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6282 TCGA-76-6285 
        9.17        16.70         3.29         2.70        17.06         8.35 
TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 
       20.98         4.83         5.03         0.23         9.27         7.73 
TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R TCGA-RR-A6KA 
        7.79         1.61        17.72        26.30         5.92         6.28 
TCGA-RR-A6KC 
       20.55 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
             0.43              0.10 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           127.59            120.56 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           11.705            12.100 
[1] "0.4 - 127.6 (11.7)" "0.1 - 120.6 (12.1)"
[1] "hr=" "1"  
D18V2, continuous
D18V3, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    33  37
  9Q GAIN WILD-TYPE 191 309
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     33   37
  9Q GAIN WILD-TYPE  191  309
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE              33               191
  MALE                37               309
[1] 2 2
[1] FALSE
D18V4, continuous
                   vv
clus                GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  9Q GAIN MUTATED                               1                   1
  9Q GAIN WILD-TYPE                            26                  17
                   vv
clus                UNTREATED PRIMARY (DE NOVO) GBM
  9Q GAIN MUTATED                                68
  9Q GAIN WILD-TYPE                             457
D18V5, multiclass
                                 clus
vv                                9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                 1                26
  TREATED PRIMARY GBM                           1                17
  UNTREATED PRIMARY (DE NOVO) GBM              68               457
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V6, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    48  22
  9Q GAIN WILD-TYPE 334 166
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     48   22
  9Q GAIN WILD-TYPE  334  166
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  NO               48               334
  YES              22               166
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9Q GAIN MUTATED       2                         3    64
  9Q GAIN WILD-TYPE    11                        46   421
D18V7, multiclass
                           clus
vv                          9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  ASIAN                                   2                11
  BLACK OR AFRICAN AMERICAN               3                46
  WHITE                                  64               421
[1] 3 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
  9Q GAIN MUTATED     2  56
  9Q GAIN WILD-TYPE  10 416
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      2   56
  9Q GAIN WILD-TYPE   10  416
                        clus
vv                       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                10
  NOT HISPANIC OR LATINO              56               416
[1] 2 2
[1] FALSE

Clustering(19) Variable = 10P GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                  0   1
  10P GAIN MUTATED     5   8
  10P GAIN WILD-TYPE  99 457
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                13                556 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 8                457 
$`10P GAIN MUTATED`
TCGA-02-0011 TCGA-02-0069 TCGA-02-0080 TCGA-02-0087 TCGA-02-0114 TCGA-06-2569 
       20.71        28.70        89.72        57.76        99.98         0.43 
TCGA-06-A7TL TCGA-08-0350 TCGA-08-0351 TCGA-08-0517 TCGA-12-1099 TCGA-14-3477 
        5.42        29.23        65.33        58.68         4.14         3.78 
TCGA-32-2632 
        8.84 

$`10P GAIN WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 
       11.77         4.73        18.35        23.18        10.59        35.41 
TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0024 
       82.59        20.61        87.06        77.65        20.12        53.10 
TCGA-02-0025 TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 
       42.74        24.59        12.16        90.58         2.83        14.14 
TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 
        3.62        10.72        10.52        18.31         6.87        14.73 
TCGA-02-0048 TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 TCGA-02-0055 TCGA-02-0057 
        3.22        15.09        12.59         6.54         2.50        19.86 
TCGA-02-0058 TCGA-02-0059 TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 TCGA-02-0070 
        8.35         9.57         6.02        19.73        26.43        25.05 
TCGA-02-0071 TCGA-02-0074 TCGA-02-0075 TCGA-02-0079 TCGA-02-0083 TCGA-02-0084 
        5.49        10.19        20.84        27.25        22.72        12.62 
TCGA-02-0085 TCGA-02-0086 TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 TCGA-02-0104 
       51.32         8.81        16.96         3.48        27.02        65.00 
TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 TCGA-02-0113 TCGA-02-0115 TCGA-02-0116 
       11.67        17.65        23.18        92.65        15.65        48.95 
TCGA-02-0258 TCGA-02-0260 TCGA-02-0266 TCGA-02-0269 TCGA-02-0271 TCGA-02-0281 
       16.54        16.93        17.72        10.75        14.47         3.98 
TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 
       13.87        14.20        15.95        12.23         9.90         7.73 
TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 
       10.62         7.33        15.91        25.71         4.37        25.12 
TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 
       10.59        12.39        14.50        10.55        47.11        11.34 
TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 TCGA-02-2466 TCGA-02-2470 TCGA-02-2483 
        9.27        16.21         3.35        16.80        12.92        15.32 
TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 
       15.45        20.32         2.70         6.15        20.38        47.61 
TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 
        6.94         3.98        22.72        33.67        12.95        25.35 
TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 
       14.30        26.70        24.23        11.90         0.20        10.29 
TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 
        2.20        11.74         2.33        20.09        17.79        10.09 
TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 
        8.61        19.46        46.59        12.33        13.94        10.45 
TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 
        3.19        10.82         9.44        11.80         3.42        56.91 
TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 
       10.65         5.85        19.66         3.29        13.12         4.47 
TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 
        3.22         4.04        91.00         4.18        88.14        20.25 
TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 
        3.65        69.90        73.84        27.22        44.58        15.42 
TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 
       10.42        38.96         4.67         7.40         5.56         0.39 
TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 
        7.66         8.42         7.63         7.40        11.84         0.53 
TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 
       15.02        24.16         0.72        19.82        13.64        13.32 
TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 
       20.42        48.69        10.82         9.01         0.26        72.36 
TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 
        4.70         9.57         3.16        35.11        12.62         5.75 
TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 
        5.75         9.80         2.10        23.57        14.20        26.40 
TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 
       46.88         7.86         2.70         2.70         0.92        43.46 
TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 
       46.19         5.65         7.17        40.41        16.57        20.78 
TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 
       26.76        23.93         6.84         4.04        26.79        11.84 
TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 TCGA-06-2557 TCGA-06-2558 
       15.32        13.61        33.90        15.32         1.08        12.49 
TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 
        4.93        17.65        12.56        30.64         5.95        16.64 
TCGA-06-2566 TCGA-06-2567 TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 
        5.98         4.37        31.50        11.74         3.55         8.35 
TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 TCGA-06-5418 
        4.54         8.81         8.98         8.55         6.71         2.73 
TCGA-06-5856 TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 TCGA-06-6389 TCGA-06-6390 
        3.75         6.15         4.57         5.23         7.79         5.39 
TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 
        1.48       120.56         7.36         8.32        12.85         4.77 
TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S0 
        1.55         4.77         4.96         4.70         1.87         3.12 
TCGA-06-A6S1 TCGA-06-A7TK TCGA-08-0244 TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 
        2.56         5.39        22.68        37.84         4.18       115.86 
TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0352 
        1.74         8.42        25.71        12.16         9.80         1.28 
TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 
        8.42        17.95        24.56        31.10        37.58        22.29 
TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 
        3.39        12.23        14.93        18.02        15.35        13.97 
TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 
        0.72        12.56         4.27        42.15        11.08        19.59 
TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 
       19.33        10.75         4.80         7.27        15.98        18.41 
TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 
        7.56        15.35        14.73        12.99        34.92        10.45 
TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 
        7.59        94.78         0.10        38.17        25.97        26.66 
TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 
       12.13         3.65        20.38        28.41        15.06        53.85 
TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 
       43.23         7.63         9.73        14.93        14.86        91.76 
TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 TCGA-12-0826 TCGA-12-0827 
       24.79        18.48        10.62        23.51        27.78        38.76 
TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 
        8.94        20.58       127.59         5.82         7.59        33.21 
TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 
       21.73        15.98        12.23        15.85         9.11        14.53 
TCGA-12-1098 TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 
        3.98        15.65        25.68        14.73         6.77        59.77 
TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 
       44.02        26.93        15.22        10.95        12.69        34.92 
TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 
       14.53        14.93         3.22         2.04        15.12        11.97 
TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 
        0.95         6.21        23.05         2.24        11.24        13.78 
TCGA-14-0812 TCGA-14-0813 TCGA-14-0817 TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 
        3.25         1.35         5.39         2.89        16.50        26.33 
TCGA-14-0867 TCGA-14-0871 TCGA-14-1034 TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 
        2.04        28.93        15.95        19.30         0.79         1.38 
TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 TCGA-14-1452 
        1.12         3.75        32.05        58.78        23.11         7.10 
TCGA-14-1453 TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 
        1.15        30.18         0.92        40.96         6.67        12.43 
TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 TCGA-14-1823 TCGA-14-1825 TCGA-14-1827 
        0.99         1.97        17.79        17.85         7.63         5.88 
TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-4157 TCGA-15-0742 TCGA-15-1444 
        7.17        17.49         7.96         3.42        13.78        50.53 
TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 
       19.10        53.19        13.28         3.91        17.59        26.07 
TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 
       16.37         4.31        29.03         4.57        10.29        14.01 
TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 
        9.14        21.24        13.97         6.41        11.77        21.90 
TCGA-19-0960 TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 
        8.61         0.66        14.27         3.39        10.75         9.07 
TCGA-19-1387 TCGA-19-1388 TCGA-19-1389 TCGA-19-1390 TCGA-19-1392 TCGA-19-1786 
        5.95        12.95         4.64        25.38         3.65         7.17 
TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 
       12.66         3.25         0.13         9.67         4.87         1.08 
TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 
        7.53         0.16         4.08        24.23         7.00         7.04 
TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 
        6.64        17.19         8.02        18.90         4.73        12.10 
TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I 
        1.78        22.49        14.07        16.80        14.96        17.79 
TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 
        3.98        28.54        10.03        13.87         9.73        31.33 
TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 
        7.13         9.37         9.40        14.86         5.49         8.88 
TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-26-A7UX TCGA-27-1830 
       18.97         1.58         7.92         2.33        19.33         5.06 
TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 
       16.60         9.86        24.23        40.54        21.30        30.05 
TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 
       14.04        11.51        24.76        10.39        10.39        16.08 
TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 
        7.59         2.86        14.40        15.78         0.20         2.53 
TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 TCGA-28-1755 
        9.21         8.35         7.63         8.48         1.22         1.55 
TCGA-28-1756 TCGA-28-1757 TCGA-28-2502 TCGA-28-2506 TCGA-28-2509 TCGA-28-2513 
        2.83         0.13         0.66         6.74         4.77         7.30 
TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 
        5.26        14.93        11.28        17.88        14.53        11.77 
TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 
       31.27        23.44        11.01        13.64         5.16        22.68 
TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 
       12.76         5.42        15.39        21.07         0.49         0.10 
TCGA-32-1978 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 
       15.85        19.50         1.18         4.67        12.69        14.86 
TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 TCGA-32-2616 
       16.93        12.23        20.78        15.02        15.95         7.36 
TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 
       22.78        25.18        21.14         3.72        12.59        19.86 
TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 
       10.85        19.23         0.85        13.35         8.94         9.53 
TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 
        0.99         4.44        11.84         0.20        15.12        12.46 
TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 
        4.14        14.76         3.45        20.91         4.34        14.33 
TCGA-74-6581 TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 
        8.22         7.50         4.80         4.54         3.09         3.65 
TCGA-76-4931 TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 
        9.17         2.53        10.78        16.70         3.29         2.70 
TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 
       11.38        17.06         8.35        20.98         4.83         5.03 
TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 
        0.23         9.27         7.73         7.79         1.61        17.72 
TCGA-87-5896 TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC 
       26.30         5.92         6.28        20.55 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
              0.43               0.10 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             99.98             127.59 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             28.70              11.84 
[1] "0.4 - 100.0 (28.7)" "0.1 - 127.6 (11.8)"
[1] "hr=" "2.8"
D19V2, continuous
D19V3, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     9   4
  10P GAIN WILD-TYPE 215 342
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      9    4
  10P GAIN WILD-TYPE  215  342
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE                9                215
  MALE                  4                342
[1] 2 2
[1] FALSE
D19V4, continuous
                    vv
clus                 GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  10P GAIN MUTATED                               1                   1
  10P GAIN WILD-TYPE                            26                  17
                    vv
clus                 UNTREATED PRIMARY (DE NOVO) GBM
  10P GAIN MUTATED                                11
  10P GAIN WILD-TYPE                             514
D19V5, multiclass
                                 clus
vv                                10P GAIN MUTATED 10P GAIN WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                  1                 26
  TREATED PRIMARY GBM                            1                 17
  UNTREATED PRIMARY (DE NOVO) GBM               11                514
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V6, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     8   5
  10P GAIN WILD-TYPE 374 183
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      8    5
  10P GAIN WILD-TYPE  374  183
     clus
vv    10P GAIN MUTATED 10P GAIN WILD-TYPE
  NO                 8                374
  YES                5                183
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10P GAIN MUTATED       1                         4     8
  10P GAIN WILD-TYPE    12                        45   477
D19V7, multiclass
                           clus
vv                          10P GAIN MUTATED 10P GAIN WILD-TYPE
  ASIAN                                    1                 12
  BLACK OR AFRICAN AMERICAN                4                 45
  WHITE                                    8                477
[1] 3 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
  10P GAIN MUTATED     1  12
  10P GAIN WILD-TYPE  11 460
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      1   12
  10P GAIN WILD-TYPE   11  460
                        clus
vv                       10P GAIN MUTATED 10P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 11
  NOT HISPANIC OR LATINO               12                460
[1] 2 2
[1] FALSE

Clustering(20) Variable = 10Q GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                  0   1
  10Q GAIN MUTATED     0   3
  10Q GAIN WILD-TYPE 104 462
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 3                566 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 3                462 
$`10Q GAIN MUTATED`
TCGA-02-0011 TCGA-12-1099 TCGA-32-2632 
       20.71         4.14         8.84 

$`10Q GAIN WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 
       11.77         4.73        18.35        23.18        10.59        35.41 
TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0024 
       82.59        20.61        87.06        77.65        20.12        53.10 
TCGA-02-0025 TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 
       42.74        24.59        12.16        90.58         2.83        14.14 
TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 
        3.62        10.72        10.52        18.31         6.87        14.73 
TCGA-02-0048 TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 TCGA-02-0055 TCGA-02-0057 
        3.22        15.09        12.59         6.54         2.50        19.86 
TCGA-02-0058 TCGA-02-0059 TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 TCGA-02-0069 
        8.35         9.57         6.02        19.73        26.43        28.70 
TCGA-02-0070 TCGA-02-0071 TCGA-02-0074 TCGA-02-0075 TCGA-02-0079 TCGA-02-0080 
       25.05         5.49        10.19        20.84        27.25        89.72 
TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 
       22.72        12.62        51.32         8.81        57.76        16.96 
TCGA-02-0099 TCGA-02-0102 TCGA-02-0104 TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 
        3.48        27.02        65.00        11.67        17.65        23.18 
TCGA-02-0113 TCGA-02-0114 TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 
       92.65        99.98        15.65        48.95        16.54        16.93 
TCGA-02-0266 TCGA-02-0269 TCGA-02-0271 TCGA-02-0281 TCGA-02-0285 TCGA-02-0289 
       17.72        10.75        14.47         3.98        13.87        14.20 
TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 
       15.95        12.23         9.90         7.73        10.62         7.33 
TCGA-02-0330 TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 
       15.91        25.71         4.37        25.12        10.59        12.39 
TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 
       14.50        10.55        47.11        11.34         9.27        16.21 
TCGA-02-0456 TCGA-02-2466 TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 
        3.35        16.80        12.92        15.32        15.45        20.32 
TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 
        2.70         6.15        20.38        47.61         6.94         3.98 
TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 
       22.72        33.67        12.95        25.35        14.30        26.70 
TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 
       24.23        11.90         0.20        10.29         2.20        11.74 
TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 
        2.33        20.09        17.79        10.09         8.61        19.46 
TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 
       46.59        12.33        13.94        10.45         3.19        10.82 
TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 
        9.44        11.80         3.42        56.91        10.65         5.85 
TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 
       19.66         3.29        13.12         4.47         3.22         4.04 
TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 
       91.00         4.18        88.14        20.25         3.65        69.90 
TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 
       73.84        27.22        44.58        15.42        10.42        38.96 
TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 
        4.67         7.40         5.56         0.39         7.66         8.42 
TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 
        7.63         7.40        11.84         0.53        15.02        24.16 
TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 
        0.72        19.82        13.64        13.32        20.42        48.69 
TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 
       10.82         9.01         0.26        72.36         4.70         9.57 
TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 
        3.16        35.11        12.62         5.75         5.75         9.80 
TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 
        2.10        23.57        14.20        26.40        46.88         7.86 
TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 
        2.70         2.70         0.92        43.46        46.19         5.65 
TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 
        7.17        40.41        16.57        20.78        26.76        23.93 
TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 
        6.84         4.04        26.79        11.84        15.32        13.61 
TCGA-06-1805 TCGA-06-1806 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 
       33.90        15.32         1.08        12.49         4.93        17.65 
TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 
       12.56        30.64         5.95        16.64         5.98         4.37 
TCGA-06-2569 TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 
        0.43        31.50        11.74         3.55         8.35         4.54 
TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 TCGA-06-5418 TCGA-06-5856 
        8.81         8.98         8.55         6.71         2.73         3.75 
TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 
        6.15         4.57         5.23         7.79         5.39         1.48 
TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 
      120.56         7.36         8.32        12.85         4.77         1.55 
TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 
        4.77         4.96         4.70         1.87         3.12         2.56 
TCGA-06-A7TK TCGA-06-A7TL TCGA-08-0244 TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 
        5.39         5.42        22.68        37.84         4.18       115.86 
TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 
        1.74         8.42        25.71        12.16         9.80        29.23 
TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 
       65.33         1.28         8.42        17.95        24.56        31.10 
TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 
       37.58        22.29         3.39        12.23        14.93        18.02 
TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 
       15.35        13.97         0.72        12.56         4.27        42.15 
TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 
       11.08        19.59        58.68        19.33        10.75         4.80 
TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 
        7.27        15.98        18.41         7.56        15.35        14.73 
TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 
       12.99        34.92        10.45         7.59        94.78         0.10 
TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 
       38.17        25.97        26.66        12.13         3.65        20.38 
TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 
       28.41        15.06        53.85        43.23         7.63         9.73 
TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 
       14.93        14.86        91.76        24.79        18.48        10.62 
TCGA-12-0822 TCGA-12-0826 TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 
       23.51        27.78        38.76         8.94        20.58       127.59 
TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 
        5.82         7.59        33.21        21.73        15.98        12.23 
TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1598 TCGA-12-1599 
       15.85         9.11        14.53         3.98        15.65        25.68 
TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 
       14.73         6.77        59.77        44.02        26.93        15.22 
TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 
       10.95        12.69        34.92        14.53        14.93         3.22 
TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 
        2.04        15.12        11.97         0.95         6.21        23.05 
TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 TCGA-14-0812 TCGA-14-0813 TCGA-14-0817 
        2.24        11.24        13.78         3.25         1.35         5.39 
TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 TCGA-14-0867 TCGA-14-0871 TCGA-14-1034 
        2.89        16.50        26.33         2.04        28.93        15.95 
TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 
       19.30         0.79         1.38         1.12         3.75        32.05 
TCGA-14-1450 TCGA-14-1451 TCGA-14-1452 TCGA-14-1453 TCGA-14-1454 TCGA-14-1455 
       58.78        23.11         7.10         1.15        30.18         0.92 
TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 
       40.96         6.67        12.43         0.99         1.97        17.79 
TCGA-14-1823 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 
       17.85         7.63         5.88         7.17        17.49         7.96 
TCGA-14-3477 TCGA-14-4157 TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 
        3.78         3.42        13.78        50.53        19.10        53.19 
TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 
       13.28         3.91        17.59        26.07        16.37         4.31 
TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 
       29.03         4.57        10.29        14.01         9.14        21.24 
TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 TCGA-19-0962 
       13.97         6.41        11.77        21.90         8.61         0.66 
TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 TCGA-19-1388 
       14.27         3.39        10.75         9.07         5.95        12.95 
TCGA-19-1389 TCGA-19-1390 TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 
        4.64        25.38         3.65         7.17        12.66         3.25 
TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 
        0.13         9.67         4.87         1.08         7.53         0.16 
TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 
        4.08        24.23         7.00         7.04         6.64        17.19 
TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 
        8.02        18.90         4.73        12.10         1.78        22.49 
TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J4 TCGA-19-A6J5 
       14.07        16.80        14.96        17.79         3.98        28.54 
TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 
       10.03        13.87         9.73        31.33         7.13         9.37 
TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 
        9.40        14.86         5.49         8.88        18.97         1.58 
TCGA-26-6173 TCGA-26-6174 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 
        7.92         2.33        19.33         5.06        16.60         9.86 
TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 
       24.23        40.54        21.30        30.05        14.04        11.51 
TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 
       24.76        10.39        10.39        16.08         7.59         2.86 
TCGA-27-2527 TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 
       14.40        15.78         0.20         2.53         9.21         8.35 
TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 
        7.63         8.48         1.22         1.55         2.83         0.13 
TCGA-28-2502 TCGA-28-2506 TCGA-28-2509 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 
        0.66         6.74         4.77         7.30         5.26        14.93 
TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 
       11.28        17.88        14.53        11.77        31.27        23.44 
TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 
       11.01        13.64         5.16        22.68        12.76         5.42 
TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 
       15.39        21.07         0.49         0.10        15.85        19.50 
TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 TCGA-32-1991 TCGA-32-2491 
        1.18         4.67        12.69        14.86        16.93        12.23 
TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 TCGA-32-2616 TCGA-32-2634 TCGA-32-2638 
       20.78        15.02        15.95         7.36        22.78        25.18 
TCGA-32-4208 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 
       21.14         3.72        12.59        19.86        10.85        19.23 
TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 
        0.85        13.35         8.94         9.53         0.99         4.44 
TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9S TCGA-4W-AA9T 
       11.84         0.20        15.12        12.46         4.14        14.76 
TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 
        3.45        20.91         4.34        14.33         8.22         7.50 
TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-4934 
        4.80         4.54         3.09         3.65         9.17         2.53 
TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 
       10.78        16.70         3.29         2.70        11.38        17.06 
TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 
        8.35        20.98         4.83         5.03         0.23         9.27 
TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R 
        7.73         7.79         1.61        17.72        26.30         5.92 
TCGA-RR-A6KA TCGA-RR-A6KC 
        6.28        20.55 

  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
              4.14               0.10 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
             20.71             127.59 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
              8.84              11.87 
[1] "4.1 - 20.7 (8.8)"   "0.1 - 127.6 (11.9)"
[1] "hr=" "1.7"
D20V2, continuous
D20V3, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     2   1
  10Q GAIN WILD-TYPE 222 345
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      2    1
  10Q GAIN WILD-TYPE  222  345
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  FEMALE                2                222
  MALE                  1                345
[1] 2 2
[1] FALSE
D20V4, continuous
[1] "Remove cluster labels:" "10Q GAIN MUTATED"      
clus
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 2                418 
        TCGA-02-0001         TCGA-02-0003         TCGA-02-0006 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-02-0007         TCGA-02-0009         TCGA-02-0010 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-02-0014         TCGA-02-0015         TCGA-02-0016 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-02-0021         TCGA-02-0023         TCGA-02-0024 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-02-0025         TCGA-02-0026         TCGA-02-0027 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-02-0028         TCGA-02-0033         TCGA-02-0034 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-02-0037         TCGA-02-0038         TCGA-02-0039 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-02-0043         TCGA-02-0046         TCGA-02-0047 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-02-0051         TCGA-02-0052         TCGA-02-0054 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-02-0055         TCGA-02-0057         TCGA-02-0058 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-02-0059         TCGA-02-0060         TCGA-02-0064 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-02-0068         TCGA-02-0069         TCGA-02-0070 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-02-0071         TCGA-02-0074         TCGA-02-0075 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-02-0079         TCGA-02-0080         TCGA-02-0083 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-02-0084         TCGA-02-0085         TCGA-02-0086 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-02-0087         TCGA-02-0089         TCGA-02-0099 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-02-0102         TCGA-02-0104         TCGA-02-0106 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-02-0107         TCGA-02-0111         TCGA-02-0113 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-02-0114         TCGA-02-0115         TCGA-02-0116 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-02-0289         TCGA-02-0290         TCGA-02-0317 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-02-0321         TCGA-02-0324         TCGA-02-0325 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-02-0326         TCGA-02-0330         TCGA-02-0332 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-02-0337         TCGA-02-0338         TCGA-02-0339 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-02-0422         TCGA-02-0430         TCGA-02-0432 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-02-0440         TCGA-02-0446         TCGA-02-0451 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-02-0456         TCGA-02-2466         TCGA-02-2470 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-02-2483         TCGA-02-2485         TCGA-02-2486 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-06-0125         TCGA-06-0126         TCGA-06-0127 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-06-0128         TCGA-06-0129         TCGA-06-0130 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-06-0138         TCGA-06-0139         TCGA-06-0140 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-06-0141         TCGA-06-0143         TCGA-06-0149 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-06-0151         TCGA-06-0154         TCGA-06-0155 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-06-0157         TCGA-06-0158         TCGA-06-0159 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-06-0162         TCGA-06-0164         TCGA-06-0165 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-06-0168         TCGA-06-0169         TCGA-06-0171 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-06-0174         TCGA-06-0175         TCGA-06-0176 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-06-0177         TCGA-06-0179         TCGA-06-0182 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-06-0184         TCGA-06-0185         TCGA-06-0187 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-06-0188         TCGA-06-0190         TCGA-06-0192 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-06-0195         TCGA-06-0208         TCGA-06-0211 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-06-0214         TCGA-06-0216         TCGA-06-0221 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-06-0238         TCGA-06-0240         TCGA-06-0241 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-06-0644         TCGA-06-0646         TCGA-06-0648 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-06-0743         TCGA-06-0744         TCGA-06-0745 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-06-0747         TCGA-06-0750         TCGA-06-0875 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-06-0876         TCGA-06-0878         TCGA-06-0879 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-06-0881         TCGA-06-0882         TCGA-06-0939 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-06-1084         TCGA-06-1086         TCGA-06-1087 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-06-1800         TCGA-06-1801         TCGA-06-1802 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-06-1805         TCGA-06-1806         TCGA-06-2557 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-06-2558         TCGA-06-2559         TCGA-06-2561 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-06-2562         TCGA-06-2563         TCGA-06-2564 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-06-2565         TCGA-06-2566         TCGA-06-2567 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-06-2569         TCGA-06-2570         TCGA-06-5408 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-06-5410         TCGA-06-5411         TCGA-06-5412 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-06-5413         TCGA-06-5414         TCGA-06-5415 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-06-5416         TCGA-06-5418         TCGA-06-5858 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-06-5859         TCGA-06-6388         TCGA-06-6389 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-06-6390         TCGA-06-6695         TCGA-06-6697 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-06-6700         TCGA-06-A5U0         TCGA-06-A6S1 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-06-A7TK         TCGA-06-A7TL         TCGA-08-0244 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-08-0245         TCGA-08-0246         TCGA-08-0344 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-08-0345         TCGA-08-0346         TCGA-08-0347 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-08-0348         TCGA-08-0350         TCGA-08-0351 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-08-0353         TCGA-08-0354         TCGA-08-0355 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-08-0356         TCGA-08-0357         TCGA-08-0358 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-08-0375         TCGA-08-0380         TCGA-08-0386 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-08-0389         TCGA-08-0390         TCGA-08-0509 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-08-0510         TCGA-08-0512         TCGA-08-0514 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-08-0517         TCGA-08-0518         TCGA-08-0521 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-08-0524         TCGA-08-0525         TCGA-08-0529 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-08-0531         TCGA-12-0615         TCGA-12-0616 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-12-0618         TCGA-12-0619         TCGA-12-0620 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-12-0656         TCGA-12-0662         TCGA-12-0670 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-12-0688         TCGA-12-0691         TCGA-12-0692 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-12-0703         TCGA-12-0769         TCGA-12-0772 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-12-0773         TCGA-12-0775         TCGA-12-0776 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-12-0778         TCGA-12-0780         TCGA-12-0819 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-12-0820         TCGA-12-0821         TCGA-12-0822 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-12-0827         TCGA-12-0828         TCGA-12-0829 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-12-1088         TCGA-12-1090         TCGA-12-1091 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-12-1092         TCGA-12-1093         TCGA-12-1094 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-12-1095         TCGA-12-1096         TCGA-12-1097 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-12-1098         TCGA-12-1599         TCGA-12-1600 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-12-1602         TCGA-12-3644         TCGA-12-3646 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-12-3648         TCGA-12-3649         TCGA-12-3650 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-12-3651         TCGA-12-3652         TCGA-12-3653 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-12-5299         TCGA-12-5301         TCGA-14-0736 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-14-0740         TCGA-14-0783         TCGA-14-0786 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-14-0787         TCGA-14-0789         TCGA-14-0790 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-14-0812         TCGA-14-0813         TCGA-14-0817 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-14-0862         TCGA-14-0865         TCGA-14-0866 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-14-0867         TCGA-14-0871         TCGA-14-1034 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-14-1037         TCGA-14-1043         TCGA-14-1395 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-14-1396         TCGA-14-1401         TCGA-14-1402 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-14-1450         TCGA-14-1451         TCGA-14-1452 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-14-1453         TCGA-14-1454         TCGA-14-1456 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-14-1458         TCGA-14-1459         TCGA-14-1795 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-14-1821         TCGA-14-1823         TCGA-14-1825 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-14-1827         TCGA-14-1829         TCGA-14-2554 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-14-2555         TCGA-14-3477         TCGA-14-4157 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-15-0742         TCGA-15-1446         TCGA-15-1447 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-15-1449         TCGA-19-0960         TCGA-19-0962 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-19-0964         TCGA-19-1386         TCGA-19-1387 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-19-1389         TCGA-19-1390         TCGA-19-1392 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-19-1786         TCGA-19-1787         TCGA-19-1789 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-19-2619         TCGA-19-2620         TCGA-19-2623 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-19-2631         TCGA-19-5947         TCGA-19-5950 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-19-5951         TCGA-19-5952         TCGA-19-5954 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-19-5956         TCGA-19-5958         TCGA-19-5959 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-19-5960         TCGA-19-A6J5         TCGA-26-1438 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-26-1440         TCGA-26-1442         TCGA-26-1443 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-26-1799         TCGA-26-5132         TCGA-26-5133 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-26-5134         TCGA-26-5139         TCGA-26-6173 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-26-6174         TCGA-27-1830         TCGA-27-1831 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-27-1832         TCGA-27-1833         TCGA-27-1834 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-27-1835         TCGA-27-1836         TCGA-27-1837 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-27-1838         TCGA-27-2518         TCGA-27-2519 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-27-2521         TCGA-27-2523         TCGA-27-2524 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-27-2526         TCGA-27-2527         TCGA-27-2528 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-28-1746         TCGA-28-1749         TCGA-28-1750 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-28-1751         TCGA-28-1752         TCGA-28-1755 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-28-1756         TCGA-28-1757         TCGA-28-2502 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-28-2506         TCGA-28-2509         TCGA-28-2513 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-28-2514         TCGA-28-5204         TCGA-28-5207 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-28-5208         TCGA-28-5211         TCGA-28-5213 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-28-5214         TCGA-28-5215         TCGA-28-5216 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-28-5219         TCGA-28-5220         TCGA-32-1976 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-32-1982         TCGA-32-1986         TCGA-32-2615 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-41-2571         TCGA-41-2573         TCGA-41-2575 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-4W-AA9T         TCGA-74-6573         TCGA-74-6575 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-74-6577         TCGA-74-6578         TCGA-74-6581 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-74-6584         TCGA-76-4925         TCGA-76-4926 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-76-4928         TCGA-76-4929         TCGA-76-4931 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-76-4934         TCGA-76-4935         TCGA-76-6191 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-76-6192         TCGA-76-6193         TCGA-76-6280 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-76-6282         TCGA-76-6285         TCGA-76-6286 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-76-6656         TCGA-76-6657         TCGA-76-6661 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-76-6662         TCGA-76-6663         TCGA-76-6664 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-81-5910 
"10Q GAIN WILD-TYPE" 
                    vv
clus                 GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  10Q GAIN MUTATED                               0                   0
  10Q GAIN WILD-TYPE                            27                  18
                    vv
clus                 UNTREATED PRIMARY (DE NOVO) GBM
  10Q GAIN MUTATED                                 3
  10Q GAIN WILD-TYPE                             522
D20V5, multiclass
                                 clus
vv                                10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                  0                 27
  TREATED PRIMARY GBM                            0                 18
  UNTREATED PRIMARY (DE NOVO) GBM                3                522
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V6, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     1   2
  10Q GAIN WILD-TYPE 381 186
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      1    2
  10Q GAIN WILD-TYPE  381  186
     clus
vv    10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  NO                 1                381
  YES                2                186
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10Q GAIN MUTATED       0                         0     3
  10Q GAIN WILD-TYPE    13                        49   482
D20V7, multiclass
                           clus
vv                          10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  ASIAN                                    0                 13
  BLACK OR AFRICAN AMERICAN                0                 49
  WHITE                                    3                482
[1] 3 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
  10Q GAIN MUTATED     1   2
  10Q GAIN WILD-TYPE  11 470
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      1    2
  10Q GAIN WILD-TYPE   11  470
                        clus
vv                       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 11
  NOT HISPANIC OR LATINO                2                470
[1] 2 2
[1] FALSE

Clustering(21) Variable = 11P GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                  0   1
  11P GAIN MUTATED     2  15
  11P GAIN WILD-TYPE 102 450
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                17                552 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                15                450 
$`11P GAIN MUTATED`
TCGA-02-0014 TCGA-02-0054 TCGA-02-0106 TCGA-06-0130 TCGA-06-0188 TCGA-06-0743 
       82.59         6.54        11.67        12.95        44.58        26.40 
TCGA-06-1087 TCGA-08-0386 TCGA-12-0826 TCGA-12-0827 TCGA-12-1093 TCGA-12-1598 
        4.04        18.02        27.78        38.76        15.98        15.65 
TCGA-19-1388 TCGA-19-4065 TCGA-27-2521 TCGA-27-2526 TCGA-28-5207 
       12.95         7.04        10.39         2.86        11.28 

$`11P GAIN WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 
       11.77         4.73        18.35        23.18        10.59        35.41 
TCGA-02-0011 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0024 
       20.71        20.61        87.06        77.65        20.12        53.10 
TCGA-02-0025 TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 
       42.74        24.59        12.16        90.58         2.83        14.14 
TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 
        3.62        10.72        10.52        18.31         6.87        14.73 
TCGA-02-0048 TCGA-02-0051 TCGA-02-0052 TCGA-02-0055 TCGA-02-0057 TCGA-02-0058 
        3.22        15.09        12.59         2.50        19.86         8.35 
TCGA-02-0059 TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 TCGA-02-0069 TCGA-02-0070 
        9.57         6.02        19.73        26.43        28.70        25.05 
TCGA-02-0071 TCGA-02-0074 TCGA-02-0075 TCGA-02-0079 TCGA-02-0080 TCGA-02-0083 
        5.49        10.19        20.84        27.25        89.72        22.72 
TCGA-02-0084 TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 
       12.62        51.32         8.81        57.76        16.96         3.48 
TCGA-02-0102 TCGA-02-0104 TCGA-02-0107 TCGA-02-0111 TCGA-02-0113 TCGA-02-0114 
       27.02        65.00        17.65        23.18        92.65        99.98 
TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 TCGA-02-0266 TCGA-02-0269 
       15.65        48.95        16.54        16.93        17.72        10.75 
TCGA-02-0271 TCGA-02-0281 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 
       14.47         3.98        13.87        14.20        15.95        12.23 
TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 
        9.90         7.73        10.62         7.33        15.91        25.71 
TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 
        4.37        25.12        10.59        12.39        14.50        10.55 
TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 TCGA-02-2466 
       47.11        11.34         9.27        16.21         3.35        16.80 
TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 
       12.92        15.32        15.45        20.32         2.70         6.15 
TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 
       20.38        47.61         6.94         3.98        22.72        33.67 
TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 
       25.35        14.30        26.70        24.23        11.90         0.20 
TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 
       10.29         2.20        11.74         2.33        20.09        17.79 
TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 
       10.09         8.61        19.46        46.59        12.33        13.94 
TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 
       10.45         3.19        10.82         9.44        11.80         3.42 
TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 
       56.91        10.65         5.85        19.66         3.29        13.12 
TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 
        4.47         3.22         4.04        91.00         4.18        88.14 
TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0189 
       20.25         3.65        69.90        73.84        27.22        15.42 
TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 
       10.42        38.96         4.67         7.40         5.56         0.39 
TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 
        7.66         8.42         7.63         7.40        11.84         0.53 
TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 
       15.02        24.16         0.72        19.82        13.64        13.32 
TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 
       20.42        48.69        10.82         9.01         0.26        72.36 
TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 
        4.70         9.57         3.16        35.11        12.62         5.75 
TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0744 
        5.75         9.80         2.10        23.57        14.20        46.88 
TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 
        7.86         2.70         2.70         0.92        43.46        46.19 
TCGA-06-0877 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 
        5.65         7.17        40.41        16.57        20.78        26.76 
TCGA-06-1084 TCGA-06-1086 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 
       23.93         6.84        26.79        11.84        15.32        13.61 
TCGA-06-1805 TCGA-06-1806 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 
       33.90        15.32         1.08        12.49         4.93        17.65 
TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 
       12.56        30.64         5.95        16.64         5.98         4.37 
TCGA-06-2569 TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 
        0.43        31.50        11.74         3.55         8.35         4.54 
TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 TCGA-06-5418 TCGA-06-5856 
        8.81         8.98         8.55         6.71         2.73         3.75 
TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 
        6.15         4.57         5.23         7.79         5.39         1.48 
TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 
      120.56         7.36         8.32        12.85         4.77         1.55 
TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 
        4.77         4.96         4.70         1.87         3.12         2.56 
TCGA-06-A7TK TCGA-06-A7TL TCGA-08-0244 TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 
        5.39         5.42        22.68        37.84         4.18       115.86 
TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 
        1.74         8.42        25.71        12.16         9.80        29.23 
TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 
       65.33         1.28         8.42        17.95        24.56        31.10 
TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0389 
       37.58        22.29         3.39        12.23        14.93        15.35 
TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 
       13.97         0.72        12.56         4.27        42.15        11.08 
TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 
       19.59        58.68        19.33        10.75         4.80         7.27 
TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 
       15.98        18.41         7.56        15.35        14.73        12.99 
TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 
       34.92        10.45         7.59        94.78         0.10        38.17 
TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 
       25.97        26.66        12.13         3.65        20.38        28.41 
TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 
       15.06        53.85        43.23         7.63         9.73        14.93 
TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 
       14.86        91.76        24.79        18.48        10.62        23.51 
TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 
        8.94        20.58       127.59         5.82         7.59        33.21 
TCGA-12-1092 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 
       21.73        12.23        15.85         9.11        14.53         3.98 
TCGA-12-1099 TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 
        4.14        25.68        14.73         6.77        59.77        44.02 
TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 
       26.93        15.22        10.95        12.69        34.92        14.53 
TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 
       14.93         3.22         2.04        15.12        11.97         0.95 
TCGA-14-0783 TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 TCGA-14-0812 
        6.21        23.05         2.24        11.24        13.78         3.25 
TCGA-14-0813 TCGA-14-0817 TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 TCGA-14-0867 
        1.35         5.39         2.89        16.50        26.33         2.04 
TCGA-14-0871 TCGA-14-1034 TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 TCGA-14-1396 
       28.93        15.95        19.30         0.79         1.38         1.12 
TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 TCGA-14-1452 TCGA-14-1453 
        3.75        32.05        58.78        23.11         7.10         1.15 
TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 TCGA-14-1794 
       30.18         0.92        40.96         6.67        12.43         0.99 
TCGA-14-1795 TCGA-14-1821 TCGA-14-1823 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 
        1.97        17.79        17.85         7.63         5.88         7.17 
TCGA-14-2554 TCGA-14-2555 TCGA-14-3477 TCGA-14-4157 TCGA-15-0742 TCGA-15-1444 
       17.49         7.96         3.78         3.42        13.78        50.53 
TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 
       19.10        53.19        13.28         3.91        17.59        26.07 
TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 
       16.37         4.31        29.03         4.57        10.29        14.01 
TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 
        9.14        21.24        13.97         6.41        11.77        21.90 
TCGA-19-0960 TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 
        8.61         0.66        14.27         3.39        10.75         9.07 
TCGA-19-1387 TCGA-19-1389 TCGA-19-1390 TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 
        5.95         4.64        25.38         3.65         7.17        12.66 
TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 
        3.25         0.13         9.67         4.87         1.08         7.53 
TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-5947 TCGA-19-5950 
        0.16         4.08        24.23         7.00         6.64        17.19 
TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 
        8.02        18.90         4.73        12.10         1.78        22.49 
TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J4 TCGA-19-A6J5 
       14.07        16.80        14.96        17.79         3.98        28.54 
TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 
       10.03        13.87         9.73        31.33         7.13         9.37 
TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 
        9.40        14.86         5.49         8.88        18.97         1.58 
TCGA-26-6173 TCGA-26-6174 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 
        7.92         2.33        19.33         5.06        16.60         9.86 
TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 
       24.23        40.54        21.30        30.05        14.04        11.51 
TCGA-27-2518 TCGA-27-2519 TCGA-27-2523 TCGA-27-2524 TCGA-27-2527 TCGA-27-2528 
       24.76        10.39        16.08         7.59        14.40        15.78 
TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 TCGA-28-1752 
        0.20         2.53         9.21         8.35         7.63         8.48 
TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 TCGA-28-2502 TCGA-28-2506 
        1.22         1.55         2.83         0.13         0.66         6.74 
TCGA-28-2509 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5208 TCGA-28-5209 
        4.77         7.30         5.26        14.93        17.88        14.53 
TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 
       11.77        31.27        23.44        11.01        13.64         5.16 
TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 
       22.68        12.76         5.42        15.39        21.07         0.49 
TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 
        0.10        15.85        19.50         1.18         4.67        12.69 
TCGA-32-1987 TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 
       14.86        16.93        12.23        20.78        15.02        15.95 
TCGA-32-2616 TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4210 
        7.36         8.84        22.78        25.18        21.14         3.72 
TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 
       12.59        19.86        10.85        19.23         0.85        13.35 
TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 
        8.94         9.53         0.99         4.44        11.84         0.20 
TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 
       15.12        12.46         4.14        14.76         3.45        20.91 
TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 
        4.34        14.33         8.22         7.50         4.80         4.54 
TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 
        3.09         3.65         9.17         2.53        10.78        16.70 
TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 
        3.29         2.70        11.38        17.06         8.35        20.98 
TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 
        4.83         5.03         0.23         9.27         7.73         7.79 
TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC 
        1.61        17.72        26.30         5.92         6.28        20.55 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              2.86               0.10 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             82.59             127.59 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             12.95              11.84 
[1] "2.9 - 82.6 (12.9)"  "0.1 - 127.6 (11.8)"
[1] "hr=" "1.2"
D21V2, continuous
D21V3, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     6  11
  11P GAIN WILD-TYPE 218 335
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      6   11
  11P GAIN WILD-TYPE  218  335
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE                6                218
  MALE                 11                335
[1] 2 2
[1] FALSE
D21V4, continuous
                    vv
clus                 GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  11P GAIN MUTATED                               0                   0
  11P GAIN WILD-TYPE                            27                  18
                    vv
clus                 UNTREATED PRIMARY (DE NOVO) GBM
  11P GAIN MUTATED                                17
  11P GAIN WILD-TYPE                             508
D21V5, multiclass
                                 clus
vv                                11P GAIN MUTATED 11P GAIN WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                  0                 27
  TREATED PRIMARY GBM                            0                 18
  UNTREATED PRIMARY (DE NOVO) GBM               17                508
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V6, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    13   4
  11P GAIN WILD-TYPE 369 184
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     13    4
  11P GAIN WILD-TYPE  369  184
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  NO                13                369
  YES                4                184
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11P GAIN MUTATED       0                         0    17
  11P GAIN WILD-TYPE    13                        49   468
D21V7, multiclass
                           clus
vv                          11P GAIN MUTATED 11P GAIN WILD-TYPE
  ASIAN                                    0                 13
  BLACK OR AFRICAN AMERICAN                0                 49
  WHITE                                   17                468
[1] 3 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
  11P GAIN MUTATED     1  15
  11P GAIN WILD-TYPE  11 457
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      1   15
  11P GAIN WILD-TYPE   11  457
                        clus
vv                       11P GAIN MUTATED 11P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 11
  NOT HISPANIC OR LATINO               15                457
[1] 2 2
[1] FALSE

Clustering(22) Variable = 11Q GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                  0   1
  11Q GAIN MUTATED     2  12
  11Q GAIN WILD-TYPE 102 453
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                14                555 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                12                453 
$`11Q GAIN MUTATED`
TCGA-02-0014 TCGA-02-0106 TCGA-02-2466 TCGA-06-0128 TCGA-06-0175 TCGA-06-1086 
       82.59        11.67        16.80        22.72         4.04         6.84 
TCGA-06-1087 TCGA-08-0386 TCGA-12-0818 TCGA-12-0826 TCGA-12-0827 TCGA-19-1388 
        4.04        18.02        91.76        27.78        38.76        12.95 
TCGA-19-4065 TCGA-27-2521 
        7.04        10.39 

$`11Q GAIN WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 
       11.77         4.73        18.35        23.18        10.59        35.41 
TCGA-02-0011 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0024 
       20.71        20.61        87.06        77.65        20.12        53.10 
TCGA-02-0025 TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 
       42.74        24.59        12.16        90.58         2.83        14.14 
TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 
        3.62        10.72        10.52        18.31         6.87        14.73 
TCGA-02-0048 TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 TCGA-02-0055 TCGA-02-0057 
        3.22        15.09        12.59         6.54         2.50        19.86 
TCGA-02-0058 TCGA-02-0059 TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 TCGA-02-0069 
        8.35         9.57         6.02        19.73        26.43        28.70 
TCGA-02-0070 TCGA-02-0071 TCGA-02-0074 TCGA-02-0075 TCGA-02-0079 TCGA-02-0080 
       25.05         5.49        10.19        20.84        27.25        89.72 
TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 
       22.72        12.62        51.32         8.81        57.76        16.96 
TCGA-02-0099 TCGA-02-0102 TCGA-02-0104 TCGA-02-0107 TCGA-02-0111 TCGA-02-0113 
        3.48        27.02        65.00        17.65        23.18        92.65 
TCGA-02-0114 TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 TCGA-02-0266 
       99.98        15.65        48.95        16.54        16.93        17.72 
TCGA-02-0269 TCGA-02-0271 TCGA-02-0281 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 
       10.75        14.47         3.98        13.87        14.20        15.95 
TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 
       12.23         9.90         7.73        10.62         7.33        15.91 
TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 
       25.71         4.37        25.12        10.59        12.39        14.50 
TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 
       10.55        47.11        11.34         9.27        16.21         3.35 
TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 
       12.92        15.32        15.45        20.32         2.70         6.15 
TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0129 TCGA-06-0130 
       20.38        47.61         6.94         3.98        33.67        12.95 
TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 
       25.35        14.30        26.70        24.23        11.90         0.20 
TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 
       10.29         2.20        11.74         2.33        20.09        17.79 
TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 
       10.09         8.61        19.46        46.59        12.33        13.94 
TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 
       10.45         3.19        10.82         9.44        11.80         3.42 
TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 
       56.91        10.65         5.85        19.66         3.29        13.12 
TCGA-06-0173 TCGA-06-0174 TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 
        4.47         3.22        91.00         4.18        88.14        20.25 
TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 
        3.65        69.90        73.84        27.22        44.58        15.42 
TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 
       10.42        38.96         4.67         7.40         5.56         0.39 
TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 
        7.66         8.42         7.63         7.40        11.84         0.53 
TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 
       15.02        24.16         0.72        19.82        13.64        13.32 
TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 
       20.42        48.69        10.82         9.01         0.26        72.36 
TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 
        4.70         9.57         3.16        35.11        12.62         5.75 
TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 
        5.75         9.80         2.10        23.57        14.20        26.40 
TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 
       46.88         7.86         2.70         2.70         0.92        43.46 
TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 
       46.19         5.65         7.17        40.41        16.57        20.78 
TCGA-06-0939 TCGA-06-1084 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 
       26.76        23.93        26.79        11.84        15.32        13.61 
TCGA-06-1805 TCGA-06-1806 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 
       33.90        15.32         1.08        12.49         4.93        17.65 
TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 
       12.56        30.64         5.95        16.64         5.98         4.37 
TCGA-06-2569 TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 
        0.43        31.50        11.74         3.55         8.35         4.54 
TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 TCGA-06-5418 TCGA-06-5856 
        8.81         8.98         8.55         6.71         2.73         3.75 
TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 
        6.15         4.57         5.23         7.79         5.39         1.48 
TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 
      120.56         7.36         8.32        12.85         4.77         1.55 
TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 
        4.77         4.96         4.70         1.87         3.12         2.56 
TCGA-06-A7TK TCGA-06-A7TL TCGA-08-0244 TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 
        5.39         5.42        22.68        37.84         4.18       115.86 
TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 
        1.74         8.42        25.71        12.16         9.80        29.23 
TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 
       65.33         1.28         8.42        17.95        24.56        31.10 
TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0389 
       37.58        22.29         3.39        12.23        14.93        15.35 
TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 
       13.97         0.72        12.56         4.27        42.15        11.08 
TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 
       19.59        58.68        19.33        10.75         4.80         7.27 
TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 
       15.98        18.41         7.56        15.35        14.73        12.99 
TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 
       34.92        10.45         7.59        94.78         0.10        38.17 
TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 
       25.97        26.66        12.13         3.65        20.38        28.41 
TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 
       15.06        53.85        43.23         7.63         9.73        14.93 
TCGA-12-0780 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 TCGA-12-0828 
       14.86        24.79        18.48        10.62        23.51         8.94 
TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 TCGA-12-1092 
       20.58       127.59         5.82         7.59        33.21        21.73 
TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 
       15.98        12.23        15.85         9.11        14.53         3.98 
TCGA-12-1099 TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 
        4.14        15.65        25.68        14.73         6.77        59.77 
TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 
       44.02        26.93        15.22        10.95        12.69        34.92 
TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 
       14.53        14.93         3.22         2.04        15.12        11.97 
TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 
        0.95         6.21        23.05         2.24        11.24        13.78 
TCGA-14-0812 TCGA-14-0813 TCGA-14-0817 TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 
        3.25         1.35         5.39         2.89        16.50        26.33 
TCGA-14-0867 TCGA-14-0871 TCGA-14-1034 TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 
        2.04        28.93        15.95        19.30         0.79         1.38 
TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 TCGA-14-1452 
        1.12         3.75        32.05        58.78        23.11         7.10 
TCGA-14-1453 TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 
        1.15        30.18         0.92        40.96         6.67        12.43 
TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 TCGA-14-1823 TCGA-14-1825 TCGA-14-1827 
        0.99         1.97        17.79        17.85         7.63         5.88 
TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-3477 TCGA-14-4157 TCGA-15-0742 
        7.17        17.49         7.96         3.78         3.42        13.78 
TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 
       50.53        19.10        53.19        13.28         3.91        17.59 
TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 
       26.07        16.37         4.31        29.03         4.57        10.29 
TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 
       14.01         9.14        21.24        13.97         6.41        11.77 
TCGA-19-0957 TCGA-19-0960 TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 
       21.90         8.61         0.66        14.27         3.39        10.75 
TCGA-19-1386 TCGA-19-1387 TCGA-19-1389 TCGA-19-1390 TCGA-19-1392 TCGA-19-1786 
        9.07         5.95         4.64        25.38         3.65         7.17 
TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 
       12.66         3.25         0.13         9.67         4.87         1.08 
TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-5947 
        7.53         0.16         4.08        24.23         7.00         6.64 
TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 
       17.19         8.02        18.90         4.73        12.10         1.78 
TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J4 
       22.49        14.07        16.80        14.96        17.79         3.98 
TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 
       28.54        10.03        13.87         9.73        31.33         7.13 
TCGA-26-1799 TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 
        9.37         9.40        14.86         5.49         8.88        18.97 
TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 
        1.58         7.92         2.33        19.33         5.06        16.60 
TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 
        9.86        24.23        40.54        21.30        30.05        14.04 
TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 
       11.51        24.76        10.39        16.08         7.59         2.86 
TCGA-27-2527 TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 
       14.40        15.78         0.20         2.53         9.21         8.35 
TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 
        7.63         8.48         1.22         1.55         2.83         0.13 
TCGA-28-2502 TCGA-28-2506 TCGA-28-2509 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 
        0.66         6.74         4.77         7.30         5.26        14.93 
TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 
       11.28        17.88        14.53        11.77        31.27        23.44 
TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 
       11.01        13.64         5.16        22.68        12.76         5.42 
TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 
       15.39        21.07         0.49         0.10        15.85        19.50 
TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 TCGA-32-1991 TCGA-32-2491 
        1.18         4.67        12.69        14.86        16.93        12.23 
TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 TCGA-32-2616 TCGA-32-2632 TCGA-32-2634 
       20.78        15.02        15.95         7.36         8.84        22.78 
TCGA-32-2638 TCGA-32-4208 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 
       25.18        21.14         3.72        12.59        19.86        10.85 
TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 
       19.23         0.85        13.35         8.94         9.53         0.99 
TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9S 
        4.44        11.84         0.20        15.12        12.46         4.14 
TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 
       14.76         3.45        20.91         4.34        14.33         8.22 
TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 
        7.50         4.80         4.54         3.09         3.65         9.17 
TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 
        2.53        10.78        16.70         3.29         2.70        11.38 
TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 
       17.06         8.35        20.98         4.83         5.03         0.23 
TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
        9.27         7.73         7.79         1.61        17.72        26.30 
TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC 
        5.92         6.28        20.55 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              4.04               0.10 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             91.76             127.59 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            14.875             11.840 
[1] "4.0 - 91.8 (14.9)"  "0.1 - 127.6 (11.8)"
[1] "hr=" "1.4"
D22V2, continuous
D22V3, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     3  11
  11Q GAIN WILD-TYPE 221 335
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      3   11
  11Q GAIN WILD-TYPE  221  335
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE                3                221
  MALE                 11                335
[1] 2 2
[1] FALSE
D22V4, continuous
                    vv
clus                 GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  11Q GAIN MUTATED                               0                   1
  11Q GAIN WILD-TYPE                            27                  17
                    vv
clus                 UNTREATED PRIMARY (DE NOVO) GBM
  11Q GAIN MUTATED                                13
  11Q GAIN WILD-TYPE                             512
D22V5, multiclass
                                 clus
vv                                11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                  0                 27
  TREATED PRIMARY GBM                            1                 17
  UNTREATED PRIMARY (DE NOVO) GBM               13                512
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V6, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    12   2
  11Q GAIN WILD-TYPE 370 186
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     12    2
  11Q GAIN WILD-TYPE  370  186
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  NO                12                370
  YES                2                186
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11Q GAIN MUTATED       0                         1    13
  11Q GAIN WILD-TYPE    13                        48   472
D22V7, multiclass
                           clus
vv                          11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  ASIAN                                    0                 13
  BLACK OR AFRICAN AMERICAN                1                 48
  WHITE                                   13                472
[1] 3 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
  11Q GAIN MUTATED     1  13
  11Q GAIN WILD-TYPE  11 459
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      1   13
  11Q GAIN WILD-TYPE   11  459
                        clus
vv                       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 11
  NOT HISPANIC OR LATINO               13                459
[1] 2 2
[1] FALSE

Clustering(23) Variable = 12P GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                  0   1
  12P GAIN MUTATED    10  49
  12P GAIN WILD-TYPE  94 416
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                59                510 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                49                416 
$`12P GAIN MUTATED`
TCGA-02-0001 TCGA-02-0024 TCGA-02-0051 TCGA-02-0054 TCGA-02-0070 TCGA-02-0074 
       11.77        53.10        15.09         6.54        25.05        10.19 
TCGA-02-0087 TCGA-02-0266 TCGA-02-0271 TCGA-02-0324 TCGA-06-0146 TCGA-06-0151 
       57.76        17.72        14.47         7.73        20.09        46.59 
TCGA-06-0162 TCGA-06-0164 TCGA-06-0184 TCGA-06-0187 TCGA-06-0188 TCGA-06-0192 
        3.42        56.91        69.90        27.22        44.58        38.96 
TCGA-06-0216 TCGA-06-0409 TCGA-06-0649 TCGA-06-0743 TCGA-06-0877 TCGA-06-1086 
       24.16        72.36         2.10        26.40         5.65         6.84 
TCGA-06-1087 TCGA-06-2561 TCGA-06-5415 TCGA-06-6389 TCGA-06-6694 TCGA-06-A7TL 
        4.04        17.65         8.55         7.79         7.36         5.42 
TCGA-08-0246 TCGA-08-0516 TCGA-12-0691 TCGA-12-0776 TCGA-12-0778 TCGA-12-1090 
        4.18        19.59        12.13         9.73        14.93         7.59 
TCGA-12-1098 TCGA-12-1598 TCGA-12-3653 TCGA-14-0740 TCGA-14-0790 TCGA-14-1396 
        3.98        15.65        14.53        11.97        13.78         1.12 
TCGA-14-1453 TCGA-14-1821 TCGA-14-1823 TCGA-14-2554 TCGA-15-1449 TCGA-16-1460 
        1.15        17.79        17.85        17.49        13.28         6.41 
TCGA-19-1787 TCGA-27-1838 TCGA-28-1756 TCGA-28-2506 TCGA-28-5207 TCGA-28-5218 
       12.66        11.51         2.83         6.74        11.28         5.16 
TCGA-32-1979 TCGA-32-2615 TCGA-32-4208 TCGA-32-5222 TCGA-74-6577 
       19.50        15.95        21.14        19.23         4.34 

$`12P GAIN WILD-TYPE`
TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 TCGA-02-0011 
        4.73        18.35        23.18        10.59        35.41        20.71 
TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0025 
       82.59        20.61        87.06        77.65        20.12        42.74 
TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 
       24.59        12.16        90.58         2.83        14.14         3.62 
TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 TCGA-02-0048 
       10.72        10.52        18.31         6.87        14.73         3.22 
TCGA-02-0052 TCGA-02-0055 TCGA-02-0057 TCGA-02-0058 TCGA-02-0059 TCGA-02-0060 
       12.59         2.50        19.86         8.35         9.57         6.02 
TCGA-02-0064 TCGA-02-0068 TCGA-02-0069 TCGA-02-0071 TCGA-02-0075 TCGA-02-0079 
       19.73        26.43        28.70         5.49        20.84        27.25 
TCGA-02-0080 TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 TCGA-02-0086 TCGA-02-0089 
       89.72        22.72        12.62        51.32         8.81        16.96 
TCGA-02-0099 TCGA-02-0102 TCGA-02-0104 TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 
        3.48        27.02        65.00        11.67        17.65        23.18 
TCGA-02-0113 TCGA-02-0114 TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 
       92.65        99.98        15.65        48.95        16.54        16.93 
TCGA-02-0269 TCGA-02-0281 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 
       10.75         3.98        13.87        14.20        15.95        12.23 
TCGA-02-0321 TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 TCGA-02-0333 
        9.90        10.62         7.33        15.91        25.71         4.37 
TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 
       25.12        10.59        12.39        14.50        10.55        47.11 
TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 TCGA-02-2466 TCGA-02-2470 
       11.34         9.27        16.21         3.35        16.80        12.92 
TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 
       15.32        15.45        20.32         2.70         6.15        20.38 
TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 
       47.61         6.94         3.98        22.72        33.67        12.95 
TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 
       25.35        14.30        26.70        24.23        11.90         0.20 
TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0147 TCGA-06-0148 
       10.29         2.20        11.74         2.33        17.79        10.09 
TCGA-06-0149 TCGA-06-0150 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 
        8.61        19.46        12.33        13.94        10.45         3.19 
TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 
       10.82         9.44        11.80        10.65         5.85        19.66 
TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 
        3.29        13.12         4.47         3.22         4.04        91.00 
TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0185 TCGA-06-0189 
        4.18        88.14        20.25         3.65        73.84        15.42 
TCGA-06-0190 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 
       10.42         4.67         7.40         5.56         0.39         7.66 
TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 
        8.42         7.63         7.40        11.84         0.53        15.02 
TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 
        0.72        19.82        13.64        13.32        20.42        48.69 
TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 
       10.82         9.01         0.26         4.70         9.57         3.16 
TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0650 
       35.11        12.62         5.75         5.75         9.80        23.57 
TCGA-06-0686 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 
       14.20        46.88         7.86         2.70         2.70         0.92 
TCGA-06-0875 TCGA-06-0876 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 
       43.46        46.19         7.17        40.41        16.57        20.78 
TCGA-06-0939 TCGA-06-1084 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 
       26.76        23.93        26.79        11.84        15.32        13.61 
TCGA-06-1805 TCGA-06-1806 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2562 
       33.90        15.32         1.08        12.49         4.93        12.56 
TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 
       30.64         5.95        16.64         5.98         4.37         0.43 
TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 
       31.50        11.74         3.55         8.35         4.54         8.81 
TCGA-06-5414 TCGA-06-5416 TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 TCGA-06-5859 
        8.98         6.71         2.73         3.75         6.15         4.57 
TCGA-06-6388 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6695 TCGA-06-6697 
        5.23         5.39         1.48       120.56         8.32        12.85 
TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A5U1 
        4.77         1.55         4.77         4.96         4.70         1.87 
TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK TCGA-08-0244 TCGA-08-0245 TCGA-08-0344 
        3.12         2.56         5.39        22.68        37.84       115.86 
TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 
        1.74         8.42        25.71        12.16         9.80        29.23 
TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 
       65.33         1.28         8.42        17.95        24.56        31.10 
TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 
       37.58        22.29         3.39        12.23        14.93        18.02 
TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 
       15.35        13.97         0.72        12.56         4.27        42.15 
TCGA-08-0514 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 
       11.08        58.68        19.33        10.75         4.80         7.27 
TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 
       15.98        18.41         7.56        15.35        14.73        12.99 
TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 
       34.92        10.45         7.59        94.78         0.10        38.17 
TCGA-12-0670 TCGA-12-0688 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 
       25.97        26.66         3.65        20.38        28.41        15.06 
TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 
       53.85        43.23         7.63        14.86        91.76        24.79 
TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 TCGA-12-0826 TCGA-12-0827 TCGA-12-0828 
       18.48        10.62        23.51        27.78        38.76         8.94 
TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 
       20.58       127.59         5.82        33.21        21.73        15.98 
TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1099 TCGA-12-1599 
       12.23        15.85         9.11        14.53         4.14        25.68 
TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 
       14.73         6.77        59.77        44.02        26.93        15.22 
TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 
       10.95        12.69        34.92        14.93         3.22         2.04 
TCGA-14-0736 TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 
       15.12         0.95         6.21        23.05         2.24        11.24 
TCGA-14-0812 TCGA-14-0813 TCGA-14-0817 TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 
        3.25         1.35         5.39         2.89        16.50        26.33 
TCGA-14-0867 TCGA-14-0871 TCGA-14-1034 TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 
        2.04        28.93        15.95        19.30         0.79         1.38 
TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 TCGA-14-1452 TCGA-14-1454 
        3.75        32.05        58.78        23.11         7.10        30.18 
TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 
        0.92        40.96         6.67        12.43         0.99         1.97 
TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2555 TCGA-14-3477 TCGA-14-4157 
        7.63         5.88         7.17         7.96         3.78         3.42 
TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 TCGA-16-0846 TCGA-16-0848 
       13.78        50.53        19.10        53.19         3.91        17.59 
TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 
       26.07        16.37         4.31        29.03         4.57        10.29 
TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-19-0955 TCGA-19-0957 
       14.01         9.14        21.24        13.97        11.77        21.90 
TCGA-19-0960 TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 
        8.61         0.66        14.27         3.39        10.75         9.07 
TCGA-19-1387 TCGA-19-1388 TCGA-19-1389 TCGA-19-1390 TCGA-19-1392 TCGA-19-1786 
        5.95        12.95         4.64        25.38         3.65         7.17 
TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 
        3.25         0.13         9.67         4.87         1.08         7.53 
TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 
        0.16         4.08        24.23         7.00         7.04         6.64 
TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 
       17.19         8.02        18.90         4.73        12.10         1.78 
TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J4 
       22.49        14.07        16.80        14.96        17.79         3.98 
TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 
       28.54        10.03        13.87         9.73        31.33         7.13 
TCGA-26-1799 TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 
        9.37         9.40        14.86         5.49         8.88        18.97 
TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 
        1.58         7.92         2.33        19.33         5.06        16.60 
TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 
        9.86        24.23        40.54        21.30        30.05        14.04 
TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 
       24.76        10.39        10.39        16.08         7.59         2.86 
TCGA-27-2527 TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 
       14.40        15.78         0.20         2.53         9.21         8.35 
TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 TCGA-28-1755 TCGA-28-1757 TCGA-28-2502 
        7.63         8.48         1.22         1.55         0.13         0.66 
TCGA-28-2509 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5208 TCGA-28-5209 
        4.77         7.30         5.26        14.93        17.88        14.53 
TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5219 
       11.77        31.27        23.44        11.01        13.64        22.68 
TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 
       12.76         5.42        15.39        21.07         0.49         0.10 
TCGA-32-1978 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 TCGA-32-1991 
       15.85         1.18         4.67        12.69        14.86        16.93 
TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2616 TCGA-32-2632 TCGA-32-2634 
       12.23        20.78        15.02         7.36         8.84        22.78 
TCGA-32-2638 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-41-2571 
       25.18         3.72        12.59        19.86        10.85         0.85 
TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 
       13.35         8.94         9.53         0.99         4.44        11.84 
TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 
        0.20        15.12        12.46         4.14        14.76         3.45 
TCGA-74-6575 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 
       20.91        14.33         8.22         7.50         4.80         4.54 
TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 
        3.09         3.65         9.17         2.53        10.78        16.70 
TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 
        3.29         2.70        11.38        17.06         8.35        20.98 
TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 
        4.83         5.03         0.23         9.27         7.73         7.79 
TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC 
        1.61        17.72        26.30         5.92         6.28        20.55 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              1.12               0.10 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             72.36             127.59 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            13.280             11.785 
[1] "1.1 - 72.4 (13.3)"  "0.1 - 127.6 (11.8)"
[1] "hr=" "1.1"
D23V2, continuous
D23V3, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    26  33
  12P GAIN WILD-TYPE 198 313
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     26   33
  12P GAIN WILD-TYPE  198  313
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE               26                198
  MALE                 33                313
[1] 2 2
[1] FALSE
D23V4, continuous
                    vv
clus                 GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  12P GAIN MUTATED                               2                   1
  12P GAIN WILD-TYPE                            25                  17
                    vv
clus                 UNTREATED PRIMARY (DE NOVO) GBM
  12P GAIN MUTATED                                56
  12P GAIN WILD-TYPE                             469
D23V5, multiclass
                                 clus
vv                                12P GAIN MUTATED 12P GAIN WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                  2                 25
  TREATED PRIMARY GBM                            1                 17
  UNTREATED PRIMARY (DE NOVO) GBM               56                469
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V6, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    42  17
  12P GAIN WILD-TYPE 340 171
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     42   17
  12P GAIN WILD-TYPE  340  171
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  NO                42                340
  YES               17                171
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12P GAIN MUTATED       1                         4    50
  12P GAIN WILD-TYPE    12                        45   435
D23V7, multiclass
                           clus
vv                          12P GAIN MUTATED 12P GAIN WILD-TYPE
  ASIAN                                    1                 12
  BLACK OR AFRICAN AMERICAN                4                 45
  WHITE                                   50                435
[1] 3 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
  12P GAIN MUTATED     1  46
  12P GAIN WILD-TYPE  11 426
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      1   46
  12P GAIN WILD-TYPE   11  426
                        clus
vv                       12P GAIN MUTATED 12P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 11
  NOT HISPANIC OR LATINO               46                426
[1] 2 2
[1] FALSE

Clustering(24) Variable = 12Q GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                  0   1
  12Q GAIN MUTATED     8  40
  12Q GAIN WILD-TYPE  96 425
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                48                521 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                40                425 
$`12Q GAIN MUTATED`
TCGA-02-0001 TCGA-02-0051 TCGA-02-0054 TCGA-02-0060 TCGA-02-0070 TCGA-02-0074 
       11.77        15.09         6.54         6.02        25.05        10.19 
TCGA-02-0087 TCGA-02-0271 TCGA-02-0324 TCGA-06-0151 TCGA-06-0164 TCGA-06-0188 
       57.76        14.47         7.73        46.59        56.91        44.58 
TCGA-06-0192 TCGA-06-0216 TCGA-06-0409 TCGA-06-0743 TCGA-06-0877 TCGA-06-1086 
       38.96        24.16        72.36        26.40         5.65         6.84 
TCGA-06-1087 TCGA-06-2561 TCGA-06-5415 TCGA-06-6391 TCGA-06-6694 TCGA-06-A7TL 
        4.04        17.65         8.55         1.48         7.36         5.42 
TCGA-08-0246 TCGA-12-0691 TCGA-12-0778 TCGA-12-1090 TCGA-12-1098 TCGA-12-3653 
        4.18        12.13        14.93         7.59         3.98        14.53 
TCGA-14-0790 TCGA-14-1396 TCGA-14-1453 TCGA-14-1821 TCGA-14-1823 TCGA-14-2554 
       13.78         1.12         1.15        17.79        17.85        17.49 
TCGA-15-1449 TCGA-19-1786 TCGA-19-1787 TCGA-27-1838 TCGA-28-2506 TCGA-28-5207 
       13.28         7.17        12.66        11.51         6.74        11.28 
TCGA-28-5218 TCGA-32-1979 TCGA-32-2615 TCGA-32-4208 TCGA-32-5222 TCGA-74-6577 
        5.16        19.50        15.95        21.14        19.23         4.34 

$`12Q GAIN WILD-TYPE`
TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 TCGA-02-0011 
        4.73        18.35        23.18        10.59        35.41        20.71 
TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0024 
       82.59        20.61        87.06        77.65        20.12        53.10 
TCGA-02-0025 TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 
       42.74        24.59        12.16        90.58         2.83        14.14 
TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 
        3.62        10.72        10.52        18.31         6.87        14.73 
TCGA-02-0048 TCGA-02-0052 TCGA-02-0055 TCGA-02-0057 TCGA-02-0058 TCGA-02-0059 
        3.22        12.59         2.50        19.86         8.35         9.57 
TCGA-02-0064 TCGA-02-0068 TCGA-02-0069 TCGA-02-0071 TCGA-02-0075 TCGA-02-0079 
       19.73        26.43        28.70         5.49        20.84        27.25 
TCGA-02-0080 TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 TCGA-02-0086 TCGA-02-0089 
       89.72        22.72        12.62        51.32         8.81        16.96 
TCGA-02-0099 TCGA-02-0102 TCGA-02-0104 TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 
        3.48        27.02        65.00        11.67        17.65        23.18 
TCGA-02-0113 TCGA-02-0114 TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 
       92.65        99.98        15.65        48.95        16.54        16.93 
TCGA-02-0266 TCGA-02-0269 TCGA-02-0281 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 
       17.72        10.75         3.98        13.87        14.20        15.95 
TCGA-02-0317 TCGA-02-0321 TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 
       12.23         9.90        10.62         7.33        15.91        25.71 
TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 
        4.37        25.12        10.59        12.39        14.50        10.55 
TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 TCGA-02-2466 
       47.11        11.34         9.27        16.21         3.35        16.80 
TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 
       12.92        15.32        15.45        20.32         2.70         6.15 
TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 
       20.38        47.61         6.94         3.98        22.72        33.67 
TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 
       12.95        25.35        14.30        26.70        24.23        11.90 
TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 
        0.20        10.29         2.20        11.74         2.33        20.09 
TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0152 TCGA-06-0154 
       17.79        10.09         8.61        19.46        12.33        13.94 
TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 
       10.45         3.19        10.82         9.44        11.80         3.42 
TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 
       10.65         5.85        19.66         3.29        13.12         4.47 
TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 
        3.22         4.04        91.00         4.18        88.14        20.25 
TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0189 TCGA-06-0190 
        3.65        69.90        73.84        27.22        15.42        10.42 
TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 
        4.67         7.40         5.56         0.39         7.66         8.42 
TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0219 
        7.63         7.40        11.84         0.53        15.02         0.72 
TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 
       19.82        13.64        13.32        20.42        48.69        10.82 
TCGA-06-0397 TCGA-06-0402 TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 
        9.01         0.26         4.70         9.57         3.16        35.11 
TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 
       12.62         5.75         5.75         9.80         2.10        23.57 
TCGA-06-0686 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 
       14.20        46.88         7.86         2.70         2.70         0.92 
TCGA-06-0875 TCGA-06-0876 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 
       43.46        46.19         7.17        40.41        16.57        20.78 
TCGA-06-0939 TCGA-06-1084 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 
       26.76        23.93        26.79        11.84        15.32        13.61 
TCGA-06-1805 TCGA-06-1806 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2562 
       33.90        15.32         1.08        12.49         4.93        12.56 
TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 
       30.64         5.95        16.64         5.98         4.37         0.43 
TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 
       31.50        11.74         3.55         8.35         4.54         8.81 
TCGA-06-5414 TCGA-06-5416 TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 TCGA-06-5859 
        8.98         6.71         2.73         3.75         6.15         4.57 
TCGA-06-6388 TCGA-06-6389 TCGA-06-6390 TCGA-06-6693 TCGA-06-6695 TCGA-06-6697 
        5.23         7.79         5.39       120.56         8.32        12.85 
TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A5U1 
        4.77         1.55         4.77         4.96         4.70         1.87 
TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK TCGA-08-0244 TCGA-08-0245 TCGA-08-0344 
        3.12         2.56         5.39        22.68        37.84       115.86 
TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 
        1.74         8.42        25.71        12.16         9.80        29.23 
TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 
       65.33         1.28         8.42        17.95        24.56        31.10 
TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 
       37.58        22.29         3.39        12.23        14.93        18.02 
TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 
       15.35        13.97         0.72        12.56         4.27        42.15 
TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 
       11.08        19.59        58.68        19.33        10.75         4.80 
TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 
        7.27        15.98        18.41         7.56        15.35        14.73 
TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 
       12.99        34.92        10.45         7.59        94.78         0.10 
TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 
       38.17        25.97        26.66         3.65        20.38        28.41 
TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0780 
       15.06        53.85        43.23         7.63         9.73        14.86 
TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 TCGA-12-0826 
       91.76        24.79        18.48        10.62        23.51        27.78 
TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 TCGA-12-1091 
       38.76         8.94        20.58       127.59         5.82        33.21 
TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 
       21.73        15.98        12.23        15.85         9.11        14.53 
TCGA-12-1099 TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 
        4.14        15.65        25.68        14.73         6.77        59.77 
TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 
       44.02        26.93        15.22        10.95        12.69        34.92 
TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 
       14.93         3.22         2.04        15.12        11.97         0.95 
TCGA-14-0783 TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 TCGA-14-0812 TCGA-14-0813 
        6.21        23.05         2.24        11.24         3.25         1.35 
TCGA-14-0817 TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 TCGA-14-0867 TCGA-14-0871 
        5.39         2.89        16.50        26.33         2.04        28.93 
TCGA-14-1034 TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 TCGA-14-1401 TCGA-14-1402 
       15.95        19.30         0.79         1.38         3.75        32.05 
TCGA-14-1450 TCGA-14-1451 TCGA-14-1452 TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 
       58.78        23.11         7.10        30.18         0.92        40.96 
TCGA-14-1458 TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1825 TCGA-14-1827 
        6.67        12.43         0.99         1.97         7.63         5.88 
TCGA-14-1829 TCGA-14-2555 TCGA-14-3477 TCGA-14-4157 TCGA-15-0742 TCGA-15-1444 
        7.17         7.96         3.78         3.42        13.78        50.53 
TCGA-15-1446 TCGA-15-1447 TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 
       19.10        53.19         3.91        17.59        26.07        16.37 
TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 
        4.31        29.03         4.57        10.29        14.01         9.14 
TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 
       21.24        13.97         6.41        11.77        21.90         8.61 
TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 
        0.66        14.27         3.39        10.75         9.07         5.95 
TCGA-19-1388 TCGA-19-1389 TCGA-19-1390 TCGA-19-1392 TCGA-19-1789 TCGA-19-1791 
       12.95         4.64        25.38         3.65         3.25         0.13 
TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 
        9.67         4.87         1.08         7.53         0.16         4.08 
TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 
       24.23         7.00         7.04         6.64        17.19         8.02 
TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 
       18.90         4.73        12.10         1.78        22.49        14.07 
TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 
       16.80        14.96        17.79         3.98        28.54        10.03 
TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 
       13.87         9.73        31.33         7.13         9.37         9.40 
TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 
       14.86         5.49         8.88        18.97         1.58         7.92 
TCGA-26-6174 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 
        2.33        19.33         5.06        16.60         9.86        24.23 
TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-2518 TCGA-27-2519 
       40.54        21.30        30.05        14.04        24.76        10.39 
TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 
       10.39        16.08         7.59         2.86        14.40        15.78 
TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 TCGA-28-1752 
        0.20         2.53         9.21         8.35         7.63         8.48 
TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 TCGA-28-2502 TCGA-28-2509 
        1.22         1.55         2.83         0.13         0.66         4.77 
TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 
        7.30         5.26        14.93        17.88        14.53        11.77 
TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5219 TCGA-28-5220 
       31.27        23.44        11.01        13.64        22.68        12.76 
TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 TCGA-32-1978 
        5.42        15.39        21.07         0.49         0.10        15.85 
TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 TCGA-32-1991 TCGA-32-2491 
        1.18         4.67        12.69        14.86        16.93        12.23 
TCGA-32-2494 TCGA-32-2495 TCGA-32-2616 TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 
       20.78        15.02         7.36         8.84        22.78        25.18 
TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-41-2571 TCGA-41-2572 
        3.72        12.59        19.86        10.85         0.85        13.35 
TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 
        8.94         9.53         0.99         4.44        11.84         0.20 
TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 
       15.12        12.46         4.14        14.76         3.45        20.91 
TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 
       14.33         8.22         7.50         4.80         4.54         3.09 
TCGA-76-4929 TCGA-76-4931 TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 
        3.65         9.17         2.53        10.78        16.70         3.29 
TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 
        2.70        11.38        17.06         8.35        20.98         4.83 
TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 
        5.03         0.23         9.27         7.73         7.79         1.61 
TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC 
       17.72        26.30         5.92         6.28        20.55 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              1.12               0.10 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             72.36             127.59 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            12.395             11.840 
[1] "1.1 - 72.4 (12.4)"  "0.1 - 127.6 (11.8)"
[1] "hr=" "1"  
D24V2, continuous
D24V3, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    23  25
  12Q GAIN WILD-TYPE 201 321
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     23   25
  12Q GAIN WILD-TYPE  201  321
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE               23                201
  MALE                 25                321
[1] 2 2
[1] FALSE
D24V4, continuous
                    vv
clus                 GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  12Q GAIN MUTATED                               2                   0
  12Q GAIN WILD-TYPE                            25                  18
                    vv
clus                 UNTREATED PRIMARY (DE NOVO) GBM
  12Q GAIN MUTATED                                46
  12Q GAIN WILD-TYPE                             479
D24V5, multiclass
                                 clus
vv                                12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                  2                 25
  TREATED PRIMARY GBM                            0                 18
  UNTREATED PRIMARY (DE NOVO) GBM               46                479
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V6, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    34  14
  12Q GAIN WILD-TYPE 348 174
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     34   14
  12Q GAIN WILD-TYPE  348  174
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  NO                34                348
  YES               14                174
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12Q GAIN MUTATED       3                         3    39
  12Q GAIN WILD-TYPE    10                        46   446
D24V7, multiclass
                           clus
vv                          12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  ASIAN                                    3                 10
  BLACK OR AFRICAN AMERICAN                3                 46
  WHITE                                   39                446
[1] 3 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
  12Q GAIN MUTATED     0  37
  12Q GAIN WILD-TYPE  12 435
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      0   37
  12Q GAIN WILD-TYPE   12  435
                        clus
vv                       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 12
  NOT HISPANIC OR LATINO               37                435
[1] 2 2
[1] FALSE

Clustering(25) Variable = 13Q GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                  0   1
  13Q GAIN MUTATED     0  10
  13Q GAIN WILD-TYPE 104 455
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                10                559 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                10                455 
$`13Q GAIN MUTATED`
TCGA-02-0001 TCGA-02-0281 TCGA-08-0386 TCGA-14-0817 TCGA-14-0871 TCGA-19-1390 
       11.77         3.98        18.02         5.39        28.93        25.38 
TCGA-19-A6J4 TCGA-26-5136 TCGA-28-5207 TCGA-32-2615 
        3.98        18.97        11.28        15.95 

$`13Q GAIN WILD-TYPE`
TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 TCGA-02-0011 
        4.73        18.35        23.18        10.59        35.41        20.71 
TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0024 
       82.59        20.61        87.06        77.65        20.12        53.10 
TCGA-02-0025 TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 
       42.74        24.59        12.16        90.58         2.83        14.14 
TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 
        3.62        10.72        10.52        18.31         6.87        14.73 
TCGA-02-0048 TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 TCGA-02-0055 TCGA-02-0057 
        3.22        15.09        12.59         6.54         2.50        19.86 
TCGA-02-0058 TCGA-02-0059 TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 TCGA-02-0069 
        8.35         9.57         6.02        19.73        26.43        28.70 
TCGA-02-0070 TCGA-02-0071 TCGA-02-0074 TCGA-02-0075 TCGA-02-0079 TCGA-02-0080 
       25.05         5.49        10.19        20.84        27.25        89.72 
TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 
       22.72        12.62        51.32         8.81        57.76        16.96 
TCGA-02-0099 TCGA-02-0102 TCGA-02-0104 TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 
        3.48        27.02        65.00        11.67        17.65        23.18 
TCGA-02-0113 TCGA-02-0114 TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 
       92.65        99.98        15.65        48.95        16.54        16.93 
TCGA-02-0266 TCGA-02-0269 TCGA-02-0271 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 
       17.72        10.75        14.47        13.87        14.20        15.95 
TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 
       12.23         9.90         7.73        10.62         7.33        15.91 
TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 
       25.71         4.37        25.12        10.59        12.39        14.50 
TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 
       10.55        47.11        11.34         9.27        16.21         3.35 
TCGA-02-2466 TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 
       16.80        12.92        15.32        15.45        20.32         2.70 
TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 
        6.15        20.38        47.61         6.94         3.98        22.72 
TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 
       33.67        12.95        25.35        14.30        26.70        24.23 
TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 
       11.90         0.20        10.29         2.20        11.74         2.33 
TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 
       20.09        17.79        10.09         8.61        19.46        46.59 
TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 
       12.33        13.94        10.45         3.19        10.82         9.44 
TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 
       11.80         3.42        56.91        10.65         5.85        19.66 
TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 
        3.29        13.12         4.47         3.22         4.04        91.00 
TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 
        4.18        88.14        20.25         3.65        69.90        73.84 
TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 
       27.22        44.58        15.42        10.42        38.96         4.67 
TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 
        7.40         5.56         0.39         7.66         8.42         7.63 
TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 
        7.40        11.84         0.53        15.02        24.16         0.72 
TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 
       19.82        13.64        13.32        20.42        48.69        10.82 
TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 
        9.01         0.26        72.36         4.70         9.57         3.16 
TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 
       35.11        12.62         5.75         5.75         9.80         2.10 
TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 
       23.57        14.20        26.40        46.88         7.86         2.70 
TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 
        2.70         0.92        43.46        46.19         5.65         7.17 
TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 
       40.41        16.57        20.78        26.76        23.93         6.84 
TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 
        4.04        26.79        11.84        15.32        13.61        33.90 
TCGA-06-1806 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 
       15.32         1.08        12.49         4.93        17.65        12.56 
TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 
       30.64         5.95        16.64         5.98         4.37         0.43 
TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 
       31.50        11.74         3.55         8.35         4.54         8.81 
TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 
        8.98         8.55         6.71         2.73         3.75         6.15 
TCGA-06-5859 TCGA-06-6388 TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 
        4.57         5.23         7.79         5.39         1.48       120.56 
TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 
        7.36         8.32        12.85         4.77         1.55         4.77 
TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK 
        4.96         4.70         1.87         3.12         2.56         5.39 
TCGA-06-A7TL TCGA-08-0244 TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 
        5.42        22.68        37.84         4.18       115.86         1.74 
TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 
        8.42        25.71        12.16         9.80        29.23        65.33 
TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 
        1.28         8.42        17.95        24.56        31.10        37.58 
TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0389 TCGA-08-0390 
       22.29         3.39        12.23        14.93        15.35        13.97 
TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 
        0.72        12.56         4.27        42.15        11.08        19.59 
TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 
       58.68        19.33        10.75         4.80         7.27        15.98 
TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 
       18.41         7.56        15.35        14.73        12.99        34.92 
TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 
       10.45         7.59        94.78         0.10        38.17        25.97 
TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 
       26.66        12.13         3.65        20.38        28.41        15.06 
TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 
       53.85        43.23         7.63         9.73        14.93        14.86 
TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 TCGA-12-0826 
       91.76        24.79        18.48        10.62        23.51        27.78 
TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 
       38.76         8.94        20.58       127.59         5.82         7.59 
TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 
       33.21        21.73        15.98        12.23        15.85         9.11 
TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 
       14.53         3.98         4.14        15.65        25.68        14.73 
TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 
        6.77        59.77        44.02        26.93        15.22        10.95 
TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 
       12.69        34.92        14.53        14.93         3.22         2.04 
TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 TCGA-14-0787 
       15.12        11.97         0.95         6.21        23.05         2.24 
TCGA-14-0789 TCGA-14-0790 TCGA-14-0812 TCGA-14-0813 TCGA-14-0862 TCGA-14-0865 
       11.24        13.78         3.25         1.35         2.89        16.50 
TCGA-14-0866 TCGA-14-0867 TCGA-14-1034 TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 
       26.33         2.04        15.95        19.30         0.79         1.38 
TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 TCGA-14-1452 
        1.12         3.75        32.05        58.78        23.11         7.10 
TCGA-14-1453 TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 
        1.15        30.18         0.92        40.96         6.67        12.43 
TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 TCGA-14-1823 TCGA-14-1825 TCGA-14-1827 
        0.99         1.97        17.79        17.85         7.63         5.88 
TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-3477 TCGA-14-4157 TCGA-15-0742 
        7.17        17.49         7.96         3.78         3.42        13.78 
TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 
       50.53        19.10        53.19        13.28         3.91        17.59 
TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 
       26.07        16.37         4.31        29.03         4.57        10.29 
TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 
       14.01         9.14        21.24        13.97         6.41        11.77 
TCGA-19-0957 TCGA-19-0960 TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 
       21.90         8.61         0.66        14.27         3.39        10.75 
TCGA-19-1386 TCGA-19-1387 TCGA-19-1388 TCGA-19-1389 TCGA-19-1392 TCGA-19-1786 
        9.07         5.95        12.95         4.64         3.65         7.17 
TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 
       12.66         3.25         0.13         9.67         4.87         1.08 
TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 
        7.53         0.16         4.08        24.23         7.00         7.04 
TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 
        6.64        17.19         8.02        18.90         4.73        12.10 
TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I 
        1.78        22.49        14.07        16.80        14.96        17.79 
TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 
       28.54        10.03        13.87         9.73        31.33         7.13 
TCGA-26-1799 TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 TCGA-26-5139 
        9.37         9.40        14.86         5.49         8.88         1.58 
TCGA-26-6173 TCGA-26-6174 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 
        7.92         2.33        19.33         5.06        16.60         9.86 
TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 
       24.23        40.54        21.30        30.05        14.04        11.51 
TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 
       24.76        10.39        10.39        16.08         7.59         2.86 
TCGA-27-2527 TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 
       14.40        15.78         0.20         2.53         9.21         8.35 
TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 
        7.63         8.48         1.22         1.55         2.83         0.13 
TCGA-28-2502 TCGA-28-2506 TCGA-28-2509 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 
        0.66         6.74         4.77         7.30         5.26        14.93 
TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 
       17.88        14.53        11.77        31.27        23.44        11.01 
TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 
       13.64         5.16        22.68        12.76         5.42        15.39 
TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 TCGA-32-1980 
       21.07         0.49         0.10        15.85        19.50         1.18 
TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 
        4.67        12.69        14.86        16.93        12.23        20.78 
TCGA-32-2495 TCGA-32-2616 TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 
       15.02         7.36         8.84        22.78        25.18        21.14 
TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 
        3.72        12.59        19.86        10.85        19.23         0.85 
TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 
       13.35         8.94         9.53         0.99         4.44        11.84 
TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 
        0.20        15.12        12.46         4.14        14.76         3.45 
TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 TCGA-76-4925 
       20.91         4.34        14.33         8.22         7.50         4.80 
TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-4934 TCGA-76-4935 
        4.54         3.09         3.65         9.17         2.53        10.78 
TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 
       16.70         3.29         2.70        11.38        17.06         8.35 
TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 
       20.98         4.83         5.03         0.23         9.27         7.73 
TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R TCGA-RR-A6KA 
        7.79         1.61        17.72        26.30         5.92         6.28 
TCGA-RR-A6KC 
       20.55 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              3.98               0.10 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             28.93             127.59 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             13.86              11.84 
[1] "4.0 - 28.9 (13.9)"  "0.1 - 127.6 (11.8)"
[1] "hr=" "1.3"
D25V2, continuous
D25V3, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     6   4
  13Q GAIN WILD-TYPE 218 342
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      6    4
  13Q GAIN WILD-TYPE  218  342
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE                6                218
  MALE                  4                342
[1] 2 2
[1] FALSE
D25V4, continuous
                    vv
clus                 GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  13Q GAIN MUTATED                               1                   0
  13Q GAIN WILD-TYPE                            26                  18
                    vv
clus                 UNTREATED PRIMARY (DE NOVO) GBM
  13Q GAIN MUTATED                                 9
  13Q GAIN WILD-TYPE                             516
D25V5, multiclass
                                 clus
vv                                13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                  1                 26
  TREATED PRIMARY GBM                            0                 18
  UNTREATED PRIMARY (DE NOVO) GBM                9                516
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V6, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     4   6
  13Q GAIN WILD-TYPE 378 182
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      4    6
  13Q GAIN WILD-TYPE  378  182
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  NO                 4                378
  YES                6                182
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  13Q GAIN MUTATED       0                         1     9
  13Q GAIN WILD-TYPE    13                        48   476
D25V7, multiclass
                           clus
vv                          13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  ASIAN                                    0                 13
  BLACK OR AFRICAN AMERICAN                1                 48
  WHITE                                    9                476
[1] 3 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
  13Q GAIN MUTATED     0   7
  13Q GAIN WILD-TYPE  12 465
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      0    7
  13Q GAIN WILD-TYPE   12  465
                        clus
vv                       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 12
  NOT HISPANIC OR LATINO                7                465
[1] 2 2
[1] FALSE

Clustering(26) Variable = 14Q GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                  0   1
  14Q GAIN MUTATED     1  21
  14Q GAIN WILD-TYPE 103 444
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                22                547 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                21                444 
$`14Q GAIN MUTATED`
TCGA-02-0059 TCGA-02-0075 TCGA-02-0102 TCGA-06-0151 TCGA-06-0159 TCGA-06-0177 
        9.57        20.84        27.02        46.59         9.44         4.18 
TCGA-06-0195 TCGA-06-0414 TCGA-06-1087 TCGA-06-2569 TCGA-08-0246 TCGA-08-0386 
        7.40        35.11         4.04         0.43         4.18        18.02 
TCGA-08-0510 TCGA-08-0514 TCGA-12-0619 TCGA-12-0776 TCGA-12-3646 TCGA-14-0867 
        4.27        11.08        34.92         9.73        44.02         2.04 
TCGA-16-0846 TCGA-19-2620 TCGA-32-2495 TCGA-32-2632 
        3.91         4.87        15.02         8.84 

$`14Q GAIN WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 
       11.77         4.73        18.35        23.18        10.59        35.41 
TCGA-02-0011 TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 
       20.71        82.59        20.61        87.06        77.65        20.12 
TCGA-02-0024 TCGA-02-0025 TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 
       53.10        42.74        24.59        12.16        90.58         2.83 
TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 
       14.14         3.62        10.72        10.52        18.31         6.87 
TCGA-02-0047 TCGA-02-0048 TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 TCGA-02-0055 
       14.73         3.22        15.09        12.59         6.54         2.50 
TCGA-02-0057 TCGA-02-0058 TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 TCGA-02-0069 
       19.86         8.35         6.02        19.73        26.43        28.70 
TCGA-02-0070 TCGA-02-0071 TCGA-02-0074 TCGA-02-0079 TCGA-02-0080 TCGA-02-0083 
       25.05         5.49        10.19        27.25        89.72        22.72 
TCGA-02-0084 TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 
       12.62        51.32         8.81        57.76        16.96         3.48 
TCGA-02-0104 TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 TCGA-02-0113 TCGA-02-0114 
       65.00        11.67        17.65        23.18        92.65        99.98 
TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 TCGA-02-0266 TCGA-02-0269 
       15.65        48.95        16.54        16.93        17.72        10.75 
TCGA-02-0271 TCGA-02-0281 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 
       14.47         3.98        13.87        14.20        15.95        12.23 
TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 
        9.90         7.73        10.62         7.33        15.91        25.71 
TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 
        4.37        25.12        10.59        12.39        14.50        10.55 
TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 TCGA-02-2466 
       47.11        11.34         9.27        16.21         3.35        16.80 
TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 
       12.92        15.32        15.45        20.32         2.70         6.15 
TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 
       20.38        47.61         6.94         3.98        22.72        33.67 
TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 
       12.95        25.35        14.30        26.70        24.23        11.90 
TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 
        0.20        10.29         2.20        11.74         2.33        20.09 
TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0152 TCGA-06-0154 
       17.79        10.09         8.61        19.46        12.33        13.94 
TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 
       10.45         3.19        10.82        11.80         3.42        56.91 
TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 
       10.65         5.85        19.66         3.29        13.12         4.47 
TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 
        3.22         4.04        91.00        88.14        20.25         3.65 
TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 
       69.90        73.84        27.22        44.58        15.42        10.42 
TCGA-06-0192 TCGA-06-0194 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 
       38.96         4.67         5.56         0.39         7.66         8.42 
TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 
        7.63         7.40        11.84         0.53        15.02        24.16 
TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 
        0.72        19.82        13.64        13.32        20.42        48.69 
TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 
       10.82         9.01         0.26        72.36         4.70         9.57 
TCGA-06-0413 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 
        3.16        12.62         5.75         5.75         9.80         2.10 
TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 
       23.57        14.20        26.40        46.88         7.86         2.70 
TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 
        2.70         0.92        43.46        46.19         5.65         7.17 
TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 
       40.41        16.57        20.78        26.76        23.93         6.84 
TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 
       26.79        11.84        15.32        13.61        33.90        15.32 
TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 
        1.08        12.49         4.93        17.65        12.56        30.64 
TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2570 TCGA-06-5408 
        5.95        16.64         5.98         4.37        31.50        11.74 
TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 
        3.55         8.35         4.54         8.81         8.98         8.55 
TCGA-06-5416 TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 
        6.71         2.73         3.75         6.15         4.57         5.23 
TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 
        7.79         5.39         1.48       120.56         7.36         8.32 
TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 
       12.85         4.77         1.55         4.77         4.96         4.70 
TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK TCGA-06-A7TL TCGA-08-0244 
        1.87         3.12         2.56         5.39         5.42        22.68 
TCGA-08-0245 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 
       37.84       115.86         1.74         8.42        25.71        12.16 
TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 
        9.80        29.23        65.33         1.28         8.42        17.95 
TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 
       24.56        31.10        37.58        22.29         3.39        12.23 
TCGA-08-0380 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0512 
       14.93        15.35        13.97         0.72        12.56        42.15 
TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 
       19.59        58.68        19.33        10.75         4.80         7.27 
TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 
       15.98        18.41         7.56        15.35        14.73        12.99 
TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 
       10.45         7.59        94.78         0.10        38.17        25.97 
TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 
       26.66        12.13         3.65        20.38        28.41        15.06 
TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 
       53.85        43.23         7.63        14.93        14.86        91.76 
TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 TCGA-12-0826 TCGA-12-0827 
       24.79        18.48        10.62        23.51        27.78        38.76 
TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 
        8.94        20.58       127.59         5.82         7.59        33.21 
TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 
       21.73        15.98        12.23        15.85         9.11        14.53 
TCGA-12-1098 TCGA-12-1099 TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 
        3.98         4.14        15.65        25.68        14.73         6.77 
TCGA-12-3644 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 
       59.77        26.93        15.22        10.95        12.69        34.92 
TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 
       14.53        14.93         3.22         2.04        15.12        11.97 
TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 
        0.95         6.21        23.05         2.24        11.24        13.78 
TCGA-14-0812 TCGA-14-0813 TCGA-14-0817 TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 
        3.25         1.35         5.39         2.89        16.50        26.33 
TCGA-14-0871 TCGA-14-1034 TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 TCGA-14-1396 
       28.93        15.95        19.30         0.79         1.38         1.12 
TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 TCGA-14-1452 TCGA-14-1453 
        3.75        32.05        58.78        23.11         7.10         1.15 
TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 TCGA-14-1794 
       30.18         0.92        40.96         6.67        12.43         0.99 
TCGA-14-1795 TCGA-14-1821 TCGA-14-1823 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 
        1.97        17.79        17.85         7.63         5.88         7.17 
TCGA-14-2554 TCGA-14-2555 TCGA-14-3477 TCGA-14-4157 TCGA-15-0742 TCGA-15-1444 
       17.49         7.96         3.78         3.42        13.78        50.53 
TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 
       19.10        53.19        13.28        17.59        26.07        16.37 
TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 
        4.31        29.03         4.57        10.29        14.01         9.14 
TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 
       21.24        13.97         6.41        11.77        21.90         8.61 
TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 
        0.66        14.27         3.39        10.75         9.07         5.95 
TCGA-19-1388 TCGA-19-1389 TCGA-19-1390 TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 
       12.95         4.64        25.38         3.65         7.17        12.66 
TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 
        3.25         0.13         9.67         1.08         7.53         0.16 
TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 
        4.08        24.23         7.00         7.04         6.64        17.19 
TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 
        8.02        18.90         4.73        12.10         1.78        22.49 
TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J4 TCGA-19-A6J5 
       14.07        16.80        14.96        17.79         3.98        28.54 
TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 
       10.03        13.87         9.73        31.33         7.13         9.37 
TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 
        9.40        14.86         5.49         8.88        18.97         1.58 
TCGA-26-6173 TCGA-26-6174 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 
        7.92         2.33        19.33         5.06        16.60         9.86 
TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 
       24.23        40.54        21.30        30.05        14.04        11.51 
TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 
       24.76        10.39        10.39        16.08         7.59         2.86 
TCGA-27-2527 TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 
       14.40        15.78         0.20         2.53         9.21         8.35 
TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 
        7.63         8.48         1.22         1.55         2.83         0.13 
TCGA-28-2502 TCGA-28-2506 TCGA-28-2509 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 
        0.66         6.74         4.77         7.30         5.26        14.93 
TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 
       11.28        17.88        14.53        11.77        31.27        23.44 
TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 
       11.01        13.64         5.16        22.68        12.76         5.42 
TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 
       15.39        21.07         0.49         0.10        15.85        19.50 
TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 TCGA-32-1991 TCGA-32-2491 
        1.18         4.67        12.69        14.86        16.93        12.23 
TCGA-32-2494 TCGA-32-2615 TCGA-32-2616 TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 
       20.78        15.95         7.36        22.78        25.18        21.14 
TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 
        3.72        12.59        19.86        10.85        19.23         0.85 
TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 
       13.35         8.94         9.53         0.99         4.44        11.84 
TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 
        0.20        15.12        12.46         4.14        14.76         3.45 
TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 TCGA-76-4925 
       20.91         4.34        14.33         8.22         7.50         4.80 
TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-4934 TCGA-76-4935 
        4.54         3.09         3.65         9.17         2.53        10.78 
TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 
       16.70         3.29         2.70        11.38        17.06         8.35 
TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 
       20.98         4.83         5.03         0.23         9.27         7.73 
TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R TCGA-RR-A6KA 
        7.79         1.61        17.72        26.30         5.92         6.28 
TCGA-RR-A6KC 
       20.55 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              0.43               0.10 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             46.59             127.59 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             9.505             12.100 
[1] "0.4 - 46.6 (9.5)"   "0.1 - 127.6 (12.1)"
[1] "hr=" "1.3"
D26V2, continuous
D26V3, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     7  15
  14Q GAIN WILD-TYPE 217 331
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      7   15
  14Q GAIN WILD-TYPE  217  331
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE                7                217
  MALE                 15                331
[1] 2 2
[1] FALSE
D26V4, continuous
                    vv
clus                 GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  14Q GAIN MUTATED                               2                   2
  14Q GAIN WILD-TYPE                            25                  16
                    vv
clus                 UNTREATED PRIMARY (DE NOVO) GBM
  14Q GAIN MUTATED                                18
  14Q GAIN WILD-TYPE                             507
D26V5, multiclass
                                 clus
vv                                14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                  2                 25
  TREATED PRIMARY GBM                            2                 16
  UNTREATED PRIMARY (DE NOVO) GBM               18                507
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V6, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    14   8
  14Q GAIN WILD-TYPE 368 180
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     14    8
  14Q GAIN WILD-TYPE  368  180
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  NO                14                368
  YES                8                180
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  14Q GAIN MUTATED       0                         1    21
  14Q GAIN WILD-TYPE    13                        48   464
D26V7, multiclass
                           clus
vv                          14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  ASIAN                                    0                 13
  BLACK OR AFRICAN AMERICAN                1                 48
  WHITE                                   21                464
[1] 3 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
  14Q GAIN MUTATED     0  21
  14Q GAIN WILD-TYPE  12 451
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      0   21
  14Q GAIN WILD-TYPE   12  451
                        clus
vv                       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 12
  NOT HISPANIC OR LATINO               21                451
[1] 2 2
[1] FALSE

Clustering(27) Variable = 15Q GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                  0   1
  15Q GAIN MUTATED     2  22
  15Q GAIN WILD-TYPE 102 443
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                24                545 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                22                443 
$`15Q GAIN MUTATED`
TCGA-02-0055 TCGA-02-0075 TCGA-02-0106 TCGA-02-0456 TCGA-02-2466 TCGA-06-0130 
        2.50        20.84        11.67         3.35        16.80        12.95 
TCGA-06-0151 TCGA-06-0166 TCGA-06-0177 TCGA-06-0414 TCGA-06-1087 TCGA-08-0392 
       46.59         5.85         4.18        35.11         4.04         0.72 
TCGA-12-0818 TCGA-12-0826 TCGA-12-3653 TCGA-14-0812 TCGA-14-1823 TCGA-14-3477 
       91.76        27.78        14.53         3.25        17.85         3.78 
TCGA-28-2509 TCGA-28-5218 TCGA-32-2615 TCGA-41-2575 TCGA-41-4097 TCGA-76-4934 
        4.77         5.16        15.95         9.53         0.20         2.53 

$`15Q GAIN WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 
       11.77         4.73        18.35        23.18        10.59        35.41 
TCGA-02-0011 TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 
       20.71        82.59        20.61        87.06        77.65        20.12 
TCGA-02-0024 TCGA-02-0025 TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 
       53.10        42.74        24.59        12.16        90.58         2.83 
TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 
       14.14         3.62        10.72        10.52        18.31         6.87 
TCGA-02-0047 TCGA-02-0048 TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 TCGA-02-0057 
       14.73         3.22        15.09        12.59         6.54        19.86 
TCGA-02-0058 TCGA-02-0059 TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 TCGA-02-0069 
        8.35         9.57         6.02        19.73        26.43        28.70 
TCGA-02-0070 TCGA-02-0071 TCGA-02-0074 TCGA-02-0079 TCGA-02-0080 TCGA-02-0083 
       25.05         5.49        10.19        27.25        89.72        22.72 
TCGA-02-0084 TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 
       12.62        51.32         8.81        57.76        16.96         3.48 
TCGA-02-0102 TCGA-02-0104 TCGA-02-0107 TCGA-02-0111 TCGA-02-0113 TCGA-02-0114 
       27.02        65.00        17.65        23.18        92.65        99.98 
TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 TCGA-02-0266 TCGA-02-0269 
       15.65        48.95        16.54        16.93        17.72        10.75 
TCGA-02-0271 TCGA-02-0281 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 
       14.47         3.98        13.87        14.20        15.95        12.23 
TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 
        9.90         7.73        10.62         7.33        15.91        25.71 
TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 
        4.37        25.12        10.59        12.39        14.50        10.55 
TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 TCGA-02-2470 TCGA-02-2483 
       47.11        11.34         9.27        16.21        12.92        15.32 
TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 
       15.45        20.32         2.70         6.15        20.38        47.61 
TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0132 TCGA-06-0133 
        6.94         3.98        22.72        33.67        25.35        14.30 
TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 
       26.70        24.23        11.90         0.20        10.29         2.20 
TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 
       11.74         2.33        20.09        17.79        10.09         8.61 
TCGA-06-0150 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 
       19.46        12.33        13.94        10.45         3.19        10.82 
TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0168 
        9.44        11.80         3.42        56.91        10.65        19.66 
TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 
        3.29        13.12         4.47         3.22         4.04        91.00 
TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 
       88.14        20.25         3.65        69.90        73.84        27.22 
TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 
       44.58        15.42        10.42        38.96         4.67         7.40 
TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 
        5.56         0.39         7.66         8.42         7.63         7.40 
TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 
       11.84         0.53        15.02        24.16         0.72        19.82 
TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 
       13.64        13.32        20.42        48.69        10.82         9.01 
TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0644 
        0.26        72.36         4.70         9.57         3.16        12.62 
TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 
        5.75         5.75         9.80         2.10        23.57        14.20 
TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 
       26.40        46.88         7.86         2.70         2.70         0.92 
TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 
       43.46        46.19         5.65         7.17        40.41        16.57 
TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1800 TCGA-06-1801 
       20.78        26.76        23.93         6.84        26.79        11.84 
TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 TCGA-06-2557 TCGA-06-2558 
       15.32        13.61        33.90        15.32         1.08        12.49 
TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 
        4.93        17.65        12.56        30.64         5.95        16.64 
TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 
        5.98         4.37         0.43        31.50        11.74         3.55 
TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 
        8.35         4.54         8.81         8.98         8.55         6.71 
TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 TCGA-06-6389 
        2.73         3.75         6.15         4.57         5.23         7.79 
TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 
        5.39         1.48       120.56         7.36         8.32        12.85 
TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A5U1 
        4.77         1.55         4.77         4.96         4.70         1.87 
TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK TCGA-06-A7TL TCGA-08-0244 TCGA-08-0245 
        3.12         2.56         5.39         5.42        22.68        37.84 
TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 
        4.18       115.86         1.74         8.42        25.71        12.16 
TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 
        9.80        29.23        65.33         1.28         8.42        17.95 
TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 
       24.56        31.10        37.58        22.29         3.39        12.23 
TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0509 TCGA-08-0510 
       14.93        18.02        15.35        13.97        12.56         4.27 
TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 
       42.15        11.08        19.59        58.68        19.33        10.75 
TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 
        4.80         7.27        15.98        18.41         7.56        15.35 
TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 
       14.73        12.99        34.92        10.45         7.59        94.78 
TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 
        0.10        38.17        25.97        26.66        12.13         3.65 
TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 
       20.38        28.41        15.06        53.85        43.23         7.63 
TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 
        9.73        14.93        14.86        24.79        18.48        10.62 
TCGA-12-0822 TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 
       23.51        38.76         8.94        20.58       127.59         5.82 
TCGA-12-1090 TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 
        7.59        33.21        21.73        15.98        12.23        15.85 
TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 TCGA-12-1598 TCGA-12-1599 
        9.11        14.53         3.98         4.14        15.65        25.68 
TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 
       14.73         6.77        59.77        44.02        26.93        15.22 
TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 
       10.95        12.69        34.92        14.93         3.22         2.04 
TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 TCGA-14-0787 
       15.12        11.97         0.95         6.21        23.05         2.24 
TCGA-14-0789 TCGA-14-0790 TCGA-14-0813 TCGA-14-0817 TCGA-14-0862 TCGA-14-0865 
       11.24        13.78         1.35         5.39         2.89        16.50 
TCGA-14-0866 TCGA-14-0867 TCGA-14-0871 TCGA-14-1034 TCGA-14-1037 TCGA-14-1043 
       26.33         2.04        28.93        15.95        19.30         0.79 
TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 
        1.38         1.12         3.75        32.05        58.78        23.11 
TCGA-14-1452 TCGA-14-1453 TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 
        7.10         1.15        30.18         0.92        40.96         6.67 
TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 TCGA-14-1825 TCGA-14-1827 
       12.43         0.99         1.97        17.79         7.63         5.88 
TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-4157 TCGA-15-0742 TCGA-15-1444 
        7.17        17.49         7.96         3.42        13.78        50.53 
TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 
       19.10        53.19        13.28         3.91        17.59        26.07 
TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 
       16.37         4.31        29.03         4.57        10.29        14.01 
TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 
        9.14        21.24        13.97         6.41        11.77        21.90 
TCGA-19-0960 TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 
        8.61         0.66        14.27         3.39        10.75         9.07 
TCGA-19-1387 TCGA-19-1388 TCGA-19-1389 TCGA-19-1390 TCGA-19-1392 TCGA-19-1786 
        5.95        12.95         4.64        25.38         3.65         7.17 
TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 
       12.66         3.25         0.13         9.67         4.87         1.08 
TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 
        7.53         0.16         4.08        24.23         7.00         7.04 
TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 
        6.64        17.19         8.02        18.90         4.73        12.10 
TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I 
        1.78        22.49        14.07        16.80        14.96        17.79 
TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 
        3.98        28.54        10.03        13.87         9.73        31.33 
TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 
        7.13         9.37         9.40        14.86         5.49         8.88 
TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-26-A7UX TCGA-27-1830 
       18.97         1.58         7.92         2.33        19.33         5.06 
TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 
       16.60         9.86        24.23        40.54        21.30        30.05 
TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 
       14.04        11.51        24.76        10.39        10.39        16.08 
TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 
        7.59         2.86        14.40        15.78         0.20         2.53 
TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 TCGA-28-1755 
        9.21         8.35         7.63         8.48         1.22         1.55 
TCGA-28-1756 TCGA-28-1757 TCGA-28-2502 TCGA-28-2506 TCGA-28-2513 TCGA-28-2514 
        2.83         0.13         0.66         6.74         7.30         5.26 
TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 
       14.93        11.28        17.88        14.53        11.77        31.27 
TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 
       23.44        11.01        13.64        22.68        12.76         5.42 
TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 
       15.39        21.07         0.49         0.10        15.85        19.50 
TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 TCGA-32-1991 TCGA-32-2491 
        1.18         4.67        12.69        14.86        16.93        12.23 
TCGA-32-2494 TCGA-32-2495 TCGA-32-2616 TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 
       20.78        15.02         7.36         8.84        22.78        25.18 
TCGA-32-4208 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 
       21.14         3.72        12.59        19.86        10.85        19.23 
TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 
        0.85        13.35         8.94         0.99         4.44        11.84 
TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 
       15.12        12.46         4.14        14.76         3.45        20.91 
TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 
        4.34        14.33         8.22         7.50         4.80         4.54 
TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 
        3.09         3.65         9.17        10.78        16.70         3.29 
TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 
        2.70        11.38        17.06         8.35        20.98         4.83 
TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 
        5.03         0.23         9.27         7.73         7.79         1.61 
TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC 
       17.72        26.30         5.92         6.28        20.55 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
               0.2                0.1 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             91.76             127.59 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              7.69              11.97 
[1] "0.2 - 91.8 (7.7)"   "0.1 - 127.6 (12.0)"
[1] "hr=" "1.3"
D27V2, continuous
D27V3, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    11  13
  15Q GAIN WILD-TYPE 213 333
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     11   13
  15Q GAIN WILD-TYPE  213  333
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE               11                213
  MALE                 13                333
[1] 2 2
[1] FALSE
D27V4, continuous
                    vv
clus                 GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  15Q GAIN MUTATED                               1                   1
  15Q GAIN WILD-TYPE                            26                  17
                    vv
clus                 UNTREATED PRIMARY (DE NOVO) GBM
  15Q GAIN MUTATED                                22
  15Q GAIN WILD-TYPE                             503
D27V5, multiclass
                                 clus
vv                                15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                  1                 26
  TREATED PRIMARY GBM                            1                 17
  UNTREATED PRIMARY (DE NOVO) GBM               22                503
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V6, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    13  11
  15Q GAIN WILD-TYPE 369 177
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     13   11
  15Q GAIN WILD-TYPE  369  177
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  NO                13                369
  YES               11                177
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  15Q GAIN MUTATED       0                         1    23
  15Q GAIN WILD-TYPE    13                        48   462
D27V7, multiclass
                           clus
vv                          15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  ASIAN                                    0                 13
  BLACK OR AFRICAN AMERICAN                1                 48
  WHITE                                   23                462
[1] 3 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
  15Q GAIN MUTATED     0  20
  15Q GAIN WILD-TYPE  12 452
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      0   20
  15Q GAIN WILD-TYPE   12  452
                        clus
vv                       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 12
  NOT HISPANIC OR LATINO               20                452
[1] 2 2
[1] FALSE

Clustering(28) Variable = 16P GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                  0   1
  16P GAIN MUTATED     7  31
  16P GAIN WILD-TYPE  97 434
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                38                531 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                31                434 
$`16P GAIN MUTATED`
TCGA-02-0051 TCGA-02-0069 TCGA-02-0075 TCGA-02-0079 TCGA-02-0106 TCGA-02-0113 
       15.09        28.70        20.84        27.25        11.67        92.65 
TCGA-06-0128 TCGA-06-0166 TCGA-06-0188 TCGA-06-0197 TCGA-06-0237 TCGA-06-0409 
       22.72         5.85        44.58         5.56        13.64        72.36 
TCGA-06-1086 TCGA-06-2558 TCGA-06-2567 TCGA-08-0245 TCGA-08-0386 TCGA-08-0510 
        6.84        12.49         4.37        37.84        18.02         4.27 
TCGA-08-0516 TCGA-12-0692 TCGA-12-0821 TCGA-12-0827 TCGA-12-1088 TCGA-12-1598 
       19.59         3.65        10.62        38.76       127.59        15.65 
TCGA-12-1602 TCGA-12-3646 TCGA-14-1454 TCGA-14-3477 TCGA-15-1447 TCGA-15-1449 
        6.77        44.02        30.18         3.78        53.19        13.28 
TCGA-16-0850 TCGA-19-1388 TCGA-19-A6J4 TCGA-27-1832 TCGA-28-2506 TCGA-28-2509 
       16.37        12.95         3.98         9.86         6.74         4.77 
TCGA-28-5207 TCGA-41-2573 
       11.28         8.94 

$`16P GAIN WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 
       11.77         4.73        18.35        23.18        10.59        35.41 
TCGA-02-0011 TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 
       20.71        82.59        20.61        87.06        77.65        20.12 
TCGA-02-0024 TCGA-02-0025 TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 
       53.10        42.74        24.59        12.16        90.58         2.83 
TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 
       14.14         3.62        10.72        10.52        18.31         6.87 
TCGA-02-0047 TCGA-02-0048 TCGA-02-0052 TCGA-02-0054 TCGA-02-0055 TCGA-02-0057 
       14.73         3.22        12.59         6.54         2.50        19.86 
TCGA-02-0058 TCGA-02-0059 TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 TCGA-02-0070 
        8.35         9.57         6.02        19.73        26.43        25.05 
TCGA-02-0071 TCGA-02-0074 TCGA-02-0080 TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 
        5.49        10.19        89.72        22.72        12.62        51.32 
TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 TCGA-02-0104 
        8.81        57.76        16.96         3.48        27.02        65.00 
TCGA-02-0107 TCGA-02-0111 TCGA-02-0114 TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 
       17.65        23.18        99.98        15.65        48.95        16.54 
TCGA-02-0260 TCGA-02-0266 TCGA-02-0269 TCGA-02-0271 TCGA-02-0281 TCGA-02-0285 
       16.93        17.72        10.75        14.47         3.98        13.87 
TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 
       14.20        15.95        12.23         9.90         7.73        10.62 
TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 
        7.33        15.91        25.71         4.37        25.12        10.59 
TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 
       12.39        14.50        10.55        47.11        11.34         9.27 
TCGA-02-0451 TCGA-02-0456 TCGA-02-2466 TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 
       16.21         3.35        16.80        12.92        15.32        15.45 
TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 
       20.32         2.70         6.15        20.38        47.61         6.94 
TCGA-06-0127 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 
        3.98        33.67        12.95        25.35        14.30        26.70 
TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 
       24.23        11.90         0.20        10.29         2.20        11.74 
TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 
        2.33        20.09        17.79        10.09         8.61        19.46 
TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 
       46.59        12.33        13.94        10.45         3.19        10.82 
TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0168 
        9.44        11.80         3.42        56.91        10.65        19.66 
TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 
        3.29        13.12         4.47         3.22         4.04        91.00 
TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 
        4.18        88.14        20.25         3.65        69.90        73.84 
TCGA-06-0187 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 
       27.22        15.42        10.42        38.96         4.67         7.40 
TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 
        0.39         7.66         8.42         7.63         7.40        11.84 
TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0238 
        0.53        15.02        24.16         0.72        19.82        13.32 
TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0410 
       20.42        48.69        10.82         9.01         0.26         4.70 
TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 
        9.57         3.16        35.11        12.62         5.75         5.75 
TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 
        9.80         2.10        23.57        14.20        26.40        46.88 
TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 
        7.86         2.70         2.70         0.92        43.46        46.19 
TCGA-06-0877 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 
        5.65         7.17        40.41        16.57        20.78        26.76 
TCGA-06-1084 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 
       23.93         4.04        26.79        11.84        15.32        13.61 
TCGA-06-1805 TCGA-06-1806 TCGA-06-2557 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 
       33.90        15.32         1.08         4.93        17.65        12.56 
TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2569 TCGA-06-2570 
       30.64         5.95        16.64         5.98         0.43        31.50 
TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 
       11.74         3.55         8.35         4.54         8.81         8.98 
TCGA-06-5415 TCGA-06-5416 TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 TCGA-06-5859 
        8.55         6.71         2.73         3.75         6.15         4.57 
TCGA-06-6388 TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 
        5.23         7.79         5.39         1.48       120.56         7.36 
TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 
        8.32        12.85         4.77         1.55         4.77         4.96 
TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK TCGA-06-A7TL 
        4.70         1.87         3.12         2.56         5.39         5.42 
TCGA-08-0244 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 
       22.68         4.18       115.86         1.74         8.42        25.71 
TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 
       12.16         9.80        29.23        65.33         1.28         8.42 
TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 
       17.95        24.56        31.10        37.58        22.29         3.39 
TCGA-08-0375 TCGA-08-0380 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 
       12.23        14.93        15.35        13.97         0.72        12.56 
TCGA-08-0512 TCGA-08-0514 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 
       42.15        11.08        58.68        19.33        10.75         4.80 
TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 
        7.27        15.98        18.41         7.56        15.35        14.73 
TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 
       12.99        34.92        10.45         7.59        94.78         0.10 
TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0703 TCGA-12-0707 
       38.17        25.97        26.66        12.13        20.38        28.41 
TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 
       15.06        53.85        43.23         7.63         9.73        14.93 
TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0822 TCGA-12-0826 
       14.86        91.76        24.79        18.48        23.51        27.78 
TCGA-12-0828 TCGA-12-0829 TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 TCGA-12-1092 
        8.94        20.58         5.82         7.59        33.21        21.73 
TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 
       15.98        12.23        15.85         9.11        14.53         3.98 
TCGA-12-1099 TCGA-12-1599 TCGA-12-1600 TCGA-12-3644 TCGA-12-3648 TCGA-12-3649 
        4.14        25.68        14.73        59.77        26.93        15.22 
TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 
       10.95        12.69        34.92        14.53        14.93         3.22 
TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 
        2.04        15.12        11.97         0.95         6.21        23.05 
TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 TCGA-14-0812 TCGA-14-0813 TCGA-14-0817 
        2.24        11.24        13.78         3.25         1.35         5.39 
TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 TCGA-14-0867 TCGA-14-0871 TCGA-14-1034 
        2.89        16.50        26.33         2.04        28.93        15.95 
TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 
       19.30         0.79         1.38         1.12         3.75        32.05 
TCGA-14-1450 TCGA-14-1451 TCGA-14-1452 TCGA-14-1453 TCGA-14-1455 TCGA-14-1456 
       58.78        23.11         7.10         1.15         0.92        40.96 
TCGA-14-1458 TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 TCGA-14-1823 
        6.67        12.43         0.99         1.97        17.79        17.85 
TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-4157 
        7.63         5.88         7.17        17.49         7.96         3.42 
TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 
       13.78        50.53        19.10         3.91        17.59        26.07 
TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 
        4.31        29.03         4.57        10.29        14.01         9.14 
TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 
       21.24        13.97         6.41        11.77        21.90         8.61 
TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 
        0.66        14.27         3.39        10.75         9.07         5.95 
TCGA-19-1389 TCGA-19-1390 TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 
        4.64        25.38         3.65         7.17        12.66         3.25 
TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 
        0.13         9.67         4.87         1.08         7.53         0.16 
TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 
        4.08        24.23         7.00         7.04         6.64        17.19 
TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 
        8.02        18.90         4.73        12.10         1.78        22.49 
TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J5 TCGA-26-1438 
       14.07        16.80        14.96        17.79        28.54        10.03 
TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 
       13.87         9.73        31.33         7.13         9.37         9.40 
TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 
       14.86         5.49         8.88        18.97         1.58         7.92 
TCGA-26-6174 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 TCGA-27-1833 TCGA-27-1834 
        2.33        19.33         5.06        16.60        24.23        40.54 
TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 
       21.30        30.05        14.04        11.51        24.76        10.39 
TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 
       10.39        16.08         7.59         2.86        14.40        15.78 
TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 TCGA-28-1752 
        0.20         2.53         9.21         8.35         7.63         8.48 
TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 TCGA-28-2502 TCGA-28-2513 
        1.22         1.55         2.83         0.13         0.66         7.30 
TCGA-28-2514 TCGA-28-5204 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 
        5.26        14.93        17.88        14.53        11.77        31.27 
TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 
       23.44        11.01        13.64         5.16        22.68        12.76 
TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 TCGA-32-1978 
        5.42        15.39        21.07         0.49         0.10        15.85 
TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 TCGA-32-1991 
       19.50         1.18         4.67        12.69        14.86        16.93 
TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 TCGA-32-2616 TCGA-32-2632 
       12.23        20.78        15.02        15.95         7.36         8.84 
TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 
       22.78        25.18        21.14         3.72        12.59        19.86 
TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2575 TCGA-41-3392 
       10.85        19.23         0.85        13.35         9.53         0.99 
TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9S 
        4.44        11.84         0.20        15.12        12.46         4.14 
TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 
       14.76         3.45        20.91         4.34        14.33         8.22 
TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 
        7.50         4.80         4.54         3.09         3.65         9.17 
TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 
        2.53        10.78        16.70         3.29         2.70        11.38 
TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 
       17.06         8.35        20.98         4.83         5.03         0.23 
TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
        9.27         7.73         7.79         1.61        17.72        26.30 
TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC 
        5.92         6.28        20.55 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              3.65               0.10 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
            127.59             120.56 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             13.46              11.80 
[1] "3.6 - 127.6 (13.5)" "0.1 - 120.6 (11.8)"
[1] "hr=" "1.5"
D28V2, continuous
D28V3, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    18  20
  16P GAIN WILD-TYPE 206 326
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     18   20
  16P GAIN WILD-TYPE  206  326
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE               18                206
  MALE                 20                326
[1] 2 2
[1] FALSE
D28V4, continuous
                    vv
clus                 GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  16P GAIN MUTATED                               1                   1
  16P GAIN WILD-TYPE                            26                  17
                    vv
clus                 UNTREATED PRIMARY (DE NOVO) GBM
  16P GAIN MUTATED                                36
  16P GAIN WILD-TYPE                             489
D28V5, multiclass
                                 clus
vv                                16P GAIN MUTATED 16P GAIN WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                  1                 26
  TREATED PRIMARY GBM                            1                 17
  UNTREATED PRIMARY (DE NOVO) GBM               36                489
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V6, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    31   7
  16P GAIN WILD-TYPE 351 181
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     31    7
  16P GAIN WILD-TYPE  351  181
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  NO                31                351
  YES                7                181
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16P GAIN MUTATED       1                         5    32
  16P GAIN WILD-TYPE    12                        44   453
D28V7, multiclass
                           clus
vv                          16P GAIN MUTATED 16P GAIN WILD-TYPE
  ASIAN                                    1                 12
  BLACK OR AFRICAN AMERICAN                5                 44
  WHITE                                   32                453
[1] 3 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
  16P GAIN MUTATED     0  34
  16P GAIN WILD-TYPE  12 438
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      0   34
  16P GAIN WILD-TYPE   12  438
                        clus
vv                       16P GAIN MUTATED 16P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 12
  NOT HISPANIC OR LATINO               34                438
[1] 2 2
[1] FALSE

Clustering(29) Variable = 16Q GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                  0   1
  16Q GAIN MUTATED     7  30
  16Q GAIN WILD-TYPE  97 435
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                37                532 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                30                435 
$`16Q GAIN MUTATED`
TCGA-02-0051 TCGA-02-0069 TCGA-02-0075 TCGA-02-0079 TCGA-02-0106 TCGA-02-0113 
       15.09        28.70        20.84        27.25        11.67        92.65 
TCGA-06-0128 TCGA-06-0166 TCGA-06-0188 TCGA-06-0197 TCGA-06-0237 TCGA-06-0409 
       22.72         5.85        44.58         5.56        13.64        72.36 
TCGA-06-0410 TCGA-06-1086 TCGA-06-2558 TCGA-06-2567 TCGA-08-0245 TCGA-08-0386 
        4.70         6.84        12.49         4.37        37.84        18.02 
TCGA-08-0510 TCGA-08-0516 TCGA-12-0821 TCGA-12-0827 TCGA-12-1598 TCGA-12-3646 
        4.27        19.59        10.62        38.76        15.65        44.02 
TCGA-14-1454 TCGA-14-1821 TCGA-14-3477 TCGA-15-1447 TCGA-15-1449 TCGA-16-0850 
       30.18        17.79         3.78        53.19        13.28        16.37 
TCGA-19-1388 TCGA-19-2620 TCGA-19-A6J4 TCGA-28-2506 TCGA-28-2509 TCGA-28-5207 
       12.95         4.87         3.98         6.74         4.77        11.28 
TCGA-41-2573 
        8.94 

$`16Q GAIN WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 
       11.77         4.73        18.35        23.18        10.59        35.41 
TCGA-02-0011 TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 
       20.71        82.59        20.61        87.06        77.65        20.12 
TCGA-02-0024 TCGA-02-0025 TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 
       53.10        42.74        24.59        12.16        90.58         2.83 
TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 
       14.14         3.62        10.72        10.52        18.31         6.87 
TCGA-02-0047 TCGA-02-0048 TCGA-02-0052 TCGA-02-0054 TCGA-02-0055 TCGA-02-0057 
       14.73         3.22        12.59         6.54         2.50        19.86 
TCGA-02-0058 TCGA-02-0059 TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 TCGA-02-0070 
        8.35         9.57         6.02        19.73        26.43        25.05 
TCGA-02-0071 TCGA-02-0074 TCGA-02-0080 TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 
        5.49        10.19        89.72        22.72        12.62        51.32 
TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 TCGA-02-0104 
        8.81        57.76        16.96         3.48        27.02        65.00 
TCGA-02-0107 TCGA-02-0111 TCGA-02-0114 TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 
       17.65        23.18        99.98        15.65        48.95        16.54 
TCGA-02-0260 TCGA-02-0266 TCGA-02-0269 TCGA-02-0271 TCGA-02-0281 TCGA-02-0285 
       16.93        17.72        10.75        14.47         3.98        13.87 
TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 
       14.20        15.95        12.23         9.90         7.73        10.62 
TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 
        7.33        15.91        25.71         4.37        25.12        10.59 
TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 
       12.39        14.50        10.55        47.11        11.34         9.27 
TCGA-02-0451 TCGA-02-0456 TCGA-02-2466 TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 
       16.21         3.35        16.80        12.92        15.32        15.45 
TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 
       20.32         2.70         6.15        20.38        47.61         6.94 
TCGA-06-0127 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 
        3.98        33.67        12.95        25.35        14.30        26.70 
TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 
       24.23        11.90         0.20        10.29         2.20        11.74 
TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 
        2.33        20.09        17.79        10.09         8.61        19.46 
TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 
       46.59        12.33        13.94        10.45         3.19        10.82 
TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0168 
        9.44        11.80         3.42        56.91        10.65        19.66 
TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 
        3.29        13.12         4.47         3.22         4.04        91.00 
TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 
        4.18        88.14        20.25         3.65        69.90        73.84 
TCGA-06-0187 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 
       27.22        15.42        10.42        38.96         4.67         7.40 
TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 
        0.39         7.66         8.42         7.63         7.40        11.84 
TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0238 
        0.53        15.02        24.16         0.72        19.82        13.32 
TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0412 
       20.42        48.69        10.82         9.01         0.26         9.57 
TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 
        3.16        35.11        12.62         5.75         5.75         9.80 
TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 
        2.10        23.57        14.20        26.40        46.88         7.86 
TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 
        2.70         2.70         0.92        43.46        46.19         5.65 
TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 
        7.17        40.41        16.57        20.78        26.76        23.93 
TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 
        4.04        26.79        11.84        15.32        13.61        33.90 
TCGA-06-1806 TCGA-06-2557 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 
       15.32         1.08         4.93        17.65        12.56        30.64 
TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2569 TCGA-06-2570 TCGA-06-5408 
        5.95        16.64         5.98         0.43        31.50        11.74 
TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 
        3.55         8.35         4.54         8.81         8.98         8.55 
TCGA-06-5416 TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 
        6.71         2.73         3.75         6.15         4.57         5.23 
TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 
        7.79         5.39         1.48       120.56         7.36         8.32 
TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 
       12.85         4.77         1.55         4.77         4.96         4.70 
TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK TCGA-06-A7TL TCGA-08-0244 
        1.87         3.12         2.56         5.39         5.42        22.68 
TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 
        4.18       115.86         1.74         8.42        25.71        12.16 
TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 
        9.80        29.23        65.33         1.28         8.42        17.95 
TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 
       24.56        31.10        37.58        22.29         3.39        12.23 
TCGA-08-0380 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0512 
       14.93        15.35        13.97         0.72        12.56        42.15 
TCGA-08-0514 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 
       11.08        58.68        19.33        10.75         4.80         7.27 
TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 
       15.98        18.41         7.56        15.35        14.73        12.99 
TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 
       34.92        10.45         7.59        94.78         0.10        38.17 
TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 
       25.97        26.66        12.13         3.65        20.38        28.41 
TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 
       15.06        53.85        43.23         7.63         9.73        14.93 
TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0822 TCGA-12-0826 
       14.86        91.76        24.79        18.48        23.51        27.78 
TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 
        8.94        20.58       127.59         5.82         7.59        33.21 
TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 
       21.73        15.98        12.23        15.85         9.11        14.53 
TCGA-12-1098 TCGA-12-1099 TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 
        3.98         4.14        25.68        14.73         6.77        59.77 
TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 
       26.93        15.22        10.95        12.69        34.92        14.53 
TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 
       14.93         3.22         2.04        15.12        11.97         0.95 
TCGA-14-0783 TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 TCGA-14-0812 
        6.21        23.05         2.24        11.24        13.78         3.25 
TCGA-14-0813 TCGA-14-0817 TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 TCGA-14-0867 
        1.35         5.39         2.89        16.50        26.33         2.04 
TCGA-14-0871 TCGA-14-1034 TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 TCGA-14-1396 
       28.93        15.95        19.30         0.79         1.38         1.12 
TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 TCGA-14-1452 TCGA-14-1453 
        3.75        32.05        58.78        23.11         7.10         1.15 
TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 
        0.92        40.96         6.67        12.43         0.99         1.97 
TCGA-14-1823 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 
       17.85         7.63         5.88         7.17        17.49         7.96 
TCGA-14-4157 TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-16-0846 TCGA-16-0848 
        3.42        13.78        50.53        19.10         3.91        17.59 
TCGA-16-0849 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 
       26.07         4.31        29.03         4.57        10.29        14.01 
TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 
        9.14        21.24        13.97         6.41        11.77        21.90 
TCGA-19-0960 TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 
        8.61         0.66        14.27         3.39        10.75         9.07 
TCGA-19-1387 TCGA-19-1389 TCGA-19-1390 TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 
        5.95         4.64        25.38         3.65         7.17        12.66 
TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 
        3.25         0.13         9.67         1.08         7.53         0.16 
TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 
        4.08        24.23         7.00         7.04         6.64        17.19 
TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 
        8.02        18.90         4.73        12.10         1.78        22.49 
TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J5 TCGA-26-1438 
       14.07        16.80        14.96        17.79        28.54        10.03 
TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 
       13.87         9.73        31.33         7.13         9.37         9.40 
TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 
       14.86         5.49         8.88        18.97         1.58         7.92 
TCGA-26-6174 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 
        2.33        19.33         5.06        16.60         9.86        24.23 
TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 
       40.54        21.30        30.05        14.04        11.51        24.76 
TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 
       10.39        10.39        16.08         7.59         2.86        14.40 
TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 
       15.78         0.20         2.53         9.21         8.35         7.63 
TCGA-28-1752 TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 TCGA-28-2502 
        8.48         1.22         1.55         2.83         0.13         0.66 
TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 
        7.30         5.26        14.93        17.88        14.53        11.77 
TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 
       31.27        23.44        11.01        13.64         5.16        22.68 
TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 
       12.76         5.42        15.39        21.07         0.49         0.10 
TCGA-32-1978 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 
       15.85        19.50         1.18         4.67        12.69        14.86 
TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 TCGA-32-2616 
       16.93        12.23        20.78        15.02        15.95         7.36 
TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4210 TCGA-32-4211 
        8.84        22.78        25.18        21.14         3.72        12.59 
TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2575 
       19.86        10.85        19.23         0.85        13.35         9.53 
TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 
        0.99         4.44        11.84         0.20        15.12        12.46 
TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 
        4.14        14.76         3.45        20.91         4.34        14.33 
TCGA-74-6581 TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 
        8.22         7.50         4.80         4.54         3.09         3.65 
TCGA-76-4931 TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 
        9.17         2.53        10.78        16.70         3.29         2.70 
TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 
       11.38        17.06         8.35        20.98         4.83         5.03 
TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 
        0.23         9.27         7.73         7.79         1.61        17.72 
TCGA-87-5896 TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC 
       26.30         5.92         6.28        20.55 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              3.78               0.10 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             92.65             127.59 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
            13.640             11.785 
[1] "3.8 - 92.7 (13.6)"  "0.1 - 127.6 (11.8)"
[1] "hr=" "1.3"
D29V2, continuous
D29V3, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    16  21
  16Q GAIN WILD-TYPE 208 325
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     16   21
  16Q GAIN WILD-TYPE  208  325
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE               16                208
  MALE                 21                325
[1] 2 2
[1] FALSE
D29V4, continuous
                    vv
clus                 GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  16Q GAIN MUTATED                               1                   1
  16Q GAIN WILD-TYPE                            26                  17
                    vv
clus                 UNTREATED PRIMARY (DE NOVO) GBM
  16Q GAIN MUTATED                                35
  16Q GAIN WILD-TYPE                             490
D29V5, multiclass
                                 clus
vv                                16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                  1                 26
  TREATED PRIMARY GBM                            1                 17
  UNTREATED PRIMARY (DE NOVO) GBM               35                490
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V6, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    30   7
  16Q GAIN WILD-TYPE 352 181
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     30    7
  16Q GAIN WILD-TYPE  352  181
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  NO                30                352
  YES                7                181
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16Q GAIN MUTATED       1                         5    31
  16Q GAIN WILD-TYPE    12                        44   454
D29V7, multiclass
                           clus
vv                          16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  ASIAN                                    1                 12
  BLACK OR AFRICAN AMERICAN                5                 44
  WHITE                                   31                454
[1] 3 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
  16Q GAIN MUTATED     0  32
  16Q GAIN WILD-TYPE  12 440
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      0   32
  16Q GAIN WILD-TYPE   12  440
                        clus
vv                       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 12
  NOT HISPANIC OR LATINO               32                440
[1] 2 2
[1] FALSE

Clustering(30) Variable = 17P GAIN MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                  0   1
  17P GAIN MUTATED     5  43
  17P GAIN WILD-TYPE  99 422
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                48                521 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                43                422 
$`17P GAIN MUTATED`
TCGA-02-0003 TCGA-02-0266 TCGA-02-0281 TCGA-02-0325 TCGA-02-0456 TCGA-02-2466 
        4.73        17.72         3.98        10.62         3.35        16.80 
TCGA-06-0151 TCGA-06-0166 TCGA-06-0173 TCGA-06-0188 TCGA-06-0195 TCGA-06-0216 
       46.59         5.85         4.47        44.58         7.40        24.16 
TCGA-06-0409 TCGA-06-0414 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-1087 
       72.36        35.11        14.20        26.40        46.88         4.04 
TCGA-06-1801 TCGA-06-2557 TCGA-06-6694 TCGA-06-A5U1 TCGA-08-0510 TCGA-12-0821 
       11.84         1.08         7.36         1.87         4.27        10.62 
TCGA-12-0822 TCGA-12-0827 TCGA-12-1096 TCGA-12-1600 TCGA-12-1602 TCGA-12-5301 
       23.51        38.76         9.11        14.73         6.77         2.04 
TCGA-14-0813 TCGA-14-0865 TCGA-14-1794 TCGA-14-3477 TCGA-16-0849 TCGA-19-1388 
        1.35        16.50         0.99         3.78        26.07        12.95 
TCGA-19-1390 TCGA-19-A6J4 TCGA-27-2521 TCGA-28-1746 TCGA-28-2506 TCGA-28-5207 
       25.38         3.98        10.39         0.20         6.74        11.28 
TCGA-28-5218 TCGA-32-2615 TCGA-32-4210 TCGA-41-2575 TCGA-41-4097 TCGA-RR-A6KA 
        5.16        15.95         3.72         9.53         0.20         6.28 

$`17P GAIN WILD-TYPE`
TCGA-02-0001 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 TCGA-02-0011 
       11.77        18.35        23.18        10.59        35.41        20.71 
TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0024 
       82.59        20.61        87.06        77.65        20.12        53.10 
TCGA-02-0025 TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 
       42.74        24.59        12.16        90.58         2.83        14.14 
TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 
        3.62        10.72        10.52        18.31         6.87        14.73 
TCGA-02-0048 TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 TCGA-02-0055 TCGA-02-0057 
        3.22        15.09        12.59         6.54         2.50        19.86 
TCGA-02-0058 TCGA-02-0059 TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 TCGA-02-0069 
        8.35         9.57         6.02        19.73        26.43        28.70 
TCGA-02-0070 TCGA-02-0071 TCGA-02-0074 TCGA-02-0075 TCGA-02-0079 TCGA-02-0080 
       25.05         5.49        10.19        20.84        27.25        89.72 
TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 
       22.72        12.62        51.32         8.81        57.76        16.96 
TCGA-02-0099 TCGA-02-0102 TCGA-02-0104 TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 
        3.48        27.02        65.00        11.67        17.65        23.18 
TCGA-02-0113 TCGA-02-0114 TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 
       92.65        99.98        15.65        48.95        16.54        16.93 
TCGA-02-0269 TCGA-02-0271 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 
       10.75        14.47        13.87        14.20        15.95        12.23 
TCGA-02-0321 TCGA-02-0324 TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 TCGA-02-0333 
        9.90         7.73         7.33        15.91        25.71         4.37 
TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 
       25.12        10.59        12.39        14.50        10.55        47.11 
TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 
       11.34         9.27        16.21        12.92        15.32        15.45 
TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 
       20.32         2.70         6.15        20.38        47.61         6.94 
TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 
        3.98        22.72        33.67        12.95        25.35        14.30 
TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 
       26.70        24.23        11.90         0.20        10.29         2.20 
TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 
       11.74         2.33        20.09        17.79        10.09         8.61 
TCGA-06-0150 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 
       19.46        12.33        13.94        10.45         3.19        10.82 
TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0168 
        9.44        11.80         3.42        56.91        10.65        19.66 
TCGA-06-0169 TCGA-06-0171 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 
        3.29        13.12         3.22         4.04        91.00         4.18 
TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 
       88.14        20.25         3.65        69.90        73.84        27.22 
TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0197 TCGA-06-0201 
       15.42        10.42        38.96         4.67         5.56         0.39 
TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 
        7.66         8.42         7.63         7.40        11.84         0.53 
TCGA-06-0214 TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 
       15.02         0.72        19.82        13.64        13.32        20.42 
TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0410 TCGA-06-0412 
       48.69        10.82         9.01         0.26         4.70         9.57 
TCGA-06-0413 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 
        3.16        12.62         5.75         5.75         9.80         2.10 
TCGA-06-0650 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 
       23.57         7.86         2.70         2.70         0.92        43.46 
TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 
       46.19         5.65         7.17        40.41        16.57        20.78 
TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1800 TCGA-06-1802 TCGA-06-1804 
       26.76        23.93         6.84        26.79        15.32        13.61 
TCGA-06-1805 TCGA-06-1806 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 
       33.90        15.32        12.49         4.93        17.65        12.56 
TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 
       30.64         5.95        16.64         5.98         4.37         0.43 
TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 
       31.50        11.74         3.55         8.35         4.54         8.81 
TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 
        8.98         8.55         6.71         2.73         3.75         6.15 
TCGA-06-5859 TCGA-06-6388 TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 
        4.57         5.23         7.79         5.39         1.48       120.56 
TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 
        8.32        12.85         4.77         1.55         4.77         4.96 
TCGA-06-A5U0 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK TCGA-06-A7TL TCGA-08-0244 
        4.70         3.12         2.56         5.39         5.42        22.68 
TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 
       37.84         4.18       115.86         1.74         8.42        25.71 
TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 
       12.16         9.80        29.23        65.33         1.28         8.42 
TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 
       17.95        24.56        31.10        37.58        22.29         3.39 
TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 
       12.23        14.93        18.02        15.35        13.97         0.72 
TCGA-08-0509 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 
       12.56        42.15        11.08        19.59        58.68        19.33 
TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 
       10.75         4.80         7.27        15.98        18.41         7.56 
TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 
       15.35        14.73        12.99        34.92        10.45         7.59 
TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 
       94.78         0.10        38.17        25.97        26.66        12.13 
TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 
        3.65        20.38        28.41        15.06        53.85        43.23 
TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 
        7.63         9.73        14.93        14.86        91.76        24.79 
TCGA-12-0820 TCGA-12-0826 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 
       18.48        27.78         8.94        20.58       127.59         5.82 
TCGA-12-1090 TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 
        7.59        33.21        21.73        15.98        12.23        15.85 
TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 TCGA-12-1598 TCGA-12-1599 TCGA-12-3644 
       14.53         3.98         4.14        15.65        25.68        59.77 
TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 
       44.02        26.93        15.22        10.95        12.69        34.92 
TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 
       14.53        14.93         3.22        15.12        11.97         0.95 
TCGA-14-0783 TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 TCGA-14-0812 
        6.21        23.05         2.24        11.24        13.78         3.25 
TCGA-14-0817 TCGA-14-0862 TCGA-14-0866 TCGA-14-0867 TCGA-14-0871 TCGA-14-1034 
        5.39         2.89        26.33         2.04        28.93        15.95 
TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 
       19.30         0.79         1.38         1.12         3.75        32.05 
TCGA-14-1450 TCGA-14-1451 TCGA-14-1452 TCGA-14-1453 TCGA-14-1454 TCGA-14-1455 
       58.78        23.11         7.10         1.15        30.18         0.92 
TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 TCGA-14-1795 TCGA-14-1821 TCGA-14-1823 
       40.96         6.67        12.43         1.97        17.79        17.85 
TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-4157 
        7.63         5.88         7.17        17.49         7.96         3.42 
TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 TCGA-16-0846 
       13.78        50.53        19.10        53.19        13.28         3.91 
TCGA-16-0848 TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 
       17.59        16.37         4.31        29.03         4.57        10.29 
TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 
       14.01         9.14        21.24        13.97         6.41        11.77 
TCGA-19-0957 TCGA-19-0960 TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 
       21.90         8.61         0.66        14.27         3.39        10.75 
TCGA-19-1386 TCGA-19-1387 TCGA-19-1389 TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 
        9.07         5.95         4.64         3.65         7.17        12.66 
TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 
        3.25         0.13         9.67         4.87         1.08         7.53 
TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 
        0.16         4.08        24.23         7.00         7.04         6.64 
TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 
       17.19         8.02        18.90         4.73        12.10         1.78 
TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J5 
       22.49        14.07        16.80        14.96        17.79        28.54 
TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 
       10.03        13.87         9.73        31.33         7.13         9.37 
TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 
        9.40        14.86         5.49         8.88        18.97         1.58 
TCGA-26-6173 TCGA-26-6174 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 
        7.92         2.33        19.33         5.06        16.60         9.86 
TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 
       24.23        40.54        21.30        30.05        14.04        11.51 
TCGA-27-2518 TCGA-27-2519 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 
       24.76        10.39        16.08         7.59         2.86        14.40 
TCGA-27-2528 TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 TCGA-28-1752 
       15.78         2.53         9.21         8.35         7.63         8.48 
TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 TCGA-28-2502 TCGA-28-2509 
        1.22         1.55         2.83         0.13         0.66         4.77 
TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 
        7.30         5.26        14.93        17.88        14.53        11.77 
TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5219 TCGA-28-5220 
       31.27        23.44        11.01        13.64        22.68        12.76 
TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 TCGA-32-1978 
        5.42        15.39        21.07         0.49         0.10        15.85 
TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 TCGA-32-1991 
       19.50         1.18         4.67        12.69        14.86        16.93 
TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2616 TCGA-32-2632 TCGA-32-2634 
       12.23        20.78        15.02         7.36         8.84        22.78 
TCGA-32-2638 TCGA-32-4208 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 
       25.18        21.14        12.59        19.86        10.85        19.23 
TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 
        0.85        13.35         8.94         0.99         4.44        11.84 
TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 
       15.12        12.46         4.14        14.76         3.45        20.91 
TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 
        4.34        14.33         8.22         7.50         4.80         4.54 
TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 
        3.09         3.65         9.17         2.53        10.78        16.70 
TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 
        3.29         2.70        11.38        17.06         8.35        20.98 
TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 
        4.83         5.03         0.23         9.27         7.73         7.79 
TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R TCGA-RR-A6KC 
        1.61        17.72        26.30         5.92        20.55 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
               0.2                0.1 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             72.36             127.59 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              9.32              12.16 
[1] "0.2 - 72.4 (9.3)"   "0.1 - 127.6 (12.2)"
[1] "hr=" "1.3"
D30V2, continuous
D30V3, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    15  33
  17P GAIN WILD-TYPE 209 313
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     15   33
  17P GAIN WILD-TYPE  209  313
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE               15                209
  MALE                 33                313
[1] 2 2
[1] FALSE
D30V4, continuous
                    vv
clus                 GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  17P GAIN MUTATED                               4                   1
  17P GAIN WILD-TYPE                            23                  17
                    vv
clus                 UNTREATED PRIMARY (DE NOVO) GBM
  17P GAIN MUTATED                                43
  17P GAIN WILD-TYPE                             482
D30V5, multiclass
                                 clus
vv                                17P GAIN MUTATED 17P GAIN WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                  4                 23
  TREATED PRIMARY GBM                            1                 17
  UNTREATED PRIMARY (DE NOVO) GBM               43                482
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V6, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    29  19
  17P GAIN WILD-TYPE 353 169
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     29   19
  17P GAIN WILD-TYPE  353  169
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  NO                29                353
  YES               19                169
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17P GAIN MUTATED       0                         6    40
  17P GAIN WILD-TYPE    13                        43   445
D30V7, multiclass
                           clus
vv                          17P GAIN MUTATED 17P GAIN WILD-TYPE
  ASIAN                                    0                 13
  BLACK OR AFRICAN AMERICAN                6                 43
  WHITE                                   40                445
[1] 3 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
  17P GAIN MUTATED     1  42
  17P GAIN WILD-TYPE  11 430
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      1   42
  17P GAIN WILD-TYPE   11  430
                        clus
vv                       17P GAIN MUTATED 17P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 11
  NOT HISPANIC OR LATINO               42                430
[1] 2 2
[1] FALSE

Clustering(31) Variable = 17Q GAIN MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                  0   1
  17Q GAIN MUTATED     4  55
  17Q GAIN WILD-TYPE 100 410
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                59                510 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                55                410 
$`17Q GAIN MUTATED`
TCGA-02-0003 TCGA-02-0266 TCGA-02-0281 TCGA-02-0325 TCGA-02-0456 TCGA-02-2466 
        4.73        17.72         3.98        10.62         3.35        16.80 
TCGA-06-0151 TCGA-06-0166 TCGA-06-0173 TCGA-06-0188 TCGA-06-0195 TCGA-06-0216 
       46.59         5.85         4.47        44.58         7.40        24.16 
TCGA-06-0237 TCGA-06-0409 TCGA-06-0410 TCGA-06-0414 TCGA-06-0686 TCGA-06-0743 
       13.64        72.36         4.70        35.11        14.20        26.40 
TCGA-06-0744 TCGA-06-1087 TCGA-06-1801 TCGA-06-2557 TCGA-06-6694 TCGA-06-A5U1 
       46.88         4.04        11.84         1.08         7.36         1.87 
TCGA-08-0510 TCGA-12-0619 TCGA-12-0821 TCGA-12-0822 TCGA-12-0827 TCGA-12-1092 
        4.27        34.92        10.62        23.51        38.76        21.73 
TCGA-12-1096 TCGA-12-1600 TCGA-12-1602 TCGA-12-5301 TCGA-14-0813 TCGA-14-0865 
        9.11        14.73         6.77         2.04         1.35        16.50 
TCGA-14-1794 TCGA-14-3477 TCGA-15-1449 TCGA-16-0846 TCGA-19-1388 TCGA-19-1390 
        0.99         3.78        13.28         3.91        12.95        25.38 
TCGA-19-A6J4 TCGA-27-1835 TCGA-27-2521 TCGA-28-1746 TCGA-28-2506 TCGA-28-5207 
        3.98        21.30        10.39         0.20         6.74        11.28 
TCGA-28-5215 TCGA-28-5218 TCGA-32-2495 TCGA-32-2615 TCGA-32-2616 TCGA-32-4210 
       11.01         5.16        15.02        15.95         7.36         3.72 
TCGA-41-2575 TCGA-41-3915 TCGA-41-4097 TCGA-76-6280 TCGA-RR-A6KA 
        9.53        11.84         0.20        11.38         6.28 

$`17Q GAIN WILD-TYPE`
TCGA-02-0001 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 TCGA-02-0011 
       11.77        18.35        23.18        10.59        35.41        20.71 
TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0024 
       82.59        20.61        87.06        77.65        20.12        53.10 
TCGA-02-0025 TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 
       42.74        24.59        12.16        90.58         2.83        14.14 
TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 
        3.62        10.72        10.52        18.31         6.87        14.73 
TCGA-02-0048 TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 TCGA-02-0055 TCGA-02-0057 
        3.22        15.09        12.59         6.54         2.50        19.86 
TCGA-02-0058 TCGA-02-0059 TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 TCGA-02-0069 
        8.35         9.57         6.02        19.73        26.43        28.70 
TCGA-02-0070 TCGA-02-0071 TCGA-02-0074 TCGA-02-0075 TCGA-02-0079 TCGA-02-0080 
       25.05         5.49        10.19        20.84        27.25        89.72 
TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 
       22.72        12.62        51.32         8.81        57.76        16.96 
TCGA-02-0099 TCGA-02-0102 TCGA-02-0104 TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 
        3.48        27.02        65.00        11.67        17.65        23.18 
TCGA-02-0113 TCGA-02-0114 TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 
       92.65        99.98        15.65        48.95        16.54        16.93 
TCGA-02-0269 TCGA-02-0271 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 
       10.75        14.47        13.87        14.20        15.95        12.23 
TCGA-02-0321 TCGA-02-0324 TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 TCGA-02-0333 
        9.90         7.73         7.33        15.91        25.71         4.37 
TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 
       25.12        10.59        12.39        14.50        10.55        47.11 
TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 
       11.34         9.27        16.21        12.92        15.32        15.45 
TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 
       20.32         2.70         6.15        20.38        47.61         6.94 
TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 
        3.98        22.72        33.67        12.95        25.35        14.30 
TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 
       26.70        24.23        11.90         0.20        10.29         2.20 
TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 
       11.74         2.33        20.09        17.79        10.09         8.61 
TCGA-06-0150 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 
       19.46        12.33        13.94        10.45         3.19        10.82 
TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0168 
        9.44        11.80         3.42        56.91        10.65        19.66 
TCGA-06-0169 TCGA-06-0171 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 
        3.29        13.12         3.22         4.04        91.00         4.18 
TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 
       88.14        20.25         3.65        69.90        73.84        27.22 
TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0197 TCGA-06-0201 
       15.42        10.42        38.96         4.67         5.56         0.39 
TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 
        7.66         8.42         7.63         7.40        11.84         0.53 
TCGA-06-0214 TCGA-06-0219 TCGA-06-0221 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 
       15.02         0.72        19.82        13.32        20.42        48.69 
TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0412 TCGA-06-0413 TCGA-06-0644 
       10.82         9.01         0.26         9.57         3.16        12.62 
TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0745 
        5.75         5.75         9.80         2.10        23.57         7.86 
TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 
        2.70         2.70         0.92        43.46        46.19         5.65 
TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 
        7.17        40.41        16.57        20.78        26.76        23.93 
TCGA-06-1086 TCGA-06-1800 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 
        6.84        26.79        15.32        13.61        33.90        15.32 
TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 
       12.49         4.93        17.65        12.56        30.64         5.95 
TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-5408 
       16.64         5.98         4.37         0.43        31.50        11.74 
TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 
        3.55         8.35         4.54         8.81         8.98         8.55 
TCGA-06-5416 TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 
        6.71         2.73         3.75         6.15         4.57         5.23 
TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6695 TCGA-06-6697 
        7.79         5.39         1.48       120.56         8.32        12.85 
TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A6S0 
        4.77         1.55         4.77         4.96         4.70         3.12 
TCGA-06-A6S1 TCGA-06-A7TK TCGA-06-A7TL TCGA-08-0244 TCGA-08-0245 TCGA-08-0246 
        2.56         5.39         5.42        22.68        37.84         4.18 
TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 
      115.86         1.74         8.42        25.71        12.16         9.80 
TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 
       29.23        65.33         1.28         8.42        17.95        24.56 
TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 
       31.10        37.58        22.29         3.39        12.23        14.93 
TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0512 
       18.02        15.35        13.97         0.72        12.56        42.15 
TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 
       11.08        19.59        58.68        19.33        10.75         4.80 
TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 
        7.27        15.98        18.41         7.56        15.35        14.73 
TCGA-12-0618 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 
       12.99        10.45         7.59        94.78         0.10        38.17 
TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 
       25.97        26.66        12.13         3.65        20.38        28.41 
TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 
       15.06        53.85        43.23         7.63         9.73        14.93 
TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0826 TCGA-12-0828 
       14.86        91.76        24.79        18.48        27.78         8.94 
TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 TCGA-12-1093 
       20.58       127.59         5.82         7.59        33.21        15.98 
TCGA-12-1094 TCGA-12-1095 TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 TCGA-12-1598 
       12.23        15.85        14.53         3.98         4.14        15.65 
TCGA-12-1599 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 
       25.68        59.77        44.02        26.93        15.22        10.95 
TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-14-0736 
       12.69        34.92        14.53        14.93         3.22        15.12 
TCGA-14-0740 TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 
       11.97         0.95         6.21        23.05         2.24        11.24 
TCGA-14-0790 TCGA-14-0812 TCGA-14-0817 TCGA-14-0862 TCGA-14-0866 TCGA-14-0867 
       13.78         3.25         5.39         2.89        26.33         2.04 
TCGA-14-0871 TCGA-14-1034 TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 TCGA-14-1396 
       28.93        15.95        19.30         0.79         1.38         1.12 
TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 TCGA-14-1452 TCGA-14-1453 
        3.75        32.05        58.78        23.11         7.10         1.15 
TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 TCGA-14-1795 
       30.18         0.92        40.96         6.67        12.43         1.97 
TCGA-14-1821 TCGA-14-1823 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 
       17.79        17.85         7.63         5.88         7.17        17.49 
TCGA-14-2555 TCGA-14-4157 TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 
        7.96         3.42        13.78        50.53        19.10        53.19 
TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 
       17.59        26.07        16.37         4.31        29.03         4.57 
TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 
       10.29        14.01         9.14        21.24        13.97         6.41 
TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 
       11.77        21.90         8.61         0.66        14.27         3.39 
TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 TCGA-19-1389 TCGA-19-1392 TCGA-19-1786 
       10.75         9.07         5.95         4.64         3.65         7.17 
TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 
       12.66         3.25         0.13         9.67         4.87         1.08 
TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 
        7.53         0.16         4.08        24.23         7.00         7.04 
TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 
        6.64        17.19         8.02        18.90         4.73        12.10 
TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I 
        1.78        22.49        14.07        16.80        14.96        17.79 
TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 
       28.54        10.03        13.87         9.73        31.33         7.13 
TCGA-26-1799 TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 
        9.37         9.40        14.86         5.49         8.88        18.97 
TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 
        1.58         7.92         2.33        19.33         5.06        16.60 
TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 
        9.86        24.23        40.54        30.05        14.04        11.51 
TCGA-27-2518 TCGA-27-2519 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 
       24.76        10.39        16.08         7.59         2.86        14.40 
TCGA-27-2528 TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 TCGA-28-1752 
       15.78         2.53         9.21         8.35         7.63         8.48 
TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 TCGA-28-2502 TCGA-28-2509 
        1.22         1.55         2.83         0.13         0.66         4.77 
TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 
        7.30         5.26        14.93        17.88        14.53        11.77 
TCGA-28-5213 TCGA-28-5214 TCGA-28-5216 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 
       31.27        23.44        13.64        22.68        12.76         5.42 
TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 
       15.39        21.07         0.49         0.10        15.85        19.50 
TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 TCGA-32-1991 TCGA-32-2491 
        1.18         4.67        12.69        14.86        16.93        12.23 
TCGA-32-2494 TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4211 
       20.78         8.84        22.78        25.18        21.14        12.59 
TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 
       19.86        10.85        19.23         0.85        13.35         8.94 
TCGA-41-3392 TCGA-41-3393 TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9S TCGA-4W-AA9T 
        0.99         4.44        15.12        12.46         4.14        14.76 
TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 
        3.45        20.91         4.34        14.33         8.22         7.50 
TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-4934 
        4.80         4.54         3.09         3.65         9.17         2.53 
TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6282 TCGA-76-6285 
       10.78        16.70         3.29         2.70        17.06         8.35 
TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 
       20.98         4.83         5.03         0.23         9.27         7.73 
TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R TCGA-RR-A6KC 
        7.79         1.61        17.72        26.30         5.92        20.55 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               0.2                0.1 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             72.36             127.59 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
            10.620             12.195 
[1] "0.2 - 72.4 (10.6)"  "0.1 - 127.6 (12.2)"
[1] "hr=" "1.4"
D31V2, continuous
D31V3, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    21  38
  17Q GAIN WILD-TYPE 203 308
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     21   38
  17Q GAIN WILD-TYPE  203  308
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE               21                203
  MALE                 38                308
[1] 2 2
[1] FALSE
D31V4, continuous
                    vv
clus                 GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  17Q GAIN MUTATED                               4                   2
  17Q GAIN WILD-TYPE                            23                  16
                    vv
clus                 UNTREATED PRIMARY (DE NOVO) GBM
  17Q GAIN MUTATED                                53
  17Q GAIN WILD-TYPE                             472
D31V5, multiclass
                                 clus
vv                                17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                  4                 23
  TREATED PRIMARY GBM                            2                 16
  UNTREATED PRIMARY (DE NOVO) GBM               53                472
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V6, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    36  23
  17Q GAIN WILD-TYPE 346 165
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     36   23
  17Q GAIN WILD-TYPE  346  165
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  NO                36                346
  YES               23                165
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17Q GAIN MUTATED       0                         6    51
  17Q GAIN WILD-TYPE    13                        43   434
D31V7, multiclass
                           clus
vv                          17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  ASIAN                                    0                 13
  BLACK OR AFRICAN AMERICAN                6                 43
  WHITE                                   51                434
[1] 3 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
  17Q GAIN MUTATED     2  50
  17Q GAIN WILD-TYPE  10 422
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      2   50
  17Q GAIN WILD-TYPE   10  422
                        clus
vv                       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                 10
  NOT HISPANIC OR LATINO               50                422
[1] 2 2
[1] FALSE

Clustering(32) Variable = 18P GAIN MUTATION ANALYSIS
D32V1, survival
                    sevent
clus2                  0   1
  18P GAIN MUTATED    11  46
  18P GAIN WILD-TYPE  93 419
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                57                512 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                46                419 
$`18P GAIN MUTATED`
TCGA-02-0025 TCGA-02-0074 TCGA-02-0104 TCGA-02-0266 TCGA-02-0271 TCGA-02-0281 
       42.74        10.19        65.00        17.72        14.47         3.98 
TCGA-02-0325 TCGA-06-0128 TCGA-06-0130 TCGA-06-0147 TCGA-06-0188 TCGA-06-0197 
       10.62        22.72        12.95        17.79        44.58         5.56 
TCGA-06-0209 TCGA-06-0238 TCGA-06-0402 TCGA-06-0410 TCGA-06-0414 TCGA-06-0686 
        7.63        13.32         0.26         4.70        35.11        14.20 
TCGA-06-1087 TCGA-06-1805 TCGA-06-2557 TCGA-06-2559 TCGA-06-5858 TCGA-06-6389 
        4.04        33.90         1.08         4.93         6.15         7.79 
TCGA-06-6698 TCGA-08-0353 TCGA-12-0657 TCGA-12-0827 TCGA-12-1090 TCGA-12-1092 
        4.77         8.42         0.10        38.76         7.59        21.73 
TCGA-12-1598 TCGA-12-1602 TCGA-12-3651 TCGA-12-3653 TCGA-12-5295 TCGA-14-0867 
       15.65         6.77        12.69        14.53        14.93         2.04 
TCGA-14-0871 TCGA-14-1794 TCGA-14-1823 TCGA-14-3477 TCGA-15-1447 TCGA-15-1449 
       28.93         0.99        17.85         3.78        53.19        13.28 
TCGA-19-0960 TCGA-19-1392 TCGA-19-1787 TCGA-19-2629 TCGA-26-5136 TCGA-27-2521 
        8.61         3.65        12.66        24.23        18.97        10.39 
TCGA-28-2506 TCGA-28-2509 TCGA-32-1973 TCGA-32-1986 TCGA-32-2632 TCGA-32-5222 
        6.74         4.77        21.07        12.69         8.84        19.23 
TCGA-41-2573 TCGA-41-3915 TCGA-76-4934 
        8.94        11.84         2.53 

$`18P GAIN WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 
       11.77         4.73        18.35        23.18        10.59        35.41 
TCGA-02-0011 TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 
       20.71        82.59        20.61        87.06        77.65        20.12 
TCGA-02-0024 TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 
       53.10        24.59        12.16        90.58         2.83        14.14 
TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 
        3.62        10.72        10.52        18.31         6.87        14.73 
TCGA-02-0048 TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 TCGA-02-0055 TCGA-02-0057 
        3.22        15.09        12.59         6.54         2.50        19.86 
TCGA-02-0058 TCGA-02-0059 TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 TCGA-02-0069 
        8.35         9.57         6.02        19.73        26.43        28.70 
TCGA-02-0070 TCGA-02-0071 TCGA-02-0075 TCGA-02-0079 TCGA-02-0080 TCGA-02-0083 
       25.05         5.49        20.84        27.25        89.72        22.72 
TCGA-02-0084 TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 
       12.62        51.32         8.81        57.76        16.96         3.48 
TCGA-02-0102 TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 TCGA-02-0113 TCGA-02-0114 
       27.02        11.67        17.65        23.18        92.65        99.98 
TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 TCGA-02-0269 TCGA-02-0285 
       15.65        48.95        16.54        16.93        10.75        13.87 
TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 TCGA-02-0326 
       14.20        15.95        12.23         9.90         7.73         7.33 
TCGA-02-0330 TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 
       15.91        25.71         4.37        25.12        10.59        12.39 
TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 
       14.50        10.55        47.11        11.34         9.27        16.21 
TCGA-02-0456 TCGA-02-2466 TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 
        3.35        16.80        12.92        15.32        15.45        20.32 
TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 
        2.70         6.15        20.38        47.61         6.94         3.98 
TCGA-06-0129 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 
       33.67        25.35        14.30        26.70        24.23        11.90 
TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 
        0.20        10.29         2.20        11.74         2.33        20.09 
TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 
       10.09         8.61        19.46        46.59        12.33        13.94 
TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 
       10.45         3.19        10.82         9.44        11.80         3.42 
TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 
       56.91        10.65         5.85        19.66         3.29        13.12 
TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 
        4.47         3.22         4.04        91.00         4.18        88.14 
TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0189 
       20.25         3.65        69.90        73.84        27.22        15.42 
TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0201 TCGA-06-0206 
       10.42        38.96         4.67         7.40         0.39         7.66 
TCGA-06-0208 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 
        8.42         7.40        11.84         0.53        15.02        24.16 
TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 
        0.72        19.82        13.64        20.42        48.69        10.82 
TCGA-06-0397 TCGA-06-0409 TCGA-06-0412 TCGA-06-0413 TCGA-06-0644 TCGA-06-0645 
        9.01        72.36         9.57         3.16        12.62         5.75 
TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0743 TCGA-06-0744 
        5.75         9.80         2.10        23.57        26.40        46.88 
TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 
        7.86         2.70         2.70         0.92        43.46        46.19 
TCGA-06-0877 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 
        5.65         7.17        40.41        16.57        20.78        26.76 
TCGA-06-1084 TCGA-06-1086 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 
       23.93         6.84        26.79        11.84        15.32        13.61 
TCGA-06-1806 TCGA-06-2558 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 
       15.32        12.49        17.65        12.56        30.64         5.95 
TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-5408 
       16.64         5.98         4.37         0.43        31.50        11.74 
TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 
        3.55         8.35         4.54         8.81         8.98         8.55 
TCGA-06-5416 TCGA-06-5418 TCGA-06-5856 TCGA-06-5859 TCGA-06-6388 TCGA-06-6390 
        6.71         2.73         3.75         4.57         5.23         5.39 
TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 TCGA-06-6699 
        1.48       120.56         7.36         8.32        12.85         1.55 
TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 
        4.77         4.96         4.70         1.87         3.12         2.56 
TCGA-06-A7TK TCGA-06-A7TL TCGA-08-0244 TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 
        5.39         5.42        22.68        37.84         4.18       115.86 
TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 
        1.74         8.42        25.71        12.16         9.80        29.23 
TCGA-08-0351 TCGA-08-0352 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 
       65.33         1.28        17.95        24.56        31.10        37.58 
TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 
       22.29         3.39        12.23        14.93        18.02        15.35 
TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 
       13.97         0.72        12.56         4.27        42.15        11.08 
TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 
       19.59        58.68        19.33        10.75         4.80         7.27 
TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 
       15.98        18.41         7.56        15.35        14.73        12.99 
TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0662 TCGA-12-0670 
       34.92        10.45         7.59        94.78        38.17        25.97 
TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 
       26.66        12.13         3.65        20.38        28.41        15.06 
TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 
       53.85        43.23         7.63         9.73        14.93        14.86 
TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 TCGA-12-0826 
       91.76        24.79        18.48        10.62        23.51        27.78 
TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 TCGA-12-1091 TCGA-12-1093 
        8.94        20.58       127.59         5.82        33.21        15.98 
TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 
       12.23        15.85         9.11        14.53         3.98         4.14 
TCGA-12-1599 TCGA-12-1600 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 
       25.68        14.73        59.77        44.02        26.93        15.22 
TCGA-12-3650 TCGA-12-3652 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 
       10.95        34.92         3.22         2.04        15.12        11.97 
TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 
        0.95         6.21        23.05         2.24        11.24        13.78 
TCGA-14-0812 TCGA-14-0813 TCGA-14-0817 TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 
        3.25         1.35         5.39         2.89        16.50        26.33 
TCGA-14-1034 TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 
       15.95        19.30         0.79         1.38         1.12         3.75 
TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 TCGA-14-1452 TCGA-14-1453 TCGA-14-1454 
       32.05        58.78        23.11         7.10         1.15        30.18 
TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 TCGA-14-1795 TCGA-14-1821 
        0.92        40.96         6.67        12.43         1.97        17.79 
TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-4157 
        7.63         5.88         7.17        17.49         7.96         3.42 
TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 
       13.78        50.53        19.10         3.91        17.59        26.07 
TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 
       16.37         4.31        29.03         4.57        10.29        14.01 
TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 
        9.14        21.24        13.97         6.41        11.77        21.90 
TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 
        0.66        14.27         3.39        10.75         9.07         5.95 
TCGA-19-1388 TCGA-19-1389 TCGA-19-1390 TCGA-19-1786 TCGA-19-1789 TCGA-19-1791 
       12.95         4.64        25.38         7.17         3.25         0.13 
TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 
        9.67         4.87         1.08         7.53         0.16         4.08 
TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 
        7.00         7.04         6.64        17.19         8.02        18.90 
TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 
        4.73        12.10         1.78        22.49        14.07        16.80 
TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 
       14.96        17.79         3.98        28.54        10.03        13.87 
TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5133 
        9.73        31.33         7.13         9.37         9.40        14.86 
TCGA-26-5134 TCGA-26-5135 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-26-A7UX 
        5.49         8.88         1.58         7.92         2.33        19.33 
TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 
        5.06        16.60         9.86        24.23        40.54        21.30 
TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2523 
       30.05        14.04        11.51        24.76        10.39        16.08 
TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 
        7.59         2.86        14.40        15.78         0.20         2.53 
TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 TCGA-28-1755 
        9.21         8.35         7.63         8.48         1.22         1.55 
TCGA-28-1756 TCGA-28-1757 TCGA-28-2502 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 
        2.83         0.13         0.66         7.30         5.26        14.93 
TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 
       11.28        17.88        14.53        11.77        31.27        23.44 
TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 
       11.01        13.64         5.16        22.68        12.76         5.42 
TCGA-32-1970 TCGA-32-1976 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 TCGA-32-1980 
       15.39         0.49         0.10        15.85        19.50         1.18 
TCGA-32-1982 TCGA-32-1987 TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 
        4.67        14.86        16.93        12.23        20.78        15.02 
TCGA-32-2615 TCGA-32-2616 TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4210 
       15.95         7.36        22.78        25.18        21.14         3.72 
TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-41-2571 TCGA-41-2572 TCGA-41-2575 
       12.59        19.86        10.85         0.85        13.35         9.53 
TCGA-41-3392 TCGA-41-3393 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9S 
        0.99         4.44         0.20        15.12        12.46         4.14 
TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 
       14.76         3.45        20.91         4.34        14.33         8.22 
TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 
        7.50         4.80         4.54         3.09         3.65         9.17 
TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 
       10.78        16.70         3.29         2.70        11.38        17.06 
TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 
        8.35        20.98         4.83         5.03         0.23         9.27 
TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R 
        7.73         7.79         1.61        17.72        26.30         5.92 
TCGA-RR-A6KA TCGA-RR-A6KC 
        6.28        20.55 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
               0.1                0.1 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             65.00             127.59 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             11.84              11.87 
[1] "0.1 - 65.0 (11.8)"  "0.1 - 127.6 (11.9)"
[1] "hr=" "1.1"
D32V2, continuous
D32V3, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    24  33
  18P GAIN WILD-TYPE 200 313
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     24   33
  18P GAIN WILD-TYPE  200  313
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE               24                200
  MALE                 33                313
[1] 2 2
[1] FALSE
D32V4, continuous
                    vv
clus                 GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  18P GAIN MUTATED                               0                   0
  18P GAIN WILD-TYPE                            27                  18
                    vv
clus                 UNTREATED PRIMARY (DE NOVO) GBM
  18P GAIN MUTATED                                57
  18P GAIN WILD-TYPE                             468
D32V5, multiclass
                                 clus
vv                                18P GAIN MUTATED 18P GAIN WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                  0                 27
  TREATED PRIMARY GBM                            0                 18
  UNTREATED PRIMARY (DE NOVO) GBM               57                468
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V6, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    40  17
  18P GAIN WILD-TYPE 342 171
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     40   17
  18P GAIN WILD-TYPE  342  171
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  NO                40                342
  YES               17                171
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18P GAIN MUTATED       0                         2    52
  18P GAIN WILD-TYPE    13                        47   433
D32V7, multiclass
                           clus
vv                          18P GAIN MUTATED 18P GAIN WILD-TYPE
  ASIAN                                    0                 13
  BLACK OR AFRICAN AMERICAN                2                 47
  WHITE                                   52                433
[1] 3 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
  18P GAIN MUTATED     2  47
  18P GAIN WILD-TYPE  10 425
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      2   47
  18P GAIN WILD-TYPE   10  425
                        clus
vv                       18P GAIN MUTATED 18P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                 10
  NOT HISPANIC OR LATINO               47                425
[1] 2 2
[1] FALSE

Clustering(33) Variable = 18Q GAIN MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                  0   1
  18Q GAIN MUTATED    12  45
  18Q GAIN WILD-TYPE  92 420
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                57                512 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                45                420 
$`18Q GAIN MUTATED`
TCGA-02-0074 TCGA-02-0104 TCGA-02-0266 TCGA-02-0271 TCGA-02-0281 TCGA-02-0325 
       10.19        65.00        17.72        14.47         3.98        10.62 
TCGA-06-0128 TCGA-06-0130 TCGA-06-0147 TCGA-06-0188 TCGA-06-0197 TCGA-06-0209 
       22.72        12.95        17.79        44.58         5.56         7.63 
TCGA-06-0238 TCGA-06-0402 TCGA-06-0410 TCGA-06-0414 TCGA-06-0686 TCGA-06-0876 
       13.32         0.26         4.70        35.11        14.20        46.19 
TCGA-06-1087 TCGA-06-1805 TCGA-06-2557 TCGA-06-5408 TCGA-06-5858 TCGA-06-6389 
        4.04        33.90         1.08        11.74         6.15         7.79 
TCGA-06-6698 TCGA-08-0353 TCGA-12-0657 TCGA-12-0827 TCGA-12-1092 TCGA-12-1598 
        4.77         8.42         0.10        38.76        21.73        15.65 
TCGA-12-1602 TCGA-12-3651 TCGA-12-3653 TCGA-12-5295 TCGA-14-0867 TCGA-14-0871 
        6.77        12.69        14.53        14.93         2.04        28.93 
TCGA-14-1794 TCGA-14-1823 TCGA-14-3477 TCGA-15-1447 TCGA-15-1449 TCGA-16-0850 
        0.99        17.85         3.78        53.19        13.28        16.37 
TCGA-19-0960 TCGA-19-1392 TCGA-19-1787 TCGA-19-2629 TCGA-26-5136 TCGA-27-2521 
        8.61         3.65        12.66        24.23        18.97        10.39 
TCGA-28-2506 TCGA-28-2509 TCGA-32-1986 TCGA-32-2632 TCGA-32-5222 TCGA-41-2573 
        6.74         4.77        12.69         8.84        19.23         8.94 
TCGA-41-2575 TCGA-41-3915 TCGA-76-4934 
        9.53        11.84         2.53 

$`18Q GAIN WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 
       11.77         4.73        18.35        23.18        10.59        35.41 
TCGA-02-0011 TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 
       20.71        82.59        20.61        87.06        77.65        20.12 
TCGA-02-0024 TCGA-02-0025 TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 
       53.10        42.74        24.59        12.16        90.58         2.83 
TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 
       14.14         3.62        10.72        10.52        18.31         6.87 
TCGA-02-0047 TCGA-02-0048 TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 TCGA-02-0055 
       14.73         3.22        15.09        12.59         6.54         2.50 
TCGA-02-0057 TCGA-02-0058 TCGA-02-0059 TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 
       19.86         8.35         9.57         6.02        19.73        26.43 
TCGA-02-0069 TCGA-02-0070 TCGA-02-0071 TCGA-02-0075 TCGA-02-0079 TCGA-02-0080 
       28.70        25.05         5.49        20.84        27.25        89.72 
TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 
       22.72        12.62        51.32         8.81        57.76        16.96 
TCGA-02-0099 TCGA-02-0102 TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 TCGA-02-0113 
        3.48        27.02        11.67        17.65        23.18        92.65 
TCGA-02-0114 TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 TCGA-02-0269 
       99.98        15.65        48.95        16.54        16.93        10.75 
TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 
       13.87        14.20        15.95        12.23         9.90         7.73 
TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 
        7.33        15.91        25.71         4.37        25.12        10.59 
TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 
       12.39        14.50        10.55        47.11        11.34         9.27 
TCGA-02-0451 TCGA-02-0456 TCGA-02-2466 TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 
       16.21         3.35        16.80        12.92        15.32        15.45 
TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 
       20.32         2.70         6.15        20.38        47.61         6.94 
TCGA-06-0127 TCGA-06-0129 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 
        3.98        33.67        25.35        14.30        26.70        24.23 
TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 
       11.90         0.20        10.29         2.20        11.74         2.33 
TCGA-06-0146 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 
       20.09        10.09         8.61        19.46        46.59        12.33 
TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 
       13.94        10.45         3.19        10.82         9.44        11.80 
TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 
        3.42        56.91        10.65         5.85        19.66         3.29 
TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 
       13.12         4.47         3.22         4.04        91.00         4.18 
TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 
       88.14        20.25         3.65        69.90        73.84        27.22 
TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0201 
       15.42        10.42        38.96         4.67         7.40         0.39 
TCGA-06-0206 TCGA-06-0208 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 
        7.66         8.42         7.40        11.84         0.53        15.02 
TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0240 TCGA-06-0241 
       24.16         0.72        19.82        13.64        20.42        48.69 
TCGA-06-0394 TCGA-06-0397 TCGA-06-0409 TCGA-06-0412 TCGA-06-0413 TCGA-06-0644 
       10.82         9.01        72.36         9.57         3.16        12.62 
TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0743 
        5.75         5.75         9.80         2.10        23.57        26.40 
TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 
       46.88         7.86         2.70         2.70         0.92        43.46 
TCGA-06-0877 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 
        5.65         7.17        40.41        16.57        20.78        26.76 
TCGA-06-1084 TCGA-06-1086 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 
       23.93         6.84        26.79        11.84        15.32        13.61 
TCGA-06-1806 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 
       15.32        12.49         4.93        17.65        12.56        30.64 
TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 
        5.95        16.64         5.98         4.37         0.43        31.50 
TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 
        3.55         8.35         4.54         8.81         8.98         8.55 
TCGA-06-5416 TCGA-06-5418 TCGA-06-5856 TCGA-06-5859 TCGA-06-6388 TCGA-06-6390 
        6.71         2.73         3.75         4.57         5.23         5.39 
TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 TCGA-06-6699 
        1.48       120.56         7.36         8.32        12.85         1.55 
TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 
        4.77         4.96         4.70         1.87         3.12         2.56 
TCGA-06-A7TK TCGA-06-A7TL TCGA-08-0244 TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 
        5.39         5.42        22.68        37.84         4.18       115.86 
TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 
        1.74         8.42        25.71        12.16         9.80        29.23 
TCGA-08-0351 TCGA-08-0352 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 
       65.33         1.28        17.95        24.56        31.10        37.58 
TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 
       22.29         3.39        12.23        14.93        18.02        15.35 
TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 
       13.97         0.72        12.56         4.27        42.15        11.08 
TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 
       19.59        58.68        19.33        10.75         4.80         7.27 
TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 
       15.98        18.41         7.56        15.35        14.73        12.99 
TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0662 TCGA-12-0670 
       34.92        10.45         7.59        94.78        38.17        25.97 
TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 
       26.66        12.13         3.65        20.38        28.41        15.06 
TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 
       53.85        43.23         7.63         9.73        14.93        14.86 
TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 TCGA-12-0826 
       91.76        24.79        18.48        10.62        23.51        27.78 
TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 
        8.94        20.58       127.59         5.82         7.59        33.21 
TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 
       15.98        12.23        15.85         9.11        14.53         3.98 
TCGA-12-1099 TCGA-12-1599 TCGA-12-1600 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 
        4.14        25.68        14.73        59.77        44.02        26.93 
TCGA-12-3649 TCGA-12-3650 TCGA-12-3652 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 
       15.22        10.95        34.92         3.22         2.04        15.12 
TCGA-14-0740 TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 
       11.97         0.95         6.21        23.05         2.24        11.24 
TCGA-14-0790 TCGA-14-0812 TCGA-14-0813 TCGA-14-0817 TCGA-14-0862 TCGA-14-0865 
       13.78         3.25         1.35         5.39         2.89        16.50 
TCGA-14-0866 TCGA-14-1034 TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 TCGA-14-1396 
       26.33        15.95        19.30         0.79         1.38         1.12 
TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 TCGA-14-1452 TCGA-14-1453 
        3.75        32.05        58.78        23.11         7.10         1.15 
TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 TCGA-14-1795 
       30.18         0.92        40.96         6.67        12.43         1.97 
TCGA-14-1821 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 
       17.79         7.63         5.88         7.17        17.49         7.96 
TCGA-14-4157 TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-16-0846 TCGA-16-0848 
        3.42        13.78        50.53        19.10         3.91        17.59 
TCGA-16-0849 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 
       26.07         4.31        29.03         4.57        10.29        14.01 
TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 
        9.14        21.24        13.97         6.41        11.77        21.90 
TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 
        0.66        14.27         3.39        10.75         9.07         5.95 
TCGA-19-1388 TCGA-19-1389 TCGA-19-1390 TCGA-19-1786 TCGA-19-1789 TCGA-19-1791 
       12.95         4.64        25.38         7.17         3.25         0.13 
TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 
        9.67         4.87         1.08         7.53         0.16         4.08 
TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 
        7.00         7.04         6.64        17.19         8.02        18.90 
TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 
        4.73        12.10         1.78        22.49        14.07        16.80 
TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 
       14.96        17.79         3.98        28.54        10.03        13.87 
TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5133 
        9.73        31.33         7.13         9.37         9.40        14.86 
TCGA-26-5134 TCGA-26-5135 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-26-A7UX 
        5.49         8.88         1.58         7.92         2.33        19.33 
TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 
        5.06        16.60         9.86        24.23        40.54        21.30 
TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2523 
       30.05        14.04        11.51        24.76        10.39        16.08 
TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 
        7.59         2.86        14.40        15.78         0.20         2.53 
TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 TCGA-28-1755 
        9.21         8.35         7.63         8.48         1.22         1.55 
TCGA-28-1756 TCGA-28-1757 TCGA-28-2502 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 
        2.83         0.13         0.66         7.30         5.26        14.93 
TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 
       11.28        17.88        14.53        11.77        31.27        23.44 
TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 
       11.01        13.64         5.16        22.68        12.76         5.42 
TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 
       15.39        21.07         0.49         0.10        15.85        19.50 
TCGA-32-1980 TCGA-32-1982 TCGA-32-1987 TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 
        1.18         4.67        14.86        16.93        12.23        20.78 
TCGA-32-2495 TCGA-32-2615 TCGA-32-2616 TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 
       15.02        15.95         7.36        22.78        25.18        21.14 
TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-41-2571 TCGA-41-2572 
        3.72        12.59        19.86        10.85         0.85        13.35 
TCGA-41-3392 TCGA-41-3393 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9S 
        0.99         4.44         0.20        15.12        12.46         4.14 
TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 
       14.76         3.45        20.91         4.34        14.33         8.22 
TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 
        7.50         4.80         4.54         3.09         3.65         9.17 
TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 
       10.78        16.70         3.29         2.70        11.38        17.06 
TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 
        8.35        20.98         4.83         5.03         0.23         9.27 
TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R 
        7.73         7.79         1.61        17.72        26.30         5.92 
TCGA-RR-A6KA TCGA-RR-A6KC 
        6.28        20.55 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
               0.1                0.1 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             65.00             127.59 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             11.84              11.87 
[1] "0.1 - 65.0 (11.8)"  "0.1 - 127.6 (11.9)"
[1] "hr=" "1.1"
D33V2, continuous
D33V3, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    27  30
  18Q GAIN WILD-TYPE 197 316
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     27   30
  18Q GAIN WILD-TYPE  197  316
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE               27                197
  MALE                 30                316
[1] 2 2
[1] FALSE
D33V4, continuous
                    vv
clus                 GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  18Q GAIN MUTATED                               0                   0
  18Q GAIN WILD-TYPE                            27                  18
                    vv
clus                 UNTREATED PRIMARY (DE NOVO) GBM
  18Q GAIN MUTATED                                57
  18Q GAIN WILD-TYPE                             468
D33V5, multiclass
                                 clus
vv                                18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                  0                 27
  TREATED PRIMARY GBM                            0                 18
  UNTREATED PRIMARY (DE NOVO) GBM               57                468
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V6, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    41  16
  18Q GAIN WILD-TYPE 341 172
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     41   16
  18Q GAIN WILD-TYPE  341  172
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  NO                41                341
  YES               16                172
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18Q GAIN MUTATED       0                         3    51
  18Q GAIN WILD-TYPE    13                        46   434
D33V7, multiclass
                           clus
vv                          18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  ASIAN                                    0                 13
  BLACK OR AFRICAN AMERICAN                3                 46
  WHITE                                   51                434
[1] 3 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
  18Q GAIN MUTATED     1  48
  18Q GAIN WILD-TYPE  11 424
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      1   48
  18Q GAIN WILD-TYPE   11  424
                        clus
vv                       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 11
  NOT HISPANIC OR LATINO               48                424
[1] 2 2
[1] FALSE

Clustering(34) Variable = 19P GAIN MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                  0   1
  19P GAIN MUTATED    40 182
  19P GAIN WILD-TYPE  64 283
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
               222                347 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
               182                283 
$`19P GAIN MUTATED`
TCGA-02-0007 TCGA-02-0009 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 
       23.18        10.59        20.61        87.06        77.65        20.12 
TCGA-02-0037 TCGA-02-0038 TCGA-02-0043 TCGA-02-0051 TCGA-02-0057 TCGA-02-0064 
        3.62        10.72        18.31        15.09        19.86        19.73 
TCGA-02-0068 TCGA-02-0070 TCGA-02-0071 TCGA-02-0074 TCGA-02-0075 TCGA-02-0102 
       26.43        25.05         5.49        10.19        20.84        27.02 
TCGA-02-0106 TCGA-02-0111 TCGA-02-0113 TCGA-02-0114 TCGA-02-0115 TCGA-02-0116 
       11.67        23.18        92.65        99.98        15.65        48.95 
TCGA-02-0258 TCGA-02-0260 TCGA-02-0266 TCGA-02-0269 TCGA-02-0285 TCGA-02-0289 
       16.54        16.93        17.72        10.75        13.87        14.20 
TCGA-02-0290 TCGA-02-0333 TCGA-02-0430 TCGA-02-2485 TCGA-06-0119 TCGA-06-0122 
       15.95         4.37        10.55        15.45         2.70         6.15 
TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0137 TCGA-06-0145 
       20.38        47.61         6.94         3.98        26.70         2.33 
TCGA-06-0147 TCGA-06-0148 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 
       17.79        10.09        19.46        46.59        12.33        13.94 
TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0164 TCGA-06-0173 
       10.45         3.19        10.82         9.44        56.91         4.47 
TCGA-06-0174 TCGA-06-0177 TCGA-06-0179 TCGA-06-0185 TCGA-06-0190 TCGA-06-0192 
        3.22         4.18        20.25        73.84        10.42        38.96 
TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0211 TCGA-06-0216 
        0.39         7.66         8.42         7.63        11.84        24.16 
TCGA-06-0221 TCGA-06-0237 TCGA-06-0394 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 
       19.82        13.64        10.82         0.26        72.36         4.70 
TCGA-06-0414 TCGA-06-0645 TCGA-06-0650 TCGA-06-0743 TCGA-06-0744 TCGA-06-0747 
       35.11         5.75        23.57        26.40        46.88         2.70 
TCGA-06-0877 TCGA-06-0879 TCGA-06-1086 TCGA-06-1087 TCGA-06-1802 TCGA-06-1806 
        5.65        40.41         6.84         4.04        15.32        15.32 
TCGA-06-2563 TCGA-06-2565 TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 TCGA-06-6388 
       30.64        16.64         8.98         8.55         6.71         5.23 
TCGA-06-6695 TCGA-06-6699 TCGA-06-A6S0 TCGA-08-0246 TCGA-08-0347 TCGA-08-0352 
        8.32         1.55         3.12         4.18        25.71         1.28 
TCGA-08-0353 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0375 TCGA-08-0386 
        8.42        24.56        31.10        37.58        12.23        18.02 
TCGA-08-0390 TCGA-08-0509 TCGA-08-0510 TCGA-08-0514 TCGA-08-0518 TCGA-08-0524 
       13.97        12.56         4.27        11.08        19.33         7.27 
TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0657 TCGA-12-0670 TCGA-12-0688 
       15.98        18.41         7.56         0.10        25.97        26.66 
TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0780 TCGA-12-0819 
       20.38        28.41        15.06        53.85        14.86        24.79 
TCGA-12-0826 TCGA-12-0829 TCGA-12-1094 TCGA-12-1099 TCGA-12-1598 TCGA-12-1599 
       27.78        20.58        12.23         4.14        15.65        25.68 
TCGA-12-1600 TCGA-12-1602 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3652 
       14.73         6.77        26.93        15.22        10.95        34.92 
TCGA-12-3653 TCGA-14-0783 TCGA-14-0789 TCGA-14-0790 TCGA-14-0817 TCGA-14-0866 
       14.53         6.21        11.24        13.78         5.39        26.33 
TCGA-14-0867 TCGA-14-1034 TCGA-14-1402 TCGA-14-1450 TCGA-14-1452 TCGA-14-1454 
        2.04        15.95        32.05        58.78         7.10        30.18 
TCGA-14-1823 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-4157 TCGA-15-1446 
       17.85         7.17        17.49         7.96         3.42        19.10 
TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 TCGA-16-1055 TCGA-16-1056 TCGA-16-1062 
       13.28         3.91        17.59        10.29        14.01        21.24 
TCGA-19-0955 TCGA-19-1386 TCGA-19-1388 TCGA-19-1390 TCGA-19-1392 TCGA-19-1786 
       11.77         9.07        12.95        25.38         3.65         7.17 
TCGA-19-1789 TCGA-19-2629 TCGA-19-5950 TCGA-19-5951 TCGA-19-5953 TCGA-19-5955 
        3.25        24.23        17.19         8.02         4.73         1.78 
TCGA-19-5958 TCGA-19-5959 TCGA-19-A60I TCGA-26-1799 TCGA-26-5139 TCGA-27-1833 
       14.07        16.80        17.79         9.37         1.58        24.23 
TCGA-27-2518 TCGA-27-2521 TCGA-27-2524 TCGA-27-2528 TCGA-28-1749 TCGA-28-1751 
       24.76        10.39         7.59        15.78         9.21         7.63 
TCGA-28-1752 TCGA-28-1753 TCGA-28-2502 TCGA-28-2506 TCGA-28-2513 TCGA-28-2514 
        8.48         1.22         0.66         6.74         7.30         5.26 
TCGA-28-5208 TCGA-28-5209 TCGA-28-5214 TCGA-28-5216 TCGA-28-5218 TCGA-28-6450 
       17.88        14.53        23.44        13.64         5.16         5.42 
TCGA-32-1970 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 TCGA-32-1982 TCGA-32-1987 
       15.39         0.10        15.85        19.50         4.67        14.86 
TCGA-32-2495 TCGA-32-2632 TCGA-32-2638 TCGA-32-4208 TCGA-32-4211 TCGA-32-5222 
       15.02         8.84        25.18        21.14        12.59        19.23 
TCGA-41-2572 TCGA-41-2575 TCGA-41-3393 TCGA-41-3915 TCGA-41-5651 TCGA-4W-AA9S 
       13.35         9.53         4.44        11.84        15.12         4.14 
TCGA-4W-AA9T TCGA-74-6578 TCGA-76-4934 TCGA-76-6280 TCGA-76-6656 TCGA-76-6661 
       14.76        14.33         2.53        11.38         4.83         0.23 
TCGA-76-6663 TCGA-76-6664 TCGA-81-5911 TCGA-87-5896 TCGA-RR-A6KA TCGA-RR-A6KC 
        7.73         7.79        17.72        26.30         6.28        20.55 

$`19P GAIN WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0010 TCGA-02-0011 TCGA-02-0014 
       11.77         4.73        18.35        35.41        20.71        82.59 
TCGA-02-0024 TCGA-02-0025 TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 
       53.10        42.74        24.59        12.16        90.58         2.83 
TCGA-02-0034 TCGA-02-0039 TCGA-02-0046 TCGA-02-0047 TCGA-02-0048 TCGA-02-0052 
       14.14        10.52         6.87        14.73         3.22        12.59 
TCGA-02-0054 TCGA-02-0055 TCGA-02-0058 TCGA-02-0059 TCGA-02-0060 TCGA-02-0069 
        6.54         2.50         8.35         9.57         6.02        28.70 
TCGA-02-0079 TCGA-02-0080 TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 TCGA-02-0086 
       27.25        89.72        22.72        12.62        51.32         8.81 
TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 TCGA-02-0104 TCGA-02-0107 TCGA-02-0271 
       57.76        16.96         3.48        65.00        17.65        14.47 
TCGA-02-0281 TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 
        3.98        12.23         9.90         7.73        10.62         7.33 
TCGA-02-0330 TCGA-02-0332 TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 
       15.91        25.71        25.12        10.59        12.39        14.50 
TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 TCGA-02-2466 
       47.11        11.34         9.27        16.21         3.35        16.80 
TCGA-02-2470 TCGA-02-2483 TCGA-02-2486 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 
       12.92        15.32        20.32        22.72        33.67        12.95 
TCGA-06-0132 TCGA-06-0133 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 
       25.35        14.30        24.23        11.90         0.20        10.29 
TCGA-06-0142 TCGA-06-0143 TCGA-06-0146 TCGA-06-0149 TCGA-06-0160 TCGA-06-0162 
        2.20        11.74        20.09         8.61        11.80         3.42 
TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0175 
       10.65         5.85        19.66         3.29        13.12         4.04 
TCGA-06-0176 TCGA-06-0178 TCGA-06-0182 TCGA-06-0184 TCGA-06-0187 TCGA-06-0188 
       91.00        88.14         3.65        69.90        27.22        44.58 
TCGA-06-0189 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0210 TCGA-06-0213 
       15.42         4.67         7.40         5.56         7.40         0.53 
TCGA-06-0214 TCGA-06-0219 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0397 
       15.02         0.72        13.32        20.42        48.69         9.01 
TCGA-06-0412 TCGA-06-0413 TCGA-06-0644 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 
        9.57         3.16        12.62         5.75         9.80         2.10 
TCGA-06-0686 TCGA-06-0745 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 
       14.20         7.86         2.70         0.92        43.46        46.19 
TCGA-06-0878 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1800 
        7.17        16.57        20.78        26.76        23.93        26.79 
TCGA-06-1801 TCGA-06-1804 TCGA-06-1805 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 
       11.84        13.61        33.90         1.08        12.49         4.93 
TCGA-06-2561 TCGA-06-2562 TCGA-06-2564 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 
       17.65        12.56         5.95         5.98         4.37         0.43 
TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 
       31.50        11.74         3.55         8.35         4.54         8.81 
TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 TCGA-06-5859 TCGA-06-6389 TCGA-06-6390 
        2.73         3.75         6.15         4.57         7.79         5.39 
TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6697 TCGA-06-6698 TCGA-06-6700 
        1.48       120.56         7.36        12.85         4.77         4.77 
TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S1 TCGA-06-A7TK TCGA-06-A7TL 
        4.96         4.70         1.87         2.56         5.39         5.42 
TCGA-08-0244 TCGA-08-0245 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0348 
       22.68        37.84       115.86         1.74         8.42        12.16 
TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0354 TCGA-08-0358 TCGA-08-0359 
        9.80        29.23        65.33        17.95        22.29         3.39 
TCGA-08-0380 TCGA-08-0389 TCGA-08-0392 TCGA-08-0512 TCGA-08-0516 TCGA-08-0517 
       14.93        15.35         0.72        42.15        19.59        58.68 
TCGA-08-0520 TCGA-08-0521 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 
       10.75         4.80        15.35        14.73        12.99        34.92 
TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0662 TCGA-12-0691 TCGA-12-0692 
       10.45         7.59        94.78        38.17        12.13         3.65 
TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0818 TCGA-12-0820 
       43.23         7.63         9.73        14.93        91.76        18.48 
TCGA-12-0821 TCGA-12-0822 TCGA-12-0827 TCGA-12-0828 TCGA-12-1088 TCGA-12-1089 
       10.62        23.51        38.76         8.94       127.59         5.82 
TCGA-12-1090 TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 TCGA-12-1095 TCGA-12-1096 
        7.59        33.21        21.73        15.98        15.85         9.11 
TCGA-12-1097 TCGA-12-1098 TCGA-12-3644 TCGA-12-3646 TCGA-12-3651 TCGA-12-5295 
       14.53         3.98        59.77        44.02        12.69        14.93 
TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 TCGA-14-0786 
        3.22         2.04        15.12        11.97         0.95        23.05 
TCGA-14-0787 TCGA-14-0812 TCGA-14-0813 TCGA-14-0862 TCGA-14-0865 TCGA-14-0871 
        2.24         3.25         1.35         2.89        16.50        28.93 
TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 TCGA-14-1451 
       19.30         0.79         1.38         1.12         3.75        23.11 
TCGA-14-1453 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 TCGA-14-1794 
        1.15         0.92        40.96         6.67        12.43         0.99 
TCGA-14-1795 TCGA-14-1821 TCGA-14-1825 TCGA-14-1827 TCGA-14-3477 TCGA-15-0742 
        1.97        17.79         7.63         5.88         3.78        13.78 
TCGA-15-1444 TCGA-15-1447 TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 
       50.53        53.19        26.07        16.37         4.31        29.03 
TCGA-16-1047 TCGA-16-1060 TCGA-16-1063 TCGA-16-1460 TCGA-19-0957 TCGA-19-0960 
        4.57         9.14        13.97         6.41        21.90         8.61 
TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 TCGA-19-1387 TCGA-19-1389 
        0.66        14.27         3.39        10.75         5.95         4.64 
TCGA-19-1787 TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 
       12.66         0.13         9.67         4.87         1.08         7.53 
TCGA-19-2624 TCGA-19-2625 TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 TCGA-19-5952 
        0.16         4.08         7.00         7.04         6.64        18.90 
TCGA-19-5954 TCGA-19-5956 TCGA-19-5960 TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 
       12.10        22.49        14.96         3.98        28.54        10.03 
TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 TCGA-26-5132 TCGA-26-5133 
       13.87         9.73        31.33         7.13         9.40        14.86 
TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 TCGA-26-6173 TCGA-26-6174 TCGA-26-A7UX 
        5.49         8.88        18.97         7.92         2.33        19.33 
TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 
        5.06        16.60         9.86        40.54        21.30        30.05 
TCGA-27-1837 TCGA-27-1838 TCGA-27-2519 TCGA-27-2523 TCGA-27-2526 TCGA-27-2527 
       14.04        11.51        10.39        16.08         2.86        14.40 
TCGA-28-1746 TCGA-28-1747 TCGA-28-1750 TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 
        0.20         2.53         8.35         1.55         2.83         0.13 
TCGA-28-2509 TCGA-28-5204 TCGA-28-5207 TCGA-28-5211 TCGA-28-5213 TCGA-28-5215 
        4.77        14.93        11.28        11.77        31.27        11.01 
TCGA-28-5219 TCGA-28-5220 TCGA-32-1973 TCGA-32-1976 TCGA-32-1980 TCGA-32-1986 
       22.68        12.76        21.07         0.49         1.18        12.69 
TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 TCGA-32-2615 TCGA-32-2616 TCGA-32-2634 
       16.93        12.23        20.78        15.95         7.36        22.78 
TCGA-32-4210 TCGA-32-4213 TCGA-32-4719 TCGA-41-2571 TCGA-41-2573 TCGA-41-3392 
        3.72        19.86        10.85         0.85         8.94         0.99 
TCGA-41-4097 TCGA-41-6646 TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6581 
        0.20        12.46         3.45        20.91         4.34         8.22 
TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 
        7.50         4.80         4.54         3.09         3.65         9.17 
TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6282 TCGA-76-6285 
       10.78        16.70         3.29         2.70        17.06         8.35 
TCGA-76-6286 TCGA-76-6657 TCGA-76-6662 TCGA-81-5910 TCGA-OX-A56R 
       20.98         5.03         9.27         1.61         5.92 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              0.10               0.13 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             99.98             127.59 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            13.825             10.780 
[1] "0.1 - 100.0 (13.8)" "0.1 - 127.6 (10.8)"
[1] "hr=" "1.1"
D34V2, continuous
D34V3, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    89 133
  19P GAIN WILD-TYPE 135 213
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     89  133
  19P GAIN WILD-TYPE  135  213
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE               89                135
  MALE                133                213
[1] 2 2
[1] FALSE
D34V4, continuous
                    vv
clus                 GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  19P GAIN MUTATED                              11                   9
  19P GAIN WILD-TYPE                            16                   9
                    vv
clus                 UNTREATED PRIMARY (DE NOVO) GBM
  19P GAIN MUTATED                               202
  19P GAIN WILD-TYPE                             323
D34V5, multiclass
                                 clus
vv                                19P GAIN MUTATED 19P GAIN WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                 11                 16
  TREATED PRIMARY GBM                            9                  9
  UNTREATED PRIMARY (DE NOVO) GBM              202                323
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V6, binary
                    cls
clus                   0   1
  19P GAIN MUTATED   150  72
  19P GAIN WILD-TYPE 232 116
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED    150   72
  19P GAIN WILD-TYPE  232  116
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  NO               150                232
  YES               72                116
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19P GAIN MUTATED       7                        20   188
  19P GAIN WILD-TYPE     6                        29   297
D34V7, multiclass
                           clus
vv                          19P GAIN MUTATED 19P GAIN WILD-TYPE
  ASIAN                                    7                  6
  BLACK OR AFRICAN AMERICAN               20                 29
  WHITE                                  188                297
[1] 3 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
  19P GAIN MUTATED     6 183
  19P GAIN WILD-TYPE   6 289
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      6  183
  19P GAIN WILD-TYPE    6  289
                        clus
vv                       19P GAIN MUTATED 19P GAIN WILD-TYPE
  HISPANIC OR LATINO                    6                  6
  NOT HISPANIC OR LATINO              183                289
[1] 2 2
[1] FALSE

Clustering(35) Variable = 19Q GAIN MUTATION ANALYSIS
D35V1, survival
                    sevent
clus2                  0   1
  19Q GAIN MUTATED    35 161
  19Q GAIN WILD-TYPE  69 304
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
               196                373 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
               161                304 
$`19Q GAIN MUTATED`
TCGA-02-0009 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0037 
       10.59        20.61        87.06        77.65        20.12         3.62 
TCGA-02-0038 TCGA-02-0043 TCGA-02-0051 TCGA-02-0057 TCGA-02-0064 TCGA-02-0068 
       10.72        18.31        15.09        19.86        19.73        26.43 
TCGA-02-0070 TCGA-02-0071 TCGA-02-0074 TCGA-02-0075 TCGA-02-0102 TCGA-02-0106 
       25.05         5.49        10.19        20.84        27.02        11.67 
TCGA-02-0111 TCGA-02-0113 TCGA-02-0115 TCGA-02-0116 TCGA-02-0260 TCGA-02-0266 
       23.18        92.65        15.65        48.95        16.93        17.72 
TCGA-02-0269 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 TCGA-02-0333 TCGA-02-0430 
       10.75        13.87        14.20        15.95         4.37        10.55 
TCGA-02-2485 TCGA-06-0119 TCGA-06-0122 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 
       15.45         2.70         6.15        47.61         6.94         3.98 
TCGA-06-0137 TCGA-06-0145 TCGA-06-0147 TCGA-06-0148 TCGA-06-0150 TCGA-06-0151 
       26.70         2.33        17.79        10.09        19.46        46.59 
TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0164 TCGA-06-0173 
       10.45         3.19        10.82         9.44        56.91         4.47 
TCGA-06-0174 TCGA-06-0177 TCGA-06-0179 TCGA-06-0182 TCGA-06-0185 TCGA-06-0190 
        3.22         4.18        20.25         3.65        73.84        10.42 
TCGA-06-0192 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0211 
       38.96         0.39         7.66         8.42         7.63        11.84 
TCGA-06-0216 TCGA-06-0237 TCGA-06-0394 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 
       24.16        13.64        10.82         0.26        72.36         4.70 
TCGA-06-0414 TCGA-06-0645 TCGA-06-0650 TCGA-06-0743 TCGA-06-0744 TCGA-06-0877 
       35.11         5.75        23.57        26.40        46.88         5.65 
TCGA-06-0879 TCGA-06-1086 TCGA-06-1087 TCGA-06-1802 TCGA-06-1806 TCGA-06-2563 
       40.41         6.84         4.04        15.32        15.32        30.64 
TCGA-06-2565 TCGA-06-5414 TCGA-06-5415 TCGA-06-6388 TCGA-06-6695 TCGA-06-A6S0 
       16.64         8.98         8.55         5.23         8.32         3.12 
TCGA-08-0246 TCGA-08-0347 TCGA-08-0352 TCGA-08-0355 TCGA-08-0356 TCGA-08-0375 
        4.18        25.71         1.28        24.56        31.10        12.23 
TCGA-08-0386 TCGA-08-0390 TCGA-08-0509 TCGA-08-0510 TCGA-08-0514 TCGA-08-0518 
       18.02        13.97        12.56         4.27        11.08        19.33 
TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0657 TCGA-12-0670 
        7.27        15.98        18.41         7.56         0.10        25.97 
TCGA-12-0688 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0778 
       26.66        20.38        28.41        15.06        53.85        14.93 
TCGA-12-0780 TCGA-12-0819 TCGA-12-0826 TCGA-12-0829 TCGA-12-1094 TCGA-12-1099 
       14.86        24.79        27.78        20.58        12.23         4.14 
TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 
       25.68        14.73         6.77        26.93        15.22        10.95 
TCGA-12-3652 TCGA-12-3653 TCGA-14-0789 TCGA-14-0790 TCGA-14-0817 TCGA-14-0866 
       34.92        14.53        11.24        13.78         5.39        26.33 
TCGA-14-0867 TCGA-14-1034 TCGA-14-1402 TCGA-14-1450 TCGA-14-1454 TCGA-14-1823 
        2.04        15.95        32.05        58.78        30.18        17.85 
TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-3477 TCGA-15-1446 TCGA-16-0846 
        7.17        17.49         7.96         3.78        19.10         3.91 
TCGA-16-0848 TCGA-16-1055 TCGA-16-1062 TCGA-19-0955 TCGA-19-1386 TCGA-19-1390 
       17.59        10.29        21.24        11.77         9.07        25.38 
TCGA-19-1392 TCGA-19-1786 TCGA-19-1789 TCGA-19-2620 TCGA-19-5950 TCGA-19-5953 
        3.65         7.17         3.25         4.87        17.19         4.73 
TCGA-19-5955 TCGA-26-1799 TCGA-26-5139 TCGA-27-1833 TCGA-27-2518 TCGA-27-2521 
        1.78         9.37         1.58        24.23        24.76        10.39 
TCGA-27-2524 TCGA-27-2528 TCGA-28-1749 TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 
        7.59        15.78         9.21         7.63         8.48         1.22 
TCGA-28-2506 TCGA-28-2513 TCGA-28-2514 TCGA-28-5208 TCGA-28-5209 TCGA-28-5214 
        6.74         7.30         5.26        17.88        14.53        23.44 
TCGA-28-5216 TCGA-28-5218 TCGA-28-6450 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 
       13.64         5.16         5.42         0.10        15.85        19.50 
TCGA-32-1982 TCGA-32-2495 TCGA-32-2632 TCGA-32-2638 TCGA-32-5222 TCGA-41-2572 
        4.67        15.02         8.84        25.18        19.23        13.35 
TCGA-41-3393 TCGA-41-3915 TCGA-41-5651 TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6578 
        4.44        11.84        15.12         4.14        14.76        14.33 
TCGA-76-4934 TCGA-76-6280 TCGA-76-6656 TCGA-76-6661 TCGA-76-6663 TCGA-76-6664 
        2.53        11.38         4.83         0.23         7.73         7.79 
TCGA-81-5911 TCGA-87-5896 TCGA-RR-A6KA TCGA-RR-A6KC 
       17.72        26.30         6.28        20.55 

$`19Q GAIN WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0010 TCGA-02-0011 
       11.77         4.73        18.35        23.18        35.41        20.71 
TCGA-02-0014 TCGA-02-0024 TCGA-02-0025 TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 
       82.59        53.10        42.74        24.59        12.16        90.58 
TCGA-02-0033 TCGA-02-0034 TCGA-02-0039 TCGA-02-0046 TCGA-02-0047 TCGA-02-0048 
        2.83        14.14        10.52         6.87        14.73         3.22 
TCGA-02-0052 TCGA-02-0054 TCGA-02-0055 TCGA-02-0058 TCGA-02-0059 TCGA-02-0060 
       12.59         6.54         2.50         8.35         9.57         6.02 
TCGA-02-0069 TCGA-02-0079 TCGA-02-0080 TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 
       28.70        27.25        89.72        22.72        12.62        51.32 
TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 TCGA-02-0104 TCGA-02-0107 
        8.81        57.76        16.96         3.48        65.00        17.65 
TCGA-02-0114 TCGA-02-0258 TCGA-02-0271 TCGA-02-0281 TCGA-02-0317 TCGA-02-0321 
       99.98        16.54        14.47         3.98        12.23         9.90 
TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 TCGA-02-0337 
        7.73        10.62         7.33        15.91        25.71        25.12 
TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 
       10.59        12.39        14.50        47.11        11.34         9.27 
TCGA-02-0451 TCGA-02-0456 TCGA-02-2466 TCGA-02-2470 TCGA-02-2483 TCGA-02-2486 
       16.21         3.35        16.80        12.92        15.32        20.32 
TCGA-06-0124 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 
       20.38        22.72        33.67        12.95        25.35        14.30 
TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 
       24.23        11.90         0.20        10.29         2.20        11.74 
TCGA-06-0146 TCGA-06-0149 TCGA-06-0152 TCGA-06-0154 TCGA-06-0160 TCGA-06-0162 
       20.09         8.61        12.33        13.94        11.80         3.42 
TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0175 
       10.65         5.85        19.66         3.29        13.12         4.04 
TCGA-06-0176 TCGA-06-0178 TCGA-06-0184 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 
       91.00        88.14        69.90        27.22        44.58        15.42 
TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0210 TCGA-06-0213 TCGA-06-0214 
        4.67         7.40         5.56         7.40         0.53        15.02 
TCGA-06-0219 TCGA-06-0221 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0397 
        0.72        19.82        13.32        20.42        48.69         9.01 
TCGA-06-0412 TCGA-06-0413 TCGA-06-0644 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 
        9.57         3.16        12.62         5.75         9.80         2.10 
TCGA-06-0686 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 
       14.20         7.86         2.70         2.70         0.92        43.46 
TCGA-06-0876 TCGA-06-0878 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 
       46.19         7.17        16.57        20.78        26.76        23.93 
TCGA-06-1800 TCGA-06-1801 TCGA-06-1804 TCGA-06-1805 TCGA-06-2557 TCGA-06-2558 
       26.79        11.84        13.61        33.90         1.08        12.49 
TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2564 TCGA-06-2566 TCGA-06-2567 
        4.93        17.65        12.56         5.95         5.98         4.37 
TCGA-06-2569 TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 
        0.43        31.50        11.74         3.55         8.35         4.54 
TCGA-06-5413 TCGA-06-5416 TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 TCGA-06-5859 
        8.81         6.71         2.73         3.75         6.15         4.57 
TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6697 
        7.79         5.39         1.48       120.56         7.36        12.85 
TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A5U1 
        4.77         1.55         4.77         4.96         4.70         1.87 
TCGA-06-A6S1 TCGA-06-A7TK TCGA-06-A7TL TCGA-08-0244 TCGA-08-0245 TCGA-08-0344 
        2.56         5.39         5.42        22.68        37.84       115.86 
TCGA-08-0345 TCGA-08-0346 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 
        1.74         8.42        12.16         9.80        29.23        65.33 
TCGA-08-0353 TCGA-08-0354 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0380 
        8.42        17.95        37.58        22.29         3.39        14.93 
TCGA-08-0389 TCGA-08-0392 TCGA-08-0512 TCGA-08-0516 TCGA-08-0517 TCGA-08-0520 
       15.35         0.72        42.15        19.59        58.68        10.75 
TCGA-08-0521 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 
        4.80        15.35        14.73        12.99        34.92        10.45 
TCGA-12-0654 TCGA-12-0656 TCGA-12-0662 TCGA-12-0691 TCGA-12-0692 TCGA-12-0773 
        7.59        94.78        38.17        12.13         3.65        43.23 
TCGA-12-0775 TCGA-12-0776 TCGA-12-0818 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 
        7.63         9.73        91.76        18.48        10.62        23.51 
TCGA-12-0827 TCGA-12-0828 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 
       38.76         8.94       127.59         5.82         7.59        33.21 
TCGA-12-1092 TCGA-12-1093 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 
       21.73        15.98        15.85         9.11        14.53         3.98 
TCGA-12-1598 TCGA-12-3644 TCGA-12-3646 TCGA-12-3651 TCGA-12-5295 TCGA-12-5299 
       15.65        59.77        44.02        12.69        14.93         3.22 
TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 
        2.04        15.12        11.97         0.95         6.21        23.05 
TCGA-14-0787 TCGA-14-0812 TCGA-14-0813 TCGA-14-0862 TCGA-14-0865 TCGA-14-0871 
        2.24         3.25         1.35         2.89        16.50        28.93 
TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 TCGA-14-1451 
       19.30         0.79         1.38         1.12         3.75        23.11 
TCGA-14-1452 TCGA-14-1453 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 
        7.10         1.15         0.92        40.96         6.67        12.43 
TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 TCGA-14-1825 TCGA-14-1827 TCGA-14-4157 
        0.99         1.97        17.79         7.63         5.88         3.42 
TCGA-15-0742 TCGA-15-1444 TCGA-15-1447 TCGA-15-1449 TCGA-16-0849 TCGA-16-0850 
       13.78        50.53        53.19        13.28        26.07        16.37 
TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1056 TCGA-16-1060 TCGA-16-1063 
        4.31        29.03         4.57        14.01         9.14        13.97 
TCGA-16-1460 TCGA-19-0957 TCGA-19-0960 TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 
        6.41        21.90         8.61         0.66        14.27         3.39 
TCGA-19-1385 TCGA-19-1387 TCGA-19-1388 TCGA-19-1389 TCGA-19-1787 TCGA-19-1791 
       10.75         5.95        12.95         4.64        12.66         0.13 
TCGA-19-2619 TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 
        9.67         1.08         7.53         0.16         4.08        24.23 
TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 TCGA-19-5951 TCGA-19-5952 TCGA-19-5954 
        7.00         7.04         6.64         8.02        18.90        12.10 
TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J4 
       22.49        14.07        16.80        14.96        17.79         3.98 
TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 
       28.54        10.03        13.87         9.73        31.33         7.13 
TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 TCGA-26-6173 
        9.40        14.86         5.49         8.88        18.97         7.92 
TCGA-26-6174 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1834 
        2.33        19.33         5.06        16.60         9.86        40.54 
TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2519 TCGA-27-2523 
       21.30        30.05        14.04        11.51        10.39        16.08 
TCGA-27-2526 TCGA-27-2527 TCGA-28-1746 TCGA-28-1747 TCGA-28-1750 TCGA-28-1755 
        2.86        14.40         0.20         2.53         8.35         1.55 
TCGA-28-1756 TCGA-28-1757 TCGA-28-2502 TCGA-28-2509 TCGA-28-5204 TCGA-28-5207 
        2.83         0.13         0.66         4.77        14.93        11.28 
TCGA-28-5211 TCGA-28-5213 TCGA-28-5215 TCGA-28-5219 TCGA-28-5220 TCGA-32-1970 
       11.77        31.27        11.01        22.68        12.76        15.39 
TCGA-32-1973 TCGA-32-1976 TCGA-32-1980 TCGA-32-1986 TCGA-32-1987 TCGA-32-1991 
       21.07         0.49         1.18        12.69        14.86        16.93 
TCGA-32-2491 TCGA-32-2494 TCGA-32-2615 TCGA-32-2616 TCGA-32-2634 TCGA-32-4208 
       12.23        20.78        15.95         7.36        22.78        21.14 
TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-41-2571 TCGA-41-2573 
        3.72        12.59        19.86        10.85         0.85         8.94 
TCGA-41-2575 TCGA-41-3392 TCGA-41-4097 TCGA-41-6646 TCGA-74-6573 TCGA-74-6575 
        9.53         0.99         0.20        12.46         3.45        20.91 
TCGA-74-6577 TCGA-74-6581 TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 
        4.34         8.22         7.50         4.80         4.54         3.09 
TCGA-76-4929 TCGA-76-4931 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 
        3.65         9.17        10.78        16.70         3.29         2.70 
TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6657 TCGA-76-6662 TCGA-81-5910 
       17.06         8.35        20.98         5.03         9.27         1.61 
TCGA-OX-A56R 
        5.92 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              0.10               0.13 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             92.65             127.59 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             13.64              11.74 
[1] "0.1 - 92.7 (13.6)"  "0.1 - 127.6 (11.7)"
[1] "hr=" "1"  
D35V2, continuous
D35V3, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    80 116
  19Q GAIN WILD-TYPE 144 230
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     80  116
  19Q GAIN WILD-TYPE  144  230
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE               80                144
  MALE                116                230
[1] 2 2
[1] FALSE
D35V4, continuous
                    vv
clus                 GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  19Q GAIN MUTATED                              10                   7
  19Q GAIN WILD-TYPE                            17                  11
                    vv
clus                 UNTREATED PRIMARY (DE NOVO) GBM
  19Q GAIN MUTATED                               179
  19Q GAIN WILD-TYPE                             346
D35V5, multiclass
                                 clus
vv                                19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                 10                 17
  TREATED PRIMARY GBM                            7                 11
  UNTREATED PRIMARY (DE NOVO) GBM              179                346
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V6, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED   128  68
  19Q GAIN WILD-TYPE 254 120
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED    128   68
  19Q GAIN WILD-TYPE  254  120
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  NO               128                254
  YES               68                120
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19Q GAIN MUTATED       7                        18   164
  19Q GAIN WILD-TYPE     6                        31   321
D35V7, multiclass
                           clus
vv                          19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  ASIAN                                    7                  6
  BLACK OR AFRICAN AMERICAN               18                 31
  WHITE                                  164                321
[1] 3 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
  19Q GAIN MUTATED     6 162
  19Q GAIN WILD-TYPE   6 310
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      6  162
  19Q GAIN WILD-TYPE    6  310
                        clus
vv                       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    6                  6
  NOT HISPANIC OR LATINO              162                310
[1] 2 2
[1] FALSE

Clustering(36) Variable = 20P GAIN MUTATION ANALYSIS
D36V1, survival
                    sevent
clus2                  0   1
  20P GAIN MUTATED    32 188
  20P GAIN WILD-TYPE  72 277
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               220                349 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               188                277 
$`20P GAIN MUTATED`
TCGA-02-0006 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0025 TCGA-02-0034 
       18.35        20.61        87.06        77.65        42.74        14.14 
TCGA-02-0037 TCGA-02-0043 TCGA-02-0054 TCGA-02-0055 TCGA-02-0057 TCGA-02-0068 
        3.62        18.31         6.54         2.50        19.86        26.43 
TCGA-02-0074 TCGA-02-0075 TCGA-02-0083 TCGA-02-0084 TCGA-02-0086 TCGA-02-0089 
       10.19        20.84        22.72        12.62         8.81        16.96 
TCGA-02-0106 TCGA-02-0111 TCGA-02-0113 TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 
       11.67        23.18        92.65        15.65        48.95        16.54 
TCGA-02-0266 TCGA-02-0269 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 TCGA-02-0333 
       17.72        10.75        13.87        14.20        15.95         4.37 
TCGA-02-0456 TCGA-02-2466 TCGA-02-2483 TCGA-06-0119 TCGA-06-0122 TCGA-06-0125 
        3.35        16.80        15.32         2.70         6.15        47.61 
TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0130 TCGA-06-0137 TCGA-06-0147 
        6.94         3.98        22.72        12.95        26.70        17.79 
TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 
       10.09         8.61        19.46        46.59        12.33        13.94 
TCGA-06-0157 TCGA-06-0158 TCGA-06-0164 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 
        3.19        10.82        56.91         3.29        13.12         4.47 
TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 TCGA-06-0179 TCGA-06-0182 
        3.22         4.04        91.00         4.18        20.25         3.65 
TCGA-06-0185 TCGA-06-0189 TCGA-06-0192 TCGA-06-0195 TCGA-06-0197 TCGA-06-0206 
       73.84        15.42        38.96         7.40         5.56         7.66 
TCGA-06-0209 TCGA-06-0211 TCGA-06-0216 TCGA-06-0237 TCGA-06-0397 TCGA-06-0402 
        7.63        11.84        24.16        13.64         9.01         0.26 
TCGA-06-0409 TCGA-06-0410 TCGA-06-0644 TCGA-06-0645 TCGA-06-0743 TCGA-06-0745 
       72.36         4.70        12.62         5.75        26.40         7.86 
TCGA-06-0747 TCGA-06-0877 TCGA-06-0882 TCGA-06-1087 TCGA-06-1802 TCGA-06-1806 
        2.70         5.65        20.78         4.04        15.32        15.32 
TCGA-06-2557 TCGA-06-2562 TCGA-06-2563 TCGA-06-2565 TCGA-06-2569 TCGA-06-5414 
        1.08        12.56        30.64        16.64         0.43         8.98 
TCGA-06-5415 TCGA-06-5856 TCGA-06-6388 TCGA-06-6390 TCGA-06-6695 TCGA-06-6697 
        8.55         3.75         5.23         5.39         8.32        12.85 
TCGA-06-6698 TCGA-06-A5U1 TCGA-06-A7TK TCGA-08-0246 TCGA-08-0352 TCGA-08-0355 
        4.77         1.87         5.39         4.18         1.28        24.56 
TCGA-08-0356 TCGA-08-0357 TCGA-08-0375 TCGA-08-0386 TCGA-08-0510 TCGA-08-0514 
       31.10        37.58        12.23        18.02         4.27        11.08 
TCGA-08-0516 TCGA-08-0518 TCGA-08-0529 TCGA-08-0531 TCGA-12-0656 TCGA-12-0670 
       19.59        19.33        18.41         7.56        94.78        25.97 
TCGA-12-0688 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0778 TCGA-12-0780 
       26.66         3.65        20.38        28.41        14.93        14.86 
TCGA-12-0819 TCGA-12-0820 TCGA-12-0826 TCGA-12-0827 TCGA-12-0829 TCGA-12-1093 
       24.79        18.48        27.78        38.76        20.58        15.98 
TCGA-12-1094 TCGA-12-1095 TCGA-12-1600 TCGA-12-1602 TCGA-12-3646 TCGA-12-3648 
       12.23        15.85        14.73         6.77        44.02        26.93 
TCGA-12-3649 TCGA-12-3652 TCGA-12-3653 TCGA-14-0740 TCGA-14-0783 TCGA-14-0786 
       15.22        34.92        14.53        11.97         6.21        23.05 
TCGA-14-0787 TCGA-14-0790 TCGA-14-0817 TCGA-14-0866 TCGA-14-0871 TCGA-14-1043 
        2.24        13.78         5.39        26.33        28.93         0.79 
TCGA-14-1395 TCGA-14-1402 TCGA-14-1452 TCGA-14-1453 TCGA-14-1823 TCGA-14-2554 
        1.38        32.05         7.10         1.15        17.85        17.49 
TCGA-14-2555 TCGA-15-0742 TCGA-15-1447 TCGA-15-1449 TCGA-16-0846 TCGA-16-0861 
        7.96        13.78        53.19        13.28         3.91         4.31 
TCGA-16-1060 TCGA-16-1062 TCGA-19-0955 TCGA-19-1386 TCGA-19-1388 TCGA-19-1392 
        9.14        21.24        11.77         9.07        12.95         3.65 
TCGA-19-1786 TCGA-19-1789 TCGA-19-2631 TCGA-19-5950 TCGA-19-5951 TCGA-19-5954 
        7.17         3.25         7.00        17.19         8.02        12.10 
TCGA-19-5958 TCGA-19-5959 TCGA-26-1439 TCGA-26-1440 TCGA-26-1799 TCGA-26-6173 
       14.07        16.80        13.87         9.73         9.37         7.92 
TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-2519 TCGA-27-2523 TCGA-27-2526 
       24.23        40.54        21.30        10.39        16.08         2.86 
TCGA-27-2527 TCGA-27-2528 TCGA-28-1749 TCGA-28-1751 TCGA-28-2506 TCGA-28-2509 
       14.40        15.78         9.21         7.63         6.74         4.77 
TCGA-28-2513 TCGA-28-5215 TCGA-28-5218 TCGA-28-6450 TCGA-32-1977 TCGA-32-1978 
        7.30        11.01         5.16         5.42         0.10        15.85 
TCGA-32-1979 TCGA-32-1980 TCGA-32-2491 TCGA-32-2495 TCGA-32-2615 TCGA-32-2632 
       19.50         1.18        12.23        15.02        15.95         8.84 
TCGA-32-2634 TCGA-32-2638 TCGA-32-4210 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 
       22.78        25.18         3.72        19.23         0.85        13.35 
TCGA-41-2575 TCGA-41-3393 TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9S TCGA-74-6575 
        9.53         4.44        15.12        12.46         4.14        20.91 
TCGA-74-6581 TCGA-76-4925 TCGA-76-4929 TCGA-76-6280 TCGA-76-6656 TCGA-76-6657 
        8.22         4.80         3.65        11.38         4.83         5.03 
TCGA-76-6661 TCGA-76-6664 TCGA-RR-A6KA TCGA-RR-A6KC 
        0.23         7.79         6.28        20.55 

$`20P GAIN WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 TCGA-02-0011 
       11.77         4.73        23.18        10.59        35.41        20.71 
TCGA-02-0014 TCGA-02-0023 TCGA-02-0024 TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 
       82.59        20.12        53.10        24.59        12.16        90.58 
TCGA-02-0033 TCGA-02-0038 TCGA-02-0039 TCGA-02-0046 TCGA-02-0047 TCGA-02-0048 
        2.83        10.72        10.52         6.87        14.73         3.22 
TCGA-02-0051 TCGA-02-0052 TCGA-02-0058 TCGA-02-0059 TCGA-02-0060 TCGA-02-0064 
       15.09        12.59         8.35         9.57         6.02        19.73 
TCGA-02-0069 TCGA-02-0070 TCGA-02-0071 TCGA-02-0079 TCGA-02-0080 TCGA-02-0085 
       28.70        25.05         5.49        27.25        89.72        51.32 
TCGA-02-0087 TCGA-02-0099 TCGA-02-0102 TCGA-02-0104 TCGA-02-0107 TCGA-02-0114 
       57.76         3.48        27.02        65.00        17.65        99.98 
TCGA-02-0260 TCGA-02-0271 TCGA-02-0281 TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 
       16.93        14.47         3.98        12.23         9.90         7.73 
TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 TCGA-02-0337 TCGA-02-0338 
       10.62         7.33        15.91        25.71        25.12        10.59 
TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 
       12.39        14.50        10.55        47.11        11.34         9.27 
TCGA-02-0451 TCGA-02-2470 TCGA-02-2485 TCGA-02-2486 TCGA-06-0124 TCGA-06-0129 
       16.21        12.92        15.45        20.32        20.38        33.67 
TCGA-06-0132 TCGA-06-0133 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 
       25.35        14.30        24.23        11.90         0.20        10.29 
TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0155 TCGA-06-0159 
        2.20        11.74         2.33        20.09        10.45         9.44 
TCGA-06-0160 TCGA-06-0162 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0178 
       11.80         3.42        10.65         5.85        19.66        88.14 
TCGA-06-0184 TCGA-06-0187 TCGA-06-0188 TCGA-06-0190 TCGA-06-0194 TCGA-06-0201 
       69.90        27.22        44.58        10.42         4.67         0.39 
TCGA-06-0208 TCGA-06-0210 TCGA-06-0213 TCGA-06-0214 TCGA-06-0219 TCGA-06-0221 
        8.42         7.40         0.53        15.02         0.72        19.82 
TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0412 TCGA-06-0413 
       13.32        20.42        48.69        10.82         9.57         3.16 
TCGA-06-0414 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 
       35.11         5.75         9.80         2.10        23.57        14.20 
TCGA-06-0744 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0878 
       46.88         2.70         0.92        43.46        46.19         7.17 
TCGA-06-0879 TCGA-06-0881 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1800 
       40.41        16.57        26.76        23.93         6.84        26.79 
TCGA-06-1801 TCGA-06-1804 TCGA-06-1805 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 
       11.84        13.61        33.90        12.49         4.93        17.65 
TCGA-06-2564 TCGA-06-2566 TCGA-06-2567 TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 
        5.95         5.98         4.37        31.50        11.74         3.55 
TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 TCGA-06-5416 TCGA-06-5418 TCGA-06-5858 
        8.35         4.54         8.81         6.71         2.73         6.15 
TCGA-06-5859 TCGA-06-6389 TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6699 
        4.57         7.79         1.48       120.56         7.36         1.55 
TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TL 
        4.77         4.96         4.70         3.12         2.56         5.42 
TCGA-08-0244 TCGA-08-0245 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 
       22.68        37.84       115.86         1.74         8.42        25.71 
TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0353 TCGA-08-0354 
       12.16         9.80        29.23        65.33         8.42        17.95 
TCGA-08-0358 TCGA-08-0359 TCGA-08-0380 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 
       22.29         3.39        14.93        15.35        13.97         0.72 
TCGA-08-0509 TCGA-08-0512 TCGA-08-0517 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 
       12.56        42.15        58.68        10.75         4.80         7.27 
TCGA-08-0525 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 
       15.98        15.35        14.73        12.99        34.92        10.45 
TCGA-12-0654 TCGA-12-0657 TCGA-12-0662 TCGA-12-0691 TCGA-12-0769 TCGA-12-0772 
        7.59         0.10        38.17        12.13        15.06        53.85 
TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0818 TCGA-12-0821 TCGA-12-0822 
       43.23         7.63         9.73        91.76        10.62        23.51 
TCGA-12-0828 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 TCGA-12-1092 
        8.94       127.59         5.82         7.59        33.21        21.73 
TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 TCGA-12-1598 TCGA-12-1599 
        9.11        14.53         3.98         4.14        15.65        25.68 
TCGA-12-3644 TCGA-12-3650 TCGA-12-3651 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 
       59.77        10.95        12.69        14.93         3.22         2.04 
TCGA-14-0736 TCGA-14-0781 TCGA-14-0789 TCGA-14-0812 TCGA-14-0813 TCGA-14-0862 
       15.12         0.95        11.24         3.25         1.35         2.89 
TCGA-14-0865 TCGA-14-0867 TCGA-14-1034 TCGA-14-1037 TCGA-14-1396 TCGA-14-1401 
       16.50         2.04        15.95        19.30         1.12         3.75 
TCGA-14-1450 TCGA-14-1451 TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 
       58.78        23.11        30.18         0.92        40.96         6.67 
TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 TCGA-14-1825 TCGA-14-1827 
       12.43         0.99         1.97        17.79         7.63         5.88 
TCGA-14-1829 TCGA-14-3477 TCGA-14-4157 TCGA-15-1444 TCGA-15-1446 TCGA-16-0848 
        7.17         3.78         3.42        50.53        19.10        17.59 
TCGA-16-0849 TCGA-16-0850 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 
       26.07        16.37        29.03         4.57        10.29        14.01 
TCGA-16-1063 TCGA-16-1460 TCGA-19-0957 TCGA-19-0960 TCGA-19-0962 TCGA-19-0963 
       13.97         6.41        21.90         8.61         0.66        14.27 
TCGA-19-0964 TCGA-19-1385 TCGA-19-1387 TCGA-19-1389 TCGA-19-1390 TCGA-19-1787 
        3.39        10.75         5.95         4.64        25.38        12.66 
TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 
        0.13         9.67         4.87         1.08         7.53         0.16 
TCGA-19-2625 TCGA-19-2629 TCGA-19-4065 TCGA-19-5947 TCGA-19-5952 TCGA-19-5953 
        4.08        24.23         7.04         6.64        18.90         4.73 
TCGA-19-5955 TCGA-19-5956 TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J4 TCGA-19-A6J5 
        1.78        22.49        14.96        17.79         3.98        28.54 
TCGA-26-1438 TCGA-26-1442 TCGA-26-1443 TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 
       10.03        31.33         7.13         9.40        14.86         5.49 
TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 TCGA-26-6174 TCGA-26-A7UX TCGA-27-1830 
        8.88        18.97         1.58         2.33        19.33         5.06 
TCGA-27-1831 TCGA-27-1832 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 
       16.60         9.86        30.05        14.04        11.51        24.76 
TCGA-27-2521 TCGA-27-2524 TCGA-28-1746 TCGA-28-1747 TCGA-28-1750 TCGA-28-1752 
       10.39         7.59         0.20         2.53         8.35         8.48 
TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 TCGA-28-2502 TCGA-28-2514 
        1.22         1.55         2.83         0.13         0.66         5.26 
TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 
       14.93        11.28        17.88        14.53        11.77        31.27 
TCGA-28-5214 TCGA-28-5216 TCGA-28-5219 TCGA-28-5220 TCGA-32-1970 TCGA-32-1973 
       23.44        13.64        22.68        12.76        15.39        21.07 
TCGA-32-1976 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 TCGA-32-1991 TCGA-32-2494 
        0.49         4.67        12.69        14.86        16.93        20.78 
TCGA-32-2616 TCGA-32-4208 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-41-2573 
        7.36        21.14        12.59        19.86        10.85         8.94 
TCGA-41-3392 TCGA-41-3915 TCGA-41-4097 TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6577 
        0.99        11.84         0.20        14.76         3.45         4.34 
TCGA-74-6578 TCGA-74-6584 TCGA-76-4926 TCGA-76-4928 TCGA-76-4931 TCGA-76-4934 
       14.33         7.50         4.54         3.09         9.17         2.53 
TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6282 TCGA-76-6285 
       10.78        16.70         3.29         2.70        17.06         8.35 
TCGA-76-6286 TCGA-76-6662 TCGA-76-6663 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
       20.98         9.27         7.73         1.61        17.72        26.30 
TCGA-OX-A56R 
        5.92 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               0.1                0.1 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             94.78             127.59 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             12.59              11.34 
[1] "0.1 - 94.8 (12.6)"  "0.1 - 127.6 (11.3)"
[1] "hr=" "1.1"
D36V2, continuous
D36V3, binary
                    cls
clus                   0   1
  20P GAIN MUTATED    92 128
  20P GAIN WILD-TYPE 132 218
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     92  128
  20P GAIN WILD-TYPE  132  218
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE               92                132
  MALE                128                218
[1] 2 2
[1] FALSE
D36V4, continuous
                    vv
clus                 GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  20P GAIN MUTATED                               9                   9
  20P GAIN WILD-TYPE                            18                   9
                    vv
clus                 UNTREATED PRIMARY (DE NOVO) GBM
  20P GAIN MUTATED                               202
  20P GAIN WILD-TYPE                             323
D36V5, multiclass
                                 clus
vv                                20P GAIN MUTATED 20P GAIN WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                  9                 18
  TREATED PRIMARY GBM                            9                  9
  UNTREATED PRIMARY (DE NOVO) GBM              202                323
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V6, binary
                    cls
clus                   0   1
  20P GAIN MUTATED   151  69
  20P GAIN WILD-TYPE 231 119
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED    151   69
  20P GAIN WILD-TYPE  231  119
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  NO               151                231
  YES               69                119
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20P GAIN MUTATED       9                        15   191
  20P GAIN WILD-TYPE     4                        34   294
D36V7, multiclass
                           clus
vv                          20P GAIN MUTATED 20P GAIN WILD-TYPE
  ASIAN                                    9                  4
  BLACK OR AFRICAN AMERICAN               15                 34
  WHITE                                  191                294
[1] 3 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
  20P GAIN MUTATED     5 189
  20P GAIN WILD-TYPE   7 283
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      5  189
  20P GAIN WILD-TYPE    7  283
                        clus
vv                       20P GAIN MUTATED 20P GAIN WILD-TYPE
  HISPANIC OR LATINO                    5                  7
  NOT HISPANIC OR LATINO              189                283
[1] 2 2
[1] FALSE

Clustering(37) Variable = 20Q GAIN MUTATION ANALYSIS
D37V1, survival
                    sevent
clus2                  0   1
  20Q GAIN MUTATED    33 185
  20Q GAIN WILD-TYPE  71 280
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               218                351 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               185                280 
$`20Q GAIN MUTATED`
TCGA-02-0006 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0025 TCGA-02-0034 
       18.35        20.61        87.06        77.65        42.74        14.14 
TCGA-02-0037 TCGA-02-0038 TCGA-02-0043 TCGA-02-0054 TCGA-02-0055 TCGA-02-0057 
        3.62        10.72        18.31         6.54         2.50        19.86 
TCGA-02-0068 TCGA-02-0069 TCGA-02-0074 TCGA-02-0075 TCGA-02-0079 TCGA-02-0083 
       26.43        28.70        10.19        20.84        27.25        22.72 
TCGA-02-0084 TCGA-02-0086 TCGA-02-0089 TCGA-02-0106 TCGA-02-0111 TCGA-02-0113 
       12.62         8.81        16.96        11.67        23.18        92.65 
TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 TCGA-02-0266 TCGA-02-0269 TCGA-02-0285 
       15.65        48.95        16.54        17.72        10.75        13.87 
TCGA-02-0289 TCGA-02-0333 TCGA-02-0456 TCGA-02-2466 TCGA-06-0119 TCGA-06-0122 
       14.20         4.37         3.35        16.80         2.70         6.15 
TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0130 TCGA-06-0137 
       47.61         6.94         3.98        22.72        12.95        26.70 
TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 
       17.79        10.09         8.61        19.46        46.59        12.33 
TCGA-06-0154 TCGA-06-0157 TCGA-06-0158 TCGA-06-0164 TCGA-06-0169 TCGA-06-0171 
       13.94         3.19        10.82        56.91         3.29        13.12 
TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 TCGA-06-0179 
        4.47         3.22         4.04        91.00         4.18        20.25 
TCGA-06-0182 TCGA-06-0185 TCGA-06-0189 TCGA-06-0192 TCGA-06-0195 TCGA-06-0197 
        3.65        73.84        15.42        38.96         7.40         5.56 
TCGA-06-0206 TCGA-06-0209 TCGA-06-0211 TCGA-06-0216 TCGA-06-0237 TCGA-06-0394 
        7.66         7.63        11.84        24.16        13.64        10.82 
TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 TCGA-06-0644 TCGA-06-0645 
        9.01         0.26        72.36         4.70        12.62         5.75 
TCGA-06-0743 TCGA-06-0745 TCGA-06-0747 TCGA-06-0877 TCGA-06-0879 TCGA-06-0882 
       26.40         7.86         2.70         5.65        40.41        20.78 
TCGA-06-1087 TCGA-06-1802 TCGA-06-1806 TCGA-06-2557 TCGA-06-2562 TCGA-06-2563 
        4.04        15.32        15.32         1.08        12.56        30.64 
TCGA-06-2565 TCGA-06-2569 TCGA-06-5414 TCGA-06-5415 TCGA-06-5856 TCGA-06-6388 
       16.64         0.43         8.98         8.55         3.75         5.23 
TCGA-06-6390 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-A5U1 TCGA-06-A7TK 
        5.39         8.32        12.85         4.77         1.87         5.39 
TCGA-08-0246 TCGA-08-0352 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0375 
        4.18         1.28        24.56        31.10        37.58        12.23 
TCGA-08-0386 TCGA-08-0510 TCGA-08-0514 TCGA-08-0516 TCGA-08-0518 TCGA-08-0529 
       18.02         4.27        11.08        19.59        19.33        18.41 
TCGA-08-0531 TCGA-12-0656 TCGA-12-0670 TCGA-12-0688 TCGA-12-0692 TCGA-12-0703 
        7.56        94.78        25.97        26.66         3.65        20.38 
TCGA-12-0707 TCGA-12-0780 TCGA-12-0819 TCGA-12-0820 TCGA-12-0826 TCGA-12-0829 
       28.41        14.86        24.79        18.48        27.78        20.58 
TCGA-12-1093 TCGA-12-1094 TCGA-12-1600 TCGA-12-1602 TCGA-12-3646 TCGA-12-3648 
       15.98        12.23        14.73         6.77        44.02        26.93 
TCGA-12-3649 TCGA-12-3652 TCGA-12-3653 TCGA-14-0783 TCGA-14-0786 TCGA-14-0787 
       15.22        34.92        14.53         6.21        23.05         2.24 
TCGA-14-0790 TCGA-14-0817 TCGA-14-0866 TCGA-14-0871 TCGA-14-1043 TCGA-14-1395 
       13.78         5.39        26.33        28.93         0.79         1.38 
TCGA-14-1402 TCGA-14-1452 TCGA-14-1823 TCGA-14-2554 TCGA-14-2555 TCGA-15-0742 
       32.05         7.10        17.85        17.49         7.96        13.78 
TCGA-15-1447 TCGA-15-1449 TCGA-16-0846 TCGA-16-1060 TCGA-19-0955 TCGA-19-0960 
       53.19        13.28         3.91         9.14        11.77         8.61 
TCGA-19-1386 TCGA-19-1388 TCGA-19-1392 TCGA-19-1786 TCGA-19-1789 TCGA-19-2631 
        9.07        12.95         3.65         7.17         3.25         7.00 
TCGA-19-5950 TCGA-19-5951 TCGA-19-5954 TCGA-19-5958 TCGA-19-5959 TCGA-26-1439 
       17.19         8.02        12.10        14.07        16.80        13.87 
TCGA-26-1440 TCGA-26-1799 TCGA-26-6173 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 
        9.73         9.37         7.92        24.23        40.54        21.30 
TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 
       10.39        10.39        16.08         2.86        14.40        15.78 
TCGA-28-1749 TCGA-28-1751 TCGA-28-2506 TCGA-28-2509 TCGA-28-2513 TCGA-28-5214 
        9.21         7.63         6.74         4.77         7.30        23.44 
TCGA-28-5215 TCGA-28-5218 TCGA-28-6450 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 
       11.01         5.16         5.42         0.10        15.85        19.50 
TCGA-32-1980 TCGA-32-2491 TCGA-32-2495 TCGA-32-2615 TCGA-32-2632 TCGA-32-2634 
        1.18        12.23        15.02        15.95         8.84        22.78 
TCGA-32-2638 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2575 TCGA-41-3393 
       25.18        19.23         0.85        13.35         9.53         4.44 
TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9S TCGA-74-6575 TCGA-74-6581 TCGA-76-4925 
       15.12        12.46         4.14        20.91         8.22         4.80 
TCGA-76-4929 TCGA-76-6280 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6664 
        3.65        11.38         4.83         5.03         0.23         7.79 
TCGA-RR-A6KA TCGA-RR-A6KC 
        6.28        20.55 

$`20Q GAIN WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 TCGA-02-0011 
       11.77         4.73        23.18        10.59        35.41        20.71 
TCGA-02-0014 TCGA-02-0023 TCGA-02-0024 TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 
       82.59        20.12        53.10        24.59        12.16        90.58 
TCGA-02-0033 TCGA-02-0039 TCGA-02-0046 TCGA-02-0047 TCGA-02-0048 TCGA-02-0051 
        2.83        10.52         6.87        14.73         3.22        15.09 
TCGA-02-0052 TCGA-02-0058 TCGA-02-0059 TCGA-02-0060 TCGA-02-0064 TCGA-02-0070 
       12.59         8.35         9.57         6.02        19.73        25.05 
TCGA-02-0071 TCGA-02-0080 TCGA-02-0085 TCGA-02-0087 TCGA-02-0099 TCGA-02-0102 
        5.49        89.72        51.32        57.76         3.48        27.02 
TCGA-02-0104 TCGA-02-0107 TCGA-02-0114 TCGA-02-0260 TCGA-02-0271 TCGA-02-0281 
       65.00        17.65        99.98        16.93        14.47         3.98 
TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 
       15.95        12.23         9.90         7.73        10.62         7.33 
TCGA-02-0330 TCGA-02-0332 TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 
       15.91        25.71        25.12        10.59        12.39        14.50 
TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 TCGA-02-2470 
       10.55        47.11        11.34         9.27        16.21        12.92 
TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 TCGA-06-0124 TCGA-06-0129 TCGA-06-0132 
       15.32        15.45        20.32        20.38        33.67        25.35 
TCGA-06-0133 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 
       14.30        24.23        11.90         0.20        10.29         2.20 
TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0155 TCGA-06-0159 TCGA-06-0160 
       11.74         2.33        20.09        10.45         9.44        11.80 
TCGA-06-0162 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0178 TCGA-06-0184 
        3.42        10.65         5.85        19.66        88.14        69.90 
TCGA-06-0187 TCGA-06-0188 TCGA-06-0190 TCGA-06-0194 TCGA-06-0201 TCGA-06-0208 
       27.22        44.58        10.42         4.67         0.39         8.42 
TCGA-06-0210 TCGA-06-0213 TCGA-06-0214 TCGA-06-0219 TCGA-06-0221 TCGA-06-0238 
        7.40         0.53        15.02         0.72        19.82        13.32 
TCGA-06-0240 TCGA-06-0241 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0646 
       20.42        48.69         9.57         3.16        35.11         5.75 
TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0744 TCGA-06-0749 
        9.80         2.10        23.57        14.20        46.88         2.70 
TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0878 TCGA-06-0881 TCGA-06-0939 
        0.92        43.46        46.19         7.17        16.57        26.76 
TCGA-06-1084 TCGA-06-1086 TCGA-06-1800 TCGA-06-1801 TCGA-06-1804 TCGA-06-1805 
       23.93         6.84        26.79        11.84        13.61        33.90 
TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2564 TCGA-06-2566 TCGA-06-2567 
       12.49         4.93        17.65         5.95         5.98         4.37 
TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 
       31.50        11.74         3.55         8.35         4.54         8.81 
TCGA-06-5416 TCGA-06-5418 TCGA-06-5858 TCGA-06-5859 TCGA-06-6389 TCGA-06-6391 
        6.71         2.73         6.15         4.57         7.79         1.48 
TCGA-06-6693 TCGA-06-6694 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 
      120.56         7.36         1.55         4.77         4.96         4.70 
TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TL TCGA-08-0244 TCGA-08-0245 TCGA-08-0344 
        3.12         2.56         5.42        22.68        37.84       115.86 
TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 
        1.74         8.42        25.71        12.16         9.80        29.23 
TCGA-08-0351 TCGA-08-0353 TCGA-08-0354 TCGA-08-0358 TCGA-08-0359 TCGA-08-0380 
       65.33         8.42        17.95        22.29         3.39        14.93 
TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0512 TCGA-08-0517 
       15.35        13.97         0.72        12.56        42.15        58.68 
TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-12-0615 TCGA-12-0616 
       10.75         4.80         7.27        15.98        15.35        14.73 
TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0657 TCGA-12-0662 
       12.99        34.92        10.45         7.59         0.10        38.17 
TCGA-12-0691 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 
       12.13        15.06        53.85        43.23         7.63         9.73 
TCGA-12-0778 TCGA-12-0818 TCGA-12-0821 TCGA-12-0822 TCGA-12-0827 TCGA-12-0828 
       14.93        91.76        10.62        23.51        38.76         8.94 
TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 TCGA-12-1092 TCGA-12-1095 
      127.59         5.82         7.59        33.21        21.73        15.85 
TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 TCGA-12-1598 TCGA-12-1599 
        9.11        14.53         3.98         4.14        15.65        25.68 
TCGA-12-3644 TCGA-12-3650 TCGA-12-3651 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 
       59.77        10.95        12.69        14.93         3.22         2.04 
TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 TCGA-14-0789 TCGA-14-0812 TCGA-14-0813 
       15.12        11.97         0.95        11.24         3.25         1.35 
TCGA-14-0862 TCGA-14-0865 TCGA-14-0867 TCGA-14-1034 TCGA-14-1037 TCGA-14-1396 
        2.89        16.50         2.04        15.95        19.30         1.12 
TCGA-14-1401 TCGA-14-1450 TCGA-14-1451 TCGA-14-1453 TCGA-14-1454 TCGA-14-1455 
        3.75        58.78        23.11         1.15        30.18         0.92 
TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 
       40.96         6.67        12.43         0.99         1.97        17.79 
TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-3477 TCGA-14-4157 TCGA-15-1444 
        7.63         5.88         7.17         3.78         3.42        50.53 
TCGA-15-1446 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 
       19.10        17.59        26.07        16.37         4.31        29.03 
TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 
        4.57        10.29        14.01        21.24        13.97         6.41 
TCGA-19-0957 TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 TCGA-19-1387 
       21.90         0.66        14.27         3.39        10.75         5.95 
TCGA-19-1389 TCGA-19-1390 TCGA-19-1787 TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 
        4.64        25.38        12.66         0.13         9.67         4.87 
TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 TCGA-19-4065 
        1.08         7.53         0.16         4.08        24.23         7.04 
TCGA-19-5947 TCGA-19-5952 TCGA-19-5953 TCGA-19-5955 TCGA-19-5956 TCGA-19-5960 
        6.64        18.90         4.73         1.78        22.49        14.96 
TCGA-19-A60I TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1442 TCGA-26-1443 
       17.79         3.98        28.54        10.03        31.33         7.13 
TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 
        9.40        14.86         5.49         8.88        18.97         1.58 
TCGA-26-6174 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1836 
        2.33        19.33         5.06        16.60         9.86        30.05 
TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2524 TCGA-28-1746 TCGA-28-1747 
       14.04        11.51        24.76         7.59         0.20         2.53 
TCGA-28-1750 TCGA-28-1752 TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 
        8.35         8.48         1.22         1.55         2.83         0.13 
TCGA-28-2502 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 
        0.66         5.26        14.93        11.28        17.88        14.53 
TCGA-28-5211 TCGA-28-5213 TCGA-28-5216 TCGA-28-5219 TCGA-28-5220 TCGA-32-1970 
       11.77        31.27        13.64        22.68        12.76        15.39 
TCGA-32-1973 TCGA-32-1976 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 TCGA-32-1991 
       21.07         0.49         4.67        12.69        14.86        16.93 
TCGA-32-2494 TCGA-32-2616 TCGA-32-4208 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 
       20.78         7.36        21.14         3.72        12.59        19.86 
TCGA-32-4719 TCGA-41-2573 TCGA-41-3392 TCGA-41-3915 TCGA-41-4097 TCGA-4W-AA9T 
       10.85         8.94         0.99        11.84         0.20        14.76 
TCGA-74-6573 TCGA-74-6577 TCGA-74-6578 TCGA-74-6584 TCGA-76-4926 TCGA-76-4928 
        3.45         4.34        14.33         7.50         4.54         3.09 
TCGA-76-4931 TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 
        9.17         2.53        10.78        16.70         3.29         2.70 
TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6662 TCGA-76-6663 TCGA-81-5910 
       17.06         8.35        20.98         9.27         7.73         1.61 
TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R 
       17.72        26.30         5.92 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               0.1                0.1 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             94.78             127.59 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             12.51              11.74 
[1] "0.1 - 94.8 (12.5)"  "0.1 - 127.6 (11.7)"
[1] "hr=" "1.1"
D37V2, continuous
D37V3, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED    92 126
  20Q GAIN WILD-TYPE 132 220
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     92  126
  20Q GAIN WILD-TYPE  132  220
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE               92                132
  MALE                126                220
[1] 2 2
[1] FALSE
D37V4, continuous
                    vv
clus                 GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  20Q GAIN MUTATED                               9                   9
  20Q GAIN WILD-TYPE                            18                   9
                    vv
clus                 UNTREATED PRIMARY (DE NOVO) GBM
  20Q GAIN MUTATED                               200
  20Q GAIN WILD-TYPE                             325
D37V5, multiclass
                                 clus
vv                                20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                  9                 18
  TREATED PRIMARY GBM                            9                  9
  UNTREATED PRIMARY (DE NOVO) GBM              200                325
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V6, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED   150  68
  20Q GAIN WILD-TYPE 232 120
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED    150   68
  20Q GAIN WILD-TYPE  232  120
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  NO               150                232
  YES               68                120
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20Q GAIN MUTATED       9                        16   188
  20Q GAIN WILD-TYPE     4                        33   297
D37V7, multiclass
                           clus
vv                          20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  ASIAN                                    9                  4
  BLACK OR AFRICAN AMERICAN               16                 33
  WHITE                                  188                297
[1] 3 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
  20Q GAIN MUTATED     5 189
  20Q GAIN WILD-TYPE   7 283
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      5  189
  20Q GAIN WILD-TYPE    7  283
                        clus
vv                       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    5                  7
  NOT HISPANIC OR LATINO              189                283
[1] 2 2
[1] FALSE

Clustering(38) Variable = 21Q GAIN MUTATION ANALYSIS
D38V1, survival
                    sevent
clus2                  0   1
  21Q GAIN MUTATED     9  54
  21Q GAIN WILD-TYPE  95 411
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                63                506 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                54                411 
$`21Q GAIN MUTATED`
TCGA-02-0001 TCGA-02-0006 TCGA-02-0025 TCGA-02-0055 TCGA-02-0069 TCGA-02-0075 
       11.77        18.35        42.74         2.50        28.70        20.84 
TCGA-02-0079 TCGA-02-0113 TCGA-02-0337 TCGA-06-0130 TCGA-06-0140 TCGA-06-0149 
       27.25        92.65        25.12        12.95         0.20         8.61 
TCGA-06-0151 TCGA-06-0159 TCGA-06-0164 TCGA-06-0168 TCGA-06-0176 TCGA-06-0177 
       46.59         9.44        56.91        19.66        91.00         4.18 
TCGA-06-0188 TCGA-06-0189 TCGA-06-0197 TCGA-06-0216 TCGA-06-0237 TCGA-06-0644 
       44.58        15.42         5.56        24.16        13.64        12.62 
TCGA-06-0743 TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 TCGA-06-1806 TCGA-06-2565 
       26.40        23.93         6.84         4.04        15.32        16.64 
TCGA-06-2567 TCGA-06-5415 TCGA-06-6698 TCGA-08-0246 TCGA-08-0386 TCGA-08-0510 
        4.37         8.55         4.77         4.18        18.02         4.27 
TCGA-12-0619 TCGA-12-0822 TCGA-12-1095 TCGA-12-1602 TCGA-12-3646 TCGA-14-0871 
       34.92        23.51        15.85         6.77        44.02        28.93 
TCGA-14-1034 TCGA-14-1454 TCGA-16-0846 TCGA-19-1388 TCGA-19-1392 TCGA-19-1787 
       15.95        30.18         3.91        12.95         3.65        12.66 
TCGA-19-A6J4 TCGA-27-1832 TCGA-27-2526 TCGA-27-2527 TCGA-28-2506 TCGA-28-2509 
        3.98         9.86         2.86        14.40         6.74         4.77 
TCGA-28-5207 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-32-2615 TCGA-32-2632 
       11.28        11.01        13.64         5.16        15.95         8.84 
TCGA-41-2575 TCGA-41-3915 TCGA-4W-AA9S 
        9.53        11.84         4.14 

$`21Q GAIN WILD-TYPE`
TCGA-02-0003 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 TCGA-02-0011 TCGA-02-0014 
        4.73        23.18        10.59        35.41        20.71        82.59 
TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0024 TCGA-02-0026 
       20.61        87.06        77.65        20.12        53.10        24.59 
TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 
       12.16        90.58         2.83        14.14         3.62        10.72 
TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 TCGA-02-0048 TCGA-02-0051 
       10.52        18.31         6.87        14.73         3.22        15.09 
TCGA-02-0052 TCGA-02-0054 TCGA-02-0057 TCGA-02-0058 TCGA-02-0059 TCGA-02-0060 
       12.59         6.54        19.86         8.35         9.57         6.02 
TCGA-02-0064 TCGA-02-0068 TCGA-02-0070 TCGA-02-0071 TCGA-02-0074 TCGA-02-0080 
       19.73        26.43        25.05         5.49        10.19        89.72 
TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 
       22.72        12.62        51.32         8.81        57.76        16.96 
TCGA-02-0099 TCGA-02-0102 TCGA-02-0104 TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 
        3.48        27.02        65.00        11.67        17.65        23.18 
TCGA-02-0114 TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 TCGA-02-0266 
       99.98        15.65        48.95        16.54        16.93        17.72 
TCGA-02-0269 TCGA-02-0271 TCGA-02-0281 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 
       10.75        14.47         3.98        13.87        14.20        15.95 
TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 
       12.23         9.90         7.73        10.62         7.33        15.91 
TCGA-02-0332 TCGA-02-0333 TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 
       25.71         4.37        10.59        12.39        14.50        10.55 
TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 TCGA-02-2466 
       47.11        11.34         9.27        16.21         3.35        16.80 
TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 
       12.92        15.32        15.45        20.32         2.70         6.15 
TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 
       20.38        47.61         6.94         3.98        22.72        33.67 
TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0141 
       25.35        14.30        26.70        24.23        11.90        10.29 
TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 
        2.20        11.74         2.33        20.09        17.79        10.09 
TCGA-06-0150 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 
       19.46        12.33        13.94        10.45         3.19        10.82 
TCGA-06-0160 TCGA-06-0162 TCGA-06-0165 TCGA-06-0166 TCGA-06-0169 TCGA-06-0171 
       11.80         3.42        10.65         5.85         3.29        13.12 
TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 
        4.47         3.22         4.04        88.14        20.25         3.65 
TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 
       69.90        73.84        27.22        10.42        38.96         4.67 
TCGA-06-0195 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 
        7.40         0.39         7.66         8.42         7.63         7.40 
TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0219 TCGA-06-0221 TCGA-06-0238 
       11.84         0.53        15.02         0.72        19.82        13.32 
TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 
       20.42        48.69        10.82         9.01         0.26        72.36 
TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0645 TCGA-06-0646 
        4.70         9.57         3.16        35.11         5.75         5.75 
TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0744 TCGA-06-0745 
        9.80         2.10        23.57        14.20        46.88         7.86 
TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 
        2.70         2.70         0.92        43.46        46.19         5.65 
TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1800 
        7.17        40.41        16.57        20.78        26.76        26.79 
TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-2557 TCGA-06-2558 
       11.84        15.32        13.61        33.90         1.08        12.49 
TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2566 
        4.93        17.65        12.56        30.64         5.95         5.98 
TCGA-06-2569 TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 
        0.43        31.50        11.74         3.55         8.35         4.54 
TCGA-06-5413 TCGA-06-5414 TCGA-06-5416 TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 
        8.81         8.98         6.71         2.73         3.75         6.15 
TCGA-06-5859 TCGA-06-6388 TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 
        4.57         5.23         7.79         5.39         1.48       120.56 
TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 
        7.36         8.32        12.85         1.55         4.77         4.96 
TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK TCGA-06-A7TL 
        4.70         1.87         3.12         2.56         5.39         5.42 
TCGA-08-0244 TCGA-08-0245 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 
       22.68        37.84       115.86         1.74         8.42        25.71 
TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 
       12.16         9.80        29.23        65.33         1.28         8.42 
TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 
       17.95        24.56        31.10        37.58        22.29         3.39 
TCGA-08-0375 TCGA-08-0380 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 
       12.23        14.93        15.35        13.97         0.72        12.56 
TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 
       42.15        11.08        19.59        58.68        19.33        10.75 
TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 
        4.80         7.27        15.98        18.41         7.56        15.35 
TCGA-12-0616 TCGA-12-0618 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 
       14.73        12.99        10.45         7.59        94.78         0.10 
TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 
       38.17        25.97        26.66        12.13         3.65        20.38 
TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 
       28.41        15.06        53.85        43.23         7.63         9.73 
TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 
       14.93        14.86        91.76        24.79        18.48        10.62 
TCGA-12-0826 TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 
       27.78        38.76         8.94        20.58       127.59         5.82 
TCGA-12-1090 TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1096 
        7.59        33.21        21.73        15.98        12.23         9.11 
TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 
       14.53         3.98         4.14        15.65        25.68        14.73 
TCGA-12-3644 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 
       59.77        26.93        15.22        10.95        12.69        34.92 
TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 
       14.53        14.93         3.22         2.04        15.12        11.97 
TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 
        0.95         6.21        23.05         2.24        11.24        13.78 
TCGA-14-0812 TCGA-14-0813 TCGA-14-0817 TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 
        3.25         1.35         5.39         2.89        16.50        26.33 
TCGA-14-0867 TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 
        2.04        19.30         0.79         1.38         1.12         3.75 
TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 TCGA-14-1452 TCGA-14-1453 TCGA-14-1455 
       32.05        58.78        23.11         7.10         1.15         0.92 
TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 
       40.96         6.67        12.43         0.99         1.97        17.79 
TCGA-14-1823 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 
       17.85         7.63         5.88         7.17        17.49         7.96 
TCGA-14-3477 TCGA-14-4157 TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 
        3.78         3.42        13.78        50.53        19.10        53.19 
TCGA-15-1449 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 
       13.28        17.59        26.07        16.37         4.31        29.03 
TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 
        4.57        10.29        14.01         9.14        21.24        13.97 
TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 TCGA-19-0962 TCGA-19-0963 
        6.41        11.77        21.90         8.61         0.66        14.27 
TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 TCGA-19-1389 TCGA-19-1390 
        3.39        10.75         9.07         5.95         4.64        25.38 
TCGA-19-1786 TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 
        7.17         3.25         0.13         9.67         4.87         1.08 
TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 
        7.53         0.16         4.08        24.23         7.00         7.04 
TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 
        6.64        17.19         8.02        18.90         4.73        12.10 
TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I 
        1.78        22.49        14.07        16.80        14.96        17.79 
TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 
       28.54        10.03        13.87         9.73        31.33         7.13 
TCGA-26-1799 TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 
        9.37         9.40        14.86         5.49         8.88        18.97 
TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 
        1.58         7.92         2.33        19.33         5.06        16.60 
TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 
       24.23        40.54        21.30        30.05        14.04        11.51 
TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2528 
       24.76        10.39        10.39        16.08         7.59        15.78 
TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 TCGA-28-1752 
        0.20         2.53         9.21         8.35         7.63         8.48 
TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 TCGA-28-2502 TCGA-28-2513 
        1.22         1.55         2.83         0.13         0.66         7.30 
TCGA-28-2514 TCGA-28-5204 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 
        5.26        14.93        17.88        14.53        11.77        31.27 
TCGA-28-5214 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 
       23.44        22.68        12.76         5.42        15.39        21.07 
TCGA-32-1976 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 
        0.49         0.10        15.85        19.50         1.18         4.67 
TCGA-32-1986 TCGA-32-1987 TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 
       12.69        14.86        16.93        12.23        20.78        15.02 
TCGA-32-2616 TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4210 TCGA-32-4211 
        7.36        22.78        25.18        21.14         3.72        12.59 
TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 
       19.86        10.85        19.23         0.85        13.35         8.94 
TCGA-41-3392 TCGA-41-3393 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9T 
        0.99         4.44         0.20        15.12        12.46        14.76 
TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 
        3.45        20.91         4.34        14.33         8.22         7.50 
TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-4934 
        4.80         4.54         3.09         3.65         9.17         2.53 
TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 
       10.78        16.70         3.29         2.70        11.38        17.06 
TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 
        8.35        20.98         4.83         5.03         0.23         9.27 
TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R 
        7.73         7.79         1.61        17.72        26.30         5.92 
TCGA-RR-A6KA TCGA-RR-A6KC 
        6.28        20.55 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
               0.2                0.1 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             92.65             127.59 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
            12.950             11.785 
[1] "0.2 - 92.7 (12.9)"  "0.1 - 127.6 (11.8)"
[1] "hr=" "1.1"
D38V2, continuous
D38V3, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    24  39
  21Q GAIN WILD-TYPE 200 307
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     24   39
  21Q GAIN WILD-TYPE  200  307
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE               24                200
  MALE                 39                307
[1] 2 2
[1] FALSE
D38V4, continuous
                    vv
clus                 GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  21Q GAIN MUTATED                               6                   1
  21Q GAIN WILD-TYPE                            21                  17
                    vv
clus                 UNTREATED PRIMARY (DE NOVO) GBM
  21Q GAIN MUTATED                                56
  21Q GAIN WILD-TYPE                             469
D38V5, multiclass
                                 clus
vv                                21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                  6                 21
  TREATED PRIMARY GBM                            1                 17
  UNTREATED PRIMARY (DE NOVO) GBM               56                469
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V6, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    42  21
  21Q GAIN WILD-TYPE 340 167
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     42   21
  21Q GAIN WILD-TYPE  340  167
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  NO                42                340
  YES               21                167
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  21Q GAIN MUTATED       4                         5    53
  21Q GAIN WILD-TYPE     9                        44   432
D38V7, multiclass
                           clus
vv                          21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  ASIAN                                    4                  9
  BLACK OR AFRICAN AMERICAN                5                 44
  WHITE                                   53                432
[1] 3 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
  21Q GAIN MUTATED     0  56
  21Q GAIN WILD-TYPE  12 416
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      0   56
  21Q GAIN WILD-TYPE   12  416
                        clus
vv                       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 12
  NOT HISPANIC OR LATINO               56                416
[1] 2 2
[1] FALSE

Clustering(39) Variable = 22Q GAIN MUTATION ANALYSIS
D39V1, survival
                    sevent
clus2                  0   1
  22Q GAIN MUTATED     7  27
  22Q GAIN WILD-TYPE  97 438
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                34                535 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                27                438 
$`22Q GAIN MUTATED`
TCGA-02-0051 TCGA-02-0055 TCGA-02-0069 TCGA-02-0074 TCGA-02-0106 TCGA-02-0281 
       15.09         2.50        28.70        10.19        11.67         3.98 
TCGA-02-0324 TCGA-06-0130 TCGA-06-0209 TCGA-06-0409 TCGA-06-0414 TCGA-06-1086 
        7.73        12.95         7.63        72.36        35.11         6.84 
TCGA-06-1087 TCGA-06-2569 TCGA-08-0510 TCGA-12-0618 TCGA-12-0827 TCGA-12-1099 
        4.04         0.43         4.27        12.99        38.76         4.14 
TCGA-12-1602 TCGA-14-0813 TCGA-14-0871 TCGA-15-1449 TCGA-16-0846 TCGA-19-1387 
        6.77         1.35        28.93        13.28         3.91         5.95 
TCGA-19-1388 TCGA-19-1390 TCGA-19-4065 TCGA-27-2521 TCGA-28-1746 TCGA-28-5215 
       12.95        25.38         7.04        10.39         0.20        11.01 
TCGA-28-5216 TCGA-28-5218 TCGA-32-2616 TCGA-32-4211 
       13.64         5.16         7.36        12.59 

$`22Q GAIN WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 
       11.77         4.73        18.35        23.18        10.59        35.41 
TCGA-02-0011 TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 
       20.71        82.59        20.61        87.06        77.65        20.12 
TCGA-02-0024 TCGA-02-0025 TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 
       53.10        42.74        24.59        12.16        90.58         2.83 
TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 
       14.14         3.62        10.72        10.52        18.31         6.87 
TCGA-02-0047 TCGA-02-0048 TCGA-02-0052 TCGA-02-0054 TCGA-02-0057 TCGA-02-0058 
       14.73         3.22        12.59         6.54        19.86         8.35 
TCGA-02-0059 TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 TCGA-02-0070 TCGA-02-0071 
        9.57         6.02        19.73        26.43        25.05         5.49 
TCGA-02-0075 TCGA-02-0079 TCGA-02-0080 TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 
       20.84        27.25        89.72        22.72        12.62        51.32 
TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 TCGA-02-0104 
        8.81        57.76        16.96         3.48        27.02        65.00 
TCGA-02-0107 TCGA-02-0111 TCGA-02-0113 TCGA-02-0114 TCGA-02-0115 TCGA-02-0116 
       17.65        23.18        92.65        99.98        15.65        48.95 
TCGA-02-0258 TCGA-02-0260 TCGA-02-0266 TCGA-02-0269 TCGA-02-0271 TCGA-02-0285 
       16.54        16.93        17.72        10.75        14.47        13.87 
TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 TCGA-02-0325 TCGA-02-0326 
       14.20        15.95        12.23         9.90        10.62         7.33 
TCGA-02-0330 TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 
       15.91        25.71         4.37        25.12        10.59        12.39 
TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 
       14.50        10.55        47.11        11.34         9.27        16.21 
TCGA-02-0456 TCGA-02-2466 TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 
        3.35        16.80        12.92        15.32        15.45        20.32 
TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 
        2.70         6.15        20.38        47.61         6.94         3.98 
TCGA-06-0128 TCGA-06-0129 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 
       22.72        33.67        25.35        14.30        26.70        24.23 
TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 
       11.90         0.20        10.29         2.20        11.74         2.33 
TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 
       20.09        17.79        10.09         8.61        19.46        46.59 
TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 
       12.33        13.94        10.45         3.19        10.82         9.44 
TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 
       11.80         3.42        56.91        10.65         5.85        19.66 
TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 
        3.29        13.12         4.47         3.22         4.04        91.00 
TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 
        4.18        88.14        20.25         3.65        69.90        73.84 
TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 
       27.22        44.58        15.42        10.42        38.96         4.67 
TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0210 
        7.40         5.56         0.39         7.66         8.42         7.40 
TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 
       11.84         0.53        15.02        24.16         0.72        19.82 
TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 
       13.64        13.32        20.42        48.69        10.82         9.01 
TCGA-06-0402 TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0644 TCGA-06-0645 
        0.26         4.70         9.57         3.16        12.62         5.75 
TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 
        5.75         9.80         2.10        23.57        14.20        26.40 
TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 
       46.88         7.86         2.70         2.70         0.92        43.46 
TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 
       46.19         5.65         7.17        40.41        16.57        20.78 
TCGA-06-0939 TCGA-06-1084 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 
       26.76        23.93        26.79        11.84        15.32        13.61 
TCGA-06-1805 TCGA-06-1806 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 
       33.90        15.32         1.08        12.49         4.93        17.65 
TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 
       12.56        30.64         5.95        16.64         5.98         4.37 
TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 
       31.50        11.74         3.55         8.35         4.54         8.81 
TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 
        8.98         8.55         6.71         2.73         3.75         6.15 
TCGA-06-5859 TCGA-06-6388 TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 
        4.57         5.23         7.79         5.39         1.48       120.56 
TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 
        7.36         8.32        12.85         4.77         1.55         4.77 
TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK 
        4.96         4.70         1.87         3.12         2.56         5.39 
TCGA-06-A7TL TCGA-08-0244 TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 
        5.42        22.68        37.84         4.18       115.86         1.74 
TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 
        8.42        25.71        12.16         9.80        29.23        65.33 
TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 
        1.28         8.42        17.95        24.56        31.10        37.58 
TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 
       22.29         3.39        12.23        14.93        18.02        15.35 
TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 
       13.97         0.72        12.56        42.15        11.08        19.59 
TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 
       58.68        19.33        10.75         4.80         7.27        15.98 
TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0619 TCGA-12-0620 
       18.41         7.56        15.35        14.73        34.92        10.45 
TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 
        7.59        94.78         0.10        38.17        25.97        26.66 
TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 
       12.13         3.65        20.38        28.41        15.06        53.85 
TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 
       43.23         7.63         9.73        14.93        14.86        91.76 
TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 TCGA-12-0826 TCGA-12-0828 
       24.79        18.48        10.62        23.51        27.78         8.94 
TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 TCGA-12-1092 
       20.58       127.59         5.82         7.59        33.21        21.73 
TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 
       15.98        12.23        15.85         9.11        14.53         3.98 
TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 
       15.65        25.68        14.73        59.77        44.02        26.93 
TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 
       15.22        10.95        12.69        34.92        14.53        14.93 
TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 TCGA-14-0783 
        3.22         2.04        15.12        11.97         0.95         6.21 
TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 TCGA-14-0812 TCGA-14-0817 
       23.05         2.24        11.24        13.78         3.25         5.39 
TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 TCGA-14-0867 TCGA-14-1034 TCGA-14-1037 
        2.89        16.50        26.33         2.04        15.95        19.30 
TCGA-14-1043 TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 
        0.79         1.38         1.12         3.75        32.05        58.78 
TCGA-14-1451 TCGA-14-1452 TCGA-14-1453 TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 
       23.11         7.10         1.15        30.18         0.92        40.96 
TCGA-14-1458 TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 TCGA-14-1823 
        6.67        12.43         0.99         1.97        17.79        17.85 
TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-3477 
        7.63         5.88         7.17        17.49         7.96         3.78 
TCGA-14-4157 TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 TCGA-16-0848 
        3.42        13.78        50.53        19.10        53.19        17.59 
TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 
       26.07        16.37         4.31        29.03         4.57        10.29 
TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 
       14.01         9.14        21.24        13.97         6.41        11.77 
TCGA-19-0957 TCGA-19-0960 TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 
       21.90         8.61         0.66        14.27         3.39        10.75 
TCGA-19-1386 TCGA-19-1389 TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 
        9.07         4.64         3.65         7.17        12.66         3.25 
TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 
        0.13         9.67         4.87         1.08         7.53         0.16 
TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 
        4.08        24.23         7.00         6.64        17.19         8.02 
TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 
       18.90         4.73        12.10         1.78        22.49        14.07 
TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 
       16.80        14.96        17.79         3.98        28.54        10.03 
TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 
       13.87         9.73        31.33         7.13         9.37         9.40 
TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 
       14.86         5.49         8.88        18.97         1.58         7.92 
TCGA-26-6174 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 
        2.33        19.33         5.06        16.60         9.86        24.23 
TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 
       40.54        21.30        30.05        14.04        11.51        24.76 
TCGA-27-2519 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 
       10.39        16.08         7.59         2.86        14.40        15.78 
TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 
        2.53         9.21         8.35         7.63         8.48         1.22 
TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 TCGA-28-2502 TCGA-28-2506 TCGA-28-2509 
        1.55         2.83         0.13         0.66         6.74         4.77 
TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 
        7.30         5.26        14.93        11.28        17.88        14.53 
TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 
       11.77        31.27        23.44        22.68        12.76         5.42 
TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 
       15.39        21.07         0.49         0.10        15.85        19.50 
TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 TCGA-32-1991 TCGA-32-2491 
        1.18         4.67        12.69        14.86        16.93        12.23 
TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 
       20.78        15.02        15.95         8.84        22.78        25.18 
TCGA-32-4208 TCGA-32-4210 TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 
       21.14         3.72        19.86        10.85        19.23         0.85 
TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 
       13.35         8.94         9.53         0.99         4.44        11.84 
TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 
        0.20        15.12        12.46         4.14        14.76         3.45 
TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 TCGA-76-4925 
       20.91         4.34        14.33         8.22         7.50         4.80 
TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-4934 TCGA-76-4935 
        4.54         3.09         3.65         9.17         2.53        10.78 
TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 
       16.70         3.29         2.70        11.38        17.06         8.35 
TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 
       20.98         4.83         5.03         0.23         9.27         7.73 
TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R TCGA-RR-A6KA 
        7.79         1.61        17.72        26.30         5.92         6.28 
TCGA-RR-A6KC 
       20.55 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
               0.2                0.1 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             72.36             127.59 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              8.96              12.13 
[1] "0.2 - 72.4 (9.0)"   "0.1 - 127.6 (12.1)"
[1] "hr=" "1.3"
D39V2, continuous
D39V3, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    13  21
  22Q GAIN WILD-TYPE 211 325
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     13   21
  22Q GAIN WILD-TYPE  211  325
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE               13                211
  MALE                 21                325
[1] 2 2
[1] FALSE
D39V4, continuous
                    vv
clus                 GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  22Q GAIN MUTATED                               0                   0
  22Q GAIN WILD-TYPE                            27                  18
                    vv
clus                 UNTREATED PRIMARY (DE NOVO) GBM
  22Q GAIN MUTATED                                34
  22Q GAIN WILD-TYPE                             491
D39V5, multiclass
                                 clus
vv                                22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                  0                 27
  TREATED PRIMARY GBM                            0                 18
  UNTREATED PRIMARY (DE NOVO) GBM               34                491
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V6, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    23  11
  22Q GAIN WILD-TYPE 359 177
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     23   11
  22Q GAIN WILD-TYPE  359  177
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  NO                23                359
  YES               11                177
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  22Q GAIN MUTATED       1                         3    29
  22Q GAIN WILD-TYPE    12                        46   456
D39V7, multiclass
                           clus
vv                          22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  ASIAN                                    1                 12
  BLACK OR AFRICAN AMERICAN                3                 46
  WHITE                                   29                456
[1] 3 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
  22Q GAIN MUTATED     2  26
  22Q GAIN WILD-TYPE  10 446
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      2   26
  22Q GAIN WILD-TYPE   10  446
                        clus
vv                       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                 10
  NOT HISPANIC OR LATINO               26                446
[1] 2 2
[1] FALSE

Clustering(40) Variable = XP GAIN MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                 0   1
  XP GAIN MUTATED     3  12
  XP GAIN WILD-TYPE 101 453
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               15               554 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               12               453 
$`XP GAIN MUTATED`
TCGA-02-0266 TCGA-02-0271 TCGA-02-0333 TCGA-06-0151 TCGA-06-6698 TCGA-12-0773 
       17.72        14.47         4.37        46.59         4.77        43.23 
TCGA-12-1098 TCGA-14-1455 TCGA-14-1823 TCGA-15-1447 TCGA-19-1787 TCGA-26-1799 
        3.98         0.92        17.85        53.19        12.66         9.37 
TCGA-28-5209 TCGA-28-5218 TCGA-32-2632 
       14.53         5.16         8.84 

$`XP GAIN WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 
       11.77         4.73        18.35        23.18        10.59        35.41 
TCGA-02-0011 TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 
       20.71        82.59        20.61        87.06        77.65        20.12 
TCGA-02-0024 TCGA-02-0025 TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 
       53.10        42.74        24.59        12.16        90.58         2.83 
TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 
       14.14         3.62        10.72        10.52        18.31         6.87 
TCGA-02-0047 TCGA-02-0048 TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 TCGA-02-0055 
       14.73         3.22        15.09        12.59         6.54         2.50 
TCGA-02-0057 TCGA-02-0058 TCGA-02-0059 TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 
       19.86         8.35         9.57         6.02        19.73        26.43 
TCGA-02-0069 TCGA-02-0070 TCGA-02-0071 TCGA-02-0074 TCGA-02-0075 TCGA-02-0079 
       28.70        25.05         5.49        10.19        20.84        27.25 
TCGA-02-0080 TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 
       89.72        22.72        12.62        51.32         8.81        57.76 
TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 TCGA-02-0104 TCGA-02-0106 TCGA-02-0107 
       16.96         3.48        27.02        65.00        11.67        17.65 
TCGA-02-0111 TCGA-02-0113 TCGA-02-0114 TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 
       23.18        92.65        99.98        15.65        48.95        16.54 
TCGA-02-0260 TCGA-02-0269 TCGA-02-0281 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 
       16.93        10.75         3.98        13.87        14.20        15.95 
TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 
       12.23         9.90         7.73        10.62         7.33        15.91 
TCGA-02-0332 TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 
       25.71        25.12        10.59        12.39        14.50        10.55 
TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 TCGA-02-2466 
       47.11        11.34         9.27        16.21         3.35        16.80 
TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 
       12.92        15.32        15.45        20.32         2.70         6.15 
TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 
       20.38        47.61         6.94         3.98        22.72        33.67 
TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 
       12.95        25.35        14.30        26.70        24.23        11.90 
TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 
        0.20        10.29         2.20        11.74         2.33        20.09 
TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0152 TCGA-06-0154 
       17.79        10.09         8.61        19.46        12.33        13.94 
TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 
       10.45         3.19        10.82         9.44        11.80         3.42 
TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 
       56.91        10.65         5.85        19.66         3.29        13.12 
TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 
        4.47         3.22         4.04        91.00         4.18        88.14 
TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 
       20.25         3.65        69.90        73.84        27.22        44.58 
TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 
       15.42        10.42        38.96         4.67         7.40         5.56 
TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 
        0.39         7.66         8.42         7.63         7.40        11.84 
TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 
        0.53        15.02        24.16         0.72        19.82        13.64 
TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 
       13.32        20.42        48.69        10.82         9.01         0.26 
TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 
       72.36         4.70         9.57         3.16        35.11        12.62 
TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 
        5.75         5.75         9.80         2.10        23.57        14.20 
TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 
       26.40        46.88         7.86         2.70         2.70         0.92 
TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 
       43.46        46.19         5.65         7.17        40.41        16.57 
TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 
       20.78        26.76        23.93         6.84         4.04        26.79 
TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 TCGA-06-2557 
       11.84        15.32        13.61        33.90        15.32         1.08 
TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 
       12.49         4.93        17.65        12.56        30.64         5.95 
TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-5408 
       16.64         5.98         4.37         0.43        31.50        11.74 
TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 
        3.55         8.35         4.54         8.81         8.98         8.55 
TCGA-06-5416 TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 
        6.71         2.73         3.75         6.15         4.57         5.23 
TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 
        7.79         5.39         1.48       120.56         7.36         8.32 
TCGA-06-6697 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A5U1 
       12.85         1.55         4.77         4.96         4.70         1.87 
TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK TCGA-06-A7TL TCGA-08-0244 TCGA-08-0245 
        3.12         2.56         5.39         5.42        22.68        37.84 
TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 
        4.18       115.86         1.74         8.42        25.71        12.16 
TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 
        9.80        29.23        65.33         1.28         8.42        17.95 
TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 
       24.56        31.10        37.58        22.29         3.39        12.23 
TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 
       14.93        18.02        15.35        13.97         0.72        12.56 
TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 
        4.27        42.15        11.08        19.59        58.68        19.33 
TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 
       10.75         4.80         7.27        15.98        18.41         7.56 
TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 
       15.35        14.73        12.99        34.92        10.45         7.59 
TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 
       94.78         0.10        38.17        25.97        26.66        12.13 
TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0775 
        3.65        20.38        28.41        15.06        53.85         7.63 
TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 
        9.73        14.93        14.86        91.76        24.79        18.48 
TCGA-12-0821 TCGA-12-0822 TCGA-12-0826 TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 
       10.62        23.51        27.78        38.76         8.94        20.58 
TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 
      127.59         5.82         7.59        33.21        21.73        15.98 
TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1099 TCGA-12-1598 
       12.23        15.85         9.11        14.53         4.14        15.65 
TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 
       25.68        14.73         6.77        59.77        44.02        26.93 
TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 
       15.22        10.95        12.69        34.92        14.53        14.93 
TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 TCGA-14-0783 
        3.22         2.04        15.12        11.97         0.95         6.21 
TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 TCGA-14-0812 TCGA-14-0813 
       23.05         2.24        11.24        13.78         3.25         1.35 
TCGA-14-0817 TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 TCGA-14-0867 TCGA-14-0871 
        5.39         2.89        16.50        26.33         2.04        28.93 
TCGA-14-1034 TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 
       15.95        19.30         0.79         1.38         1.12         3.75 
TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 TCGA-14-1452 TCGA-14-1453 TCGA-14-1454 
       32.05        58.78        23.11         7.10         1.15        30.18 
TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 
       40.96         6.67        12.43         0.99         1.97        17.79 
TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-3477 
        7.63         5.88         7.17        17.49         7.96         3.78 
TCGA-14-4157 TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-15-1449 TCGA-16-0846 
        3.42        13.78        50.53        19.10        13.28         3.91 
TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 
       17.59        26.07        16.37         4.31        29.03         4.57 
TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 
       10.29        14.01         9.14        21.24        13.97         6.41 
TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 
       11.77        21.90         8.61         0.66        14.27         3.39 
TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 TCGA-19-1388 TCGA-19-1389 TCGA-19-1390 
       10.75         9.07         5.95        12.95         4.64        25.38 
TCGA-19-1392 TCGA-19-1786 TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 
        3.65         7.17         3.25         0.13         9.67         4.87 
TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 
        1.08         7.53         0.16         4.08        24.23         7.00 
TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 
        7.04         6.64        17.19         8.02        18.90         4.73 
TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 
       12.10         1.78        22.49        14.07        16.80        14.96 
TCGA-19-A60I TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 
       17.79         3.98        28.54        10.03        13.87         9.73 
TCGA-26-1442 TCGA-26-1443 TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 
       31.33         7.13         9.40        14.86         5.49         8.88 
TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-26-A7UX TCGA-27-1830 
       18.97         1.58         7.92         2.33        19.33         5.06 
TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 
       16.60         9.86        24.23        40.54        21.30        30.05 
TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 
       14.04        11.51        24.76        10.39        10.39        16.08 
TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 
        7.59         2.86        14.40        15.78         0.20         2.53 
TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 TCGA-28-1755 
        9.21         8.35         7.63         8.48         1.22         1.55 
TCGA-28-1756 TCGA-28-1757 TCGA-28-2502 TCGA-28-2506 TCGA-28-2509 TCGA-28-2513 
        2.83         0.13         0.66         6.74         4.77         7.30 
TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5211 TCGA-28-5213 
        5.26        14.93        11.28        17.88        11.77        31.27 
TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 
       23.44        11.01        13.64        22.68        12.76         5.42 
TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 
       15.39        21.07         0.49         0.10        15.85        19.50 
TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 TCGA-32-1991 TCGA-32-2491 
        1.18         4.67        12.69        14.86        16.93        12.23 
TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 TCGA-32-2616 TCGA-32-2634 TCGA-32-2638 
       20.78        15.02        15.95         7.36        22.78        25.18 
TCGA-32-4208 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 
       21.14         3.72        12.59        19.86        10.85        19.23 
TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 
        0.85        13.35         8.94         9.53         0.99         4.44 
TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9S TCGA-4W-AA9T 
       11.84         0.20        15.12        12.46         4.14        14.76 
TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 
        3.45        20.91         4.34        14.33         8.22         7.50 
TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-4934 
        4.80         4.54         3.09         3.65         9.17         2.53 
TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 
       10.78        16.70         3.29         2.70        11.38        17.06 
TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 
        8.35        20.98         4.83         5.03         0.23         9.27 
TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R 
        7.73         7.79         1.61        17.72        26.30         5.92 
TCGA-RR-A6KA TCGA-RR-A6KC 
        6.28        20.55 

  XP GAIN MUTATED XP GAIN WILD-TYPE 
             0.92              0.10 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
            53.19            127.59 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
            12.66             11.84 
[1] "0.9 - 53.2 (12.7)"  "0.1 - 127.6 (11.8)"
[1] "hr=" "1.1"
D40V2, continuous
D40V3, binary
                   cls
clus                  0   1
  XP GAIN MUTATED     7   8
  XP GAIN WILD-TYPE 217 338
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      7    8
  XP GAIN WILD-TYPE  217  338
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  FEMALE               7               217
  MALE                 8               338
[1] 2 2
[1] FALSE
D40V4, continuous
                   vv
clus                GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  XP GAIN MUTATED                               1                   0
  XP GAIN WILD-TYPE                            26                  18
                   vv
clus                UNTREATED PRIMARY (DE NOVO) GBM
  XP GAIN MUTATED                                14
  XP GAIN WILD-TYPE                             511
D40V5, multiclass
                                 clus
vv                                XP GAIN MUTATED XP GAIN WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                 1                26
  TREATED PRIMARY GBM                           0                18
  UNTREATED PRIMARY (DE NOVO) GBM              14               511
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V6, binary
                   cls
clus                  0   1
  XP GAIN MUTATED     9   6
  XP GAIN WILD-TYPE 373 182
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      9    6
  XP GAIN WILD-TYPE  373  182
     clus
vv    XP GAIN MUTATED XP GAIN WILD-TYPE
  NO                9               373
  YES               6               182
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XP GAIN MUTATED       0                         0    13
  XP GAIN WILD-TYPE    13                        49   472
D40V7, multiclass
                           clus
vv                          XP GAIN MUTATED XP GAIN WILD-TYPE
  ASIAN                                   0                13
  BLACK OR AFRICAN AMERICAN               0                49
  WHITE                                  13               472
[1] 3 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
  XP GAIN MUTATED     1   8
  XP GAIN WILD-TYPE  11 464
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      1    8
  XP GAIN WILD-TYPE   11  464
                        clus
vv                       XP GAIN MUTATED XP GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                11
  NOT HISPANIC OR LATINO               8               464
[1] 2 2
[1] FALSE

Clustering(41) Variable = XQ GAIN MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                 0   1
  XQ GAIN MUTATED     2  14
  XQ GAIN WILD-TYPE 102 451
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               16               553 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               14               451 
$`XQ GAIN MUTATED`
TCGA-02-0058 TCGA-02-0266 TCGA-02-0271 TCGA-02-0333 TCGA-06-0151 TCGA-06-0743 
        8.35        17.72        14.47         4.37        46.59        26.40 
TCGA-06-6698 TCGA-12-0773 TCGA-14-1455 TCGA-14-1823 TCGA-19-1787 TCGA-26-1799 
        4.77        43.23         0.92        17.85        12.66         9.37 
TCGA-28-5209 TCGA-28-5218 TCGA-32-2632 TCGA-32-4210 
       14.53         5.16         8.84         3.72 

$`XQ GAIN WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 
       11.77         4.73        18.35        23.18        10.59        35.41 
TCGA-02-0011 TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 
       20.71        82.59        20.61        87.06        77.65        20.12 
TCGA-02-0024 TCGA-02-0025 TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 
       53.10        42.74        24.59        12.16        90.58         2.83 
TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 
       14.14         3.62        10.72        10.52        18.31         6.87 
TCGA-02-0047 TCGA-02-0048 TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 TCGA-02-0055 
       14.73         3.22        15.09        12.59         6.54         2.50 
TCGA-02-0057 TCGA-02-0059 TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 TCGA-02-0069 
       19.86         9.57         6.02        19.73        26.43        28.70 
TCGA-02-0070 TCGA-02-0071 TCGA-02-0074 TCGA-02-0075 TCGA-02-0079 TCGA-02-0080 
       25.05         5.49        10.19        20.84        27.25        89.72 
TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 
       22.72        12.62        51.32         8.81        57.76        16.96 
TCGA-02-0099 TCGA-02-0102 TCGA-02-0104 TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 
        3.48        27.02        65.00        11.67        17.65        23.18 
TCGA-02-0113 TCGA-02-0114 TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 
       92.65        99.98        15.65        48.95        16.54        16.93 
TCGA-02-0269 TCGA-02-0281 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 
       10.75         3.98        13.87        14.20        15.95        12.23 
TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 
        9.90         7.73        10.62         7.33        15.91        25.71 
TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 
       25.12        10.59        12.39        14.50        10.55        47.11 
TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 TCGA-02-2466 TCGA-02-2470 
       11.34         9.27        16.21         3.35        16.80        12.92 
TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 
       15.32        15.45        20.32         2.70         6.15        20.38 
TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 
       47.61         6.94         3.98        22.72        33.67        12.95 
TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 
       25.35        14.30        26.70        24.23        11.90         0.20 
TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 
       10.29         2.20        11.74         2.33        20.09        17.79 
TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 
       10.09         8.61        19.46        12.33        13.94        10.45 
TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 
        3.19        10.82         9.44        11.80         3.42        56.91 
TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 
       10.65         5.85        19.66         3.29        13.12         4.47 
TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 
        3.22         4.04        91.00         4.18        88.14        20.25 
TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 
        3.65        69.90        73.84        27.22        44.58        15.42 
TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 
       10.42        38.96         4.67         7.40         5.56         0.39 
TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 
        7.66         8.42         7.63         7.40        11.84         0.53 
TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 
       15.02        24.16         0.72        19.82        13.64        13.32 
TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 
       20.42        48.69        10.82         9.01         0.26        72.36 
TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 
        4.70         9.57         3.16        35.11        12.62         5.75 
TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0744 
        5.75         9.80         2.10        23.57        14.20        46.88 
TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 
        7.86         2.70         2.70         0.92        43.46        46.19 
TCGA-06-0877 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 
        5.65         7.17        40.41        16.57        20.78        26.76 
TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 
       23.93         6.84         4.04        26.79        11.84        15.32 
TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 
       13.61        33.90        15.32         1.08        12.49         4.93 
TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 
       17.65        12.56        30.64         5.95        16.64         5.98 
TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 
        4.37         0.43        31.50        11.74         3.55         8.35 
TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 TCGA-06-5418 
        4.54         8.81         8.98         8.55         6.71         2.73 
TCGA-06-5856 TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 TCGA-06-6389 TCGA-06-6390 
        3.75         6.15         4.57         5.23         7.79         5.39 
TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 TCGA-06-6699 
        1.48       120.56         7.36         8.32        12.85         1.55 
TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 
        4.77         4.96         4.70         1.87         3.12         2.56 
TCGA-06-A7TK TCGA-06-A7TL TCGA-08-0244 TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 
        5.39         5.42        22.68        37.84         4.18       115.86 
TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 
        1.74         8.42        25.71        12.16         9.80        29.23 
TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 
       65.33         1.28         8.42        17.95        24.56        31.10 
TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 
       37.58        22.29         3.39        12.23        14.93        18.02 
TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 
       15.35        13.97         0.72        12.56         4.27        42.15 
TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 
       11.08        19.59        58.68        19.33        10.75         4.80 
TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 
        7.27        15.98        18.41         7.56        15.35        14.73 
TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 
       12.99        34.92        10.45         7.59        94.78         0.10 
TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 
       38.17        25.97        26.66        12.13         3.65        20.38 
TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 
       28.41        15.06        53.85         7.63         9.73        14.93 
TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 
       14.86        91.76        24.79        18.48        10.62        23.51 
TCGA-12-0826 TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 
       27.78        38.76         8.94        20.58       127.59         5.82 
TCGA-12-1090 TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 
        7.59        33.21        21.73        15.98        12.23        15.85 
TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 TCGA-12-1598 TCGA-12-1599 
        9.11        14.53         3.98         4.14        15.65        25.68 
TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 
       14.73         6.77        59.77        44.02        26.93        15.22 
TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 
       10.95        12.69        34.92        14.53        14.93         3.22 
TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 
        2.04        15.12        11.97         0.95         6.21        23.05 
TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 TCGA-14-0812 TCGA-14-0813 TCGA-14-0817 
        2.24        11.24        13.78         3.25         1.35         5.39 
TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 TCGA-14-0867 TCGA-14-0871 TCGA-14-1034 
        2.89        16.50        26.33         2.04        28.93        15.95 
TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 
       19.30         0.79         1.38         1.12         3.75        32.05 
TCGA-14-1450 TCGA-14-1451 TCGA-14-1452 TCGA-14-1453 TCGA-14-1454 TCGA-14-1456 
       58.78        23.11         7.10         1.15        30.18        40.96 
TCGA-14-1458 TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 TCGA-14-1825 
        6.67        12.43         0.99         1.97        17.79         7.63 
TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-3477 TCGA-14-4157 
        5.88         7.17        17.49         7.96         3.78         3.42 
TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 TCGA-16-0846 
       13.78        50.53        19.10        53.19        13.28         3.91 
TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 
       17.59        26.07        16.37         4.31        29.03         4.57 
TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 
       10.29        14.01         9.14        21.24        13.97         6.41 
TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 
       11.77        21.90         8.61         0.66        14.27         3.39 
TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 TCGA-19-1388 TCGA-19-1389 TCGA-19-1390 
       10.75         9.07         5.95        12.95         4.64        25.38 
TCGA-19-1392 TCGA-19-1786 TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 
        3.65         7.17         3.25         0.13         9.67         4.87 
TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 
        1.08         7.53         0.16         4.08        24.23         7.00 
TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 
        7.04         6.64        17.19         8.02        18.90         4.73 
TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 
       12.10         1.78        22.49        14.07        16.80        14.96 
TCGA-19-A60I TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 
       17.79         3.98        28.54        10.03        13.87         9.73 
TCGA-26-1442 TCGA-26-1443 TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 
       31.33         7.13         9.40        14.86         5.49         8.88 
TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-26-A7UX TCGA-27-1830 
       18.97         1.58         7.92         2.33        19.33         5.06 
TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 
       16.60         9.86        24.23        40.54        21.30        30.05 
TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 
       14.04        11.51        24.76        10.39        10.39        16.08 
TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 
        7.59         2.86        14.40        15.78         0.20         2.53 
TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 TCGA-28-1755 
        9.21         8.35         7.63         8.48         1.22         1.55 
TCGA-28-1756 TCGA-28-1757 TCGA-28-2502 TCGA-28-2506 TCGA-28-2509 TCGA-28-2513 
        2.83         0.13         0.66         6.74         4.77         7.30 
TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5211 TCGA-28-5213 
        5.26        14.93        11.28        17.88        11.77        31.27 
TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 
       23.44        11.01        13.64        22.68        12.76         5.42 
TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 
       15.39        21.07         0.49         0.10        15.85        19.50 
TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 TCGA-32-1991 TCGA-32-2491 
        1.18         4.67        12.69        14.86        16.93        12.23 
TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 TCGA-32-2616 TCGA-32-2634 TCGA-32-2638 
       20.78        15.02        15.95         7.36        22.78        25.18 
TCGA-32-4208 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 
       21.14        12.59        19.86        10.85        19.23         0.85 
TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 
       13.35         8.94         9.53         0.99         4.44        11.84 
TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 
        0.20        15.12        12.46         4.14        14.76         3.45 
TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 TCGA-76-4925 
       20.91         4.34        14.33         8.22         7.50         4.80 
TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-4934 TCGA-76-4935 
        4.54         3.09         3.65         9.17         2.53        10.78 
TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 
       16.70         3.29         2.70        11.38        17.06         8.35 
TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 
       20.98         4.83         5.03         0.23         9.27         7.73 
TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R TCGA-RR-A6KA 
        7.79         1.61        17.72        26.30         5.92         6.28 
TCGA-RR-A6KC 
       20.55 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             0.92              0.10 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            46.59            127.59 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
           11.015            11.840 
[1] "0.9 - 46.6 (11.0)"  "0.1 - 127.6 (11.8)"
[1] "hr=" "1.2"
D41V2, continuous
D41V3, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     6  10
  XQ GAIN WILD-TYPE 218 336
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      6   10
  XQ GAIN WILD-TYPE  218  336
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE               6               218
  MALE                10               336
[1] 2 2
[1] FALSE
D41V4, continuous
                   vv
clus                GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  XQ GAIN MUTATED                               1                   1
  XQ GAIN WILD-TYPE                            26                  17
                   vv
clus                UNTREATED PRIMARY (DE NOVO) GBM
  XQ GAIN MUTATED                                14
  XQ GAIN WILD-TYPE                             511
D41V5, multiclass
                                 clus
vv                                XQ GAIN MUTATED XQ GAIN WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                 1                26
  TREATED PRIMARY GBM                           1                17
  UNTREATED PRIMARY (DE NOVO) GBM              14               511
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V6, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     8   8
  XQ GAIN WILD-TYPE 374 180
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      8    8
  XQ GAIN WILD-TYPE  374  180
     clus
vv    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  NO                8               374
  YES               8               180
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XQ GAIN MUTATED       0                         0    14
  XQ GAIN WILD-TYPE    13                        49   471
D41V7, multiclass
                           clus
vv                          XQ GAIN MUTATED XQ GAIN WILD-TYPE
  ASIAN                                   0                13
  BLACK OR AFRICAN AMERICAN               0                49
  WHITE                                  14               471
[1] 3 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
  XQ GAIN MUTATED     1  10
  XQ GAIN WILD-TYPE  11 462
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      1   10
  XQ GAIN WILD-TYPE   11  462
                        clus
vv                       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                11
  NOT HISPANIC OR LATINO              10               462
[1] 2 2
[1] FALSE

Clustering(42) Variable = 1P LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                 0   1
  1P LOSS MUTATED     2  13
  1P LOSS WILD-TYPE 102 452
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               15               554 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               13               452 
$`1P LOSS MUTATED`
TCGA-02-0028 TCGA-02-0269 TCGA-02-0281 TCGA-06-5411 TCGA-08-0244 TCGA-08-0344 
       90.58        10.75         3.98         8.35        22.68       115.86 
TCGA-08-0392 TCGA-08-0510 TCGA-14-0740 TCGA-19-1387 TCGA-19-1388 TCGA-19-1390 
        0.72         4.27        11.97         5.95        12.95        25.38 
TCGA-19-2629 TCGA-41-4097 TCGA-74-6575 
       24.23         0.20        20.91 

$`1P LOSS WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 
       11.77         4.73        18.35        23.18        10.59        35.41 
TCGA-02-0011 TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 
       20.71        82.59        20.61        87.06        77.65        20.12 
TCGA-02-0024 TCGA-02-0025 TCGA-02-0026 TCGA-02-0027 TCGA-02-0033 TCGA-02-0034 
       53.10        42.74        24.59        12.16         2.83        14.14 
TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 
        3.62        10.72        10.52        18.31         6.87        14.73 
TCGA-02-0048 TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 TCGA-02-0055 TCGA-02-0057 
        3.22        15.09        12.59         6.54         2.50        19.86 
TCGA-02-0058 TCGA-02-0059 TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 TCGA-02-0069 
        8.35         9.57         6.02        19.73        26.43        28.70 
TCGA-02-0070 TCGA-02-0071 TCGA-02-0074 TCGA-02-0075 TCGA-02-0079 TCGA-02-0080 
       25.05         5.49        10.19        20.84        27.25        89.72 
TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 
       22.72        12.62        51.32         8.81        57.76        16.96 
TCGA-02-0099 TCGA-02-0102 TCGA-02-0104 TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 
        3.48        27.02        65.00        11.67        17.65        23.18 
TCGA-02-0113 TCGA-02-0114 TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 
       92.65        99.98        15.65        48.95        16.54        16.93 
TCGA-02-0266 TCGA-02-0271 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 
       17.72        14.47        13.87        14.20        15.95        12.23 
TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 
        9.90         7.73        10.62         7.33        15.91        25.71 
TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 
        4.37        25.12        10.59        12.39        14.50        10.55 
TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 TCGA-02-2466 
       47.11        11.34         9.27        16.21         3.35        16.80 
TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 
       12.92        15.32        15.45        20.32         2.70         6.15 
TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 
       20.38        47.61         6.94         3.98        22.72        33.67 
TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 
       12.95        25.35        14.30        26.70        24.23        11.90 
TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 
        0.20        10.29         2.20        11.74         2.33        20.09 
TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 
       17.79        10.09         8.61        19.46        46.59        12.33 
TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 
       13.94        10.45         3.19        10.82         9.44        11.80 
TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 
        3.42        56.91        10.65         5.85        19.66         3.29 
TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 
       13.12         4.47         3.22         4.04        91.00         4.18 
TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 
       88.14        20.25         3.65        69.90        73.84        27.22 
TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 
       44.58        15.42        10.42        38.96         4.67         7.40 
TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 
        5.56         0.39         7.66         8.42         7.63         7.40 
TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 
       11.84         0.53        15.02        24.16         0.72        19.82 
TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 
       13.64        13.32        20.42        48.69        10.82         9.01 
TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 
        0.26        72.36         4.70         9.57         3.16        35.11 
TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 
       12.62         5.75         5.75         9.80         2.10        23.57 
TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 
       14.20        26.40        46.88         7.86         2.70         2.70 
TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 TCGA-06-0879 
        0.92        43.46        46.19         5.65         7.17        40.41 
TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 
       16.57        20.78        26.76        23.93         6.84         4.04 
TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 
       26.79        11.84        15.32        13.61        33.90        15.32 
TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 
        1.08        12.49         4.93        17.65        12.56        30.64 
TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 
        5.95        16.64         5.98         4.37         0.43        31.50 
TCGA-06-5408 TCGA-06-5410 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 
       11.74         3.55         4.54         8.81         8.98         8.55 
TCGA-06-5416 TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 
        6.71         2.73         3.75         6.15         4.57         5.23 
TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 
        7.79         5.39         1.48       120.56         7.36         8.32 
TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 
       12.85         4.77         1.55         4.77         4.96         4.70 
TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK TCGA-06-A7TL TCGA-08-0245 
        1.87         3.12         2.56         5.39         5.42        37.84 
TCGA-08-0246 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 
        4.18         1.74         8.42        25.71        12.16         9.80 
TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 
       29.23        65.33         1.28         8.42        17.95        24.56 
TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 
       31.10        37.58        22.29         3.39        12.23        14.93 
TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0509 TCGA-08-0512 TCGA-08-0514 
       18.02        15.35        13.97        12.56        42.15        11.08 
TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 
       19.59        58.68        19.33        10.75         4.80         7.27 
TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 
       15.98        18.41         7.56        15.35        14.73        12.99 
TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 
       34.92        10.45         7.59        94.78         0.10        38.17 
TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 
       25.97        26.66        12.13         3.65        20.38        28.41 
TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 
       15.06        53.85        43.23         7.63         9.73        14.93 
TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 
       14.86        91.76        24.79        18.48        10.62        23.51 
TCGA-12-0826 TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 
       27.78        38.76         8.94        20.58       127.59         5.82 
TCGA-12-1090 TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 
        7.59        33.21        21.73        15.98        12.23        15.85 
TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 TCGA-12-1598 TCGA-12-1599 
        9.11        14.53         3.98         4.14        15.65        25.68 
TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 
       14.73         6.77        59.77        44.02        26.93        15.22 
TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 
       10.95        12.69        34.92        14.53        14.93         3.22 
TCGA-12-5301 TCGA-14-0736 TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 TCGA-14-0787 
        2.04        15.12         0.95         6.21        23.05         2.24 
TCGA-14-0789 TCGA-14-0790 TCGA-14-0812 TCGA-14-0813 TCGA-14-0817 TCGA-14-0862 
       11.24        13.78         3.25         1.35         5.39         2.89 
TCGA-14-0865 TCGA-14-0866 TCGA-14-0867 TCGA-14-0871 TCGA-14-1034 TCGA-14-1037 
       16.50        26.33         2.04        28.93        15.95        19.30 
TCGA-14-1043 TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 
        0.79         1.38         1.12         3.75        32.05        58.78 
TCGA-14-1451 TCGA-14-1452 TCGA-14-1453 TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 
       23.11         7.10         1.15        30.18         0.92        40.96 
TCGA-14-1458 TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 TCGA-14-1823 
        6.67        12.43         0.99         1.97        17.79        17.85 
TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-3477 
        7.63         5.88         7.17        17.49         7.96         3.78 
TCGA-14-4157 TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 
        3.42        13.78        50.53        19.10        53.19        13.28 
TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 
        3.91        17.59        26.07        16.37         4.31        29.03 
TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 
        4.57        10.29        14.01         9.14        21.24        13.97 
TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 TCGA-19-0962 TCGA-19-0963 
        6.41        11.77        21.90         8.61         0.66        14.27 
TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 TCGA-19-1389 TCGA-19-1392 TCGA-19-1786 
        3.39        10.75         9.07         4.64         3.65         7.17 
TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 
       12.66         3.25         0.13         9.67         4.87         1.08 
TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 
        7.53         0.16         4.08         7.00         7.04         6.64 
TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 
       17.19         8.02        18.90         4.73        12.10         1.78 
TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J4 
       22.49        14.07        16.80        14.96        17.79         3.98 
TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 
       28.54        10.03        13.87         9.73        31.33         7.13 
TCGA-26-1799 TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 
        9.37         9.40        14.86         5.49         8.88        18.97 
TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 
        1.58         7.92         2.33        19.33         5.06        16.60 
TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 
        9.86        24.23        40.54        21.30        30.05        14.04 
TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 
       11.51        24.76        10.39        10.39        16.08         7.59 
TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 
        2.86        14.40        15.78         0.20         2.53         9.21 
TCGA-28-1750 TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 
        8.35         7.63         8.48         1.22         1.55         2.83 
TCGA-28-1757 TCGA-28-2502 TCGA-28-2506 TCGA-28-2509 TCGA-28-2513 TCGA-28-2514 
        0.13         0.66         6.74         4.77         7.30         5.26 
TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 
       14.93        11.28        17.88        14.53        11.77        31.27 
TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 
       23.44        11.01        13.64         5.16        22.68        12.76 
TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 TCGA-32-1978 
        5.42        15.39        21.07         0.49         0.10        15.85 
TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 TCGA-32-1991 
       19.50         1.18         4.67        12.69        14.86        16.93 
TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 TCGA-32-2616 TCGA-32-2632 
       12.23        20.78        15.02        15.95         7.36         8.84 
TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 
       22.78        25.18        21.14         3.72        12.59        19.86 
TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 
       10.85        19.23         0.85        13.35         8.94         9.53 
TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9S 
        0.99         4.44        11.84        15.12        12.46         4.14 
TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 
       14.76         3.45         4.34        14.33         8.22         7.50 
TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-4934 
        4.80         4.54         3.09         3.65         9.17         2.53 
TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 
       10.78        16.70         3.29         2.70        11.38        17.06 
TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 
        8.35        20.98         4.83         5.03         0.23         9.27 
TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R 
        7.73         7.79         1.61        17.72        26.30         5.92 
TCGA-RR-A6KA TCGA-RR-A6KC 
        6.28        20.55 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
              0.2               0.1 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           115.86            127.59 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            11.97             11.84 
[1] "0.2 - 115.9 (12.0)" "0.1 - 127.6 (11.8)"
[1] "hr=" "1.3"
D42V2, continuous
D42V3, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     4  11
  1P LOSS WILD-TYPE 220 335
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      4   11
  1P LOSS WILD-TYPE  220  335
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE               4               220
  MALE                11               335
[1] 2 2
[1] FALSE
D42V4, continuous
                   vv
clus                GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  1P LOSS MUTATED                               0                   1
  1P LOSS WILD-TYPE                            27                  17
                   vv
clus                UNTREATED PRIMARY (DE NOVO) GBM
  1P LOSS MUTATED                                14
  1P LOSS WILD-TYPE                             511
D42V5, multiclass
                                 clus
vv                                1P LOSS MUTATED 1P LOSS WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                 0                27
  TREATED PRIMARY GBM                           1                17
  UNTREATED PRIMARY (DE NOVO) GBM              14               511
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V6, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     9   6
  1P LOSS WILD-TYPE 373 182
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      9    6
  1P LOSS WILD-TYPE  373  182
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  NO                9               373
  YES               6               182
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1P LOSS MUTATED       0                         0    14
  1P LOSS WILD-TYPE    13                        49   471
D42V7, multiclass
                           clus
vv                          1P LOSS MUTATED 1P LOSS WILD-TYPE
  ASIAN                                   0                13
  BLACK OR AFRICAN AMERICAN               0                49
  WHITE                                  14               471
[1] 3 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
  1P LOSS MUTATED     0  13
  1P LOSS WILD-TYPE  12 459
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      0   13
  1P LOSS WILD-TYPE   12  459
                        clus
vv                       1P LOSS MUTATED 1P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                12
  NOT HISPANIC OR LATINO              13               459
[1] 2 2
[1] FALSE

Clustering(43) Variable = 1Q LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                 0   1
  1Q LOSS MUTATED     2  12
  1Q LOSS WILD-TYPE 102 453
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               14               555 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               12               453 
$`1Q LOSS MUTATED`
TCGA-02-0269 TCGA-02-0281 TCGA-06-5411 TCGA-08-0244 TCGA-08-0392 TCGA-08-0510 
       10.75         3.98         8.35        22.68         0.72         4.27 
TCGA-14-0740 TCGA-14-1034 TCGA-19-1387 TCGA-19-1388 TCGA-19-1390 TCGA-19-2629 
       11.97        15.95         5.95        12.95        25.38        24.23 
TCGA-41-4097 TCGA-74-6575 
        0.20        20.91 

$`1Q LOSS WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 
       11.77         4.73        18.35        23.18        10.59        35.41 
TCGA-02-0011 TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 
       20.71        82.59        20.61        87.06        77.65        20.12 
TCGA-02-0024 TCGA-02-0025 TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 
       53.10        42.74        24.59        12.16        90.58         2.83 
TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 
       14.14         3.62        10.72        10.52        18.31         6.87 
TCGA-02-0047 TCGA-02-0048 TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 TCGA-02-0055 
       14.73         3.22        15.09        12.59         6.54         2.50 
TCGA-02-0057 TCGA-02-0058 TCGA-02-0059 TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 
       19.86         8.35         9.57         6.02        19.73        26.43 
TCGA-02-0069 TCGA-02-0070 TCGA-02-0071 TCGA-02-0074 TCGA-02-0075 TCGA-02-0079 
       28.70        25.05         5.49        10.19        20.84        27.25 
TCGA-02-0080 TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 
       89.72        22.72        12.62        51.32         8.81        57.76 
TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 TCGA-02-0104 TCGA-02-0106 TCGA-02-0107 
       16.96         3.48        27.02        65.00        11.67        17.65 
TCGA-02-0111 TCGA-02-0113 TCGA-02-0114 TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 
       23.18        92.65        99.98        15.65        48.95        16.54 
TCGA-02-0260 TCGA-02-0266 TCGA-02-0271 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 
       16.93        17.72        14.47        13.87        14.20        15.95 
TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 
       12.23         9.90         7.73        10.62         7.33        15.91 
TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 
       25.71         4.37        25.12        10.59        12.39        14.50 
TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 
       10.55        47.11        11.34         9.27        16.21         3.35 
TCGA-02-2466 TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 
       16.80        12.92        15.32        15.45        20.32         2.70 
TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 
        6.15        20.38        47.61         6.94         3.98        22.72 
TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 
       33.67        12.95        25.35        14.30        26.70        24.23 
TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 
       11.90         0.20        10.29         2.20        11.74         2.33 
TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 
       20.09        17.79        10.09         8.61        19.46        46.59 
TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 
       12.33        13.94        10.45         3.19        10.82         9.44 
TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 
       11.80         3.42        56.91        10.65         5.85        19.66 
TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 
        3.29        13.12         4.47         3.22         4.04        91.00 
TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 
        4.18        88.14        20.25         3.65        69.90        73.84 
TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 
       27.22        44.58        15.42        10.42        38.96         4.67 
TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 
        7.40         5.56         0.39         7.66         8.42         7.63 
TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 
        7.40        11.84         0.53        15.02        24.16         0.72 
TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 
       19.82        13.64        13.32        20.42        48.69        10.82 
TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 
        9.01         0.26        72.36         4.70         9.57         3.16 
TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 
       35.11        12.62         5.75         5.75         9.80         2.10 
TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 
       23.57        14.20        26.40        46.88         7.86         2.70 
TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 
        2.70         0.92        43.46        46.19         5.65         7.17 
TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 
       40.41        16.57        20.78        26.76        23.93         6.84 
TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 
        4.04        26.79        11.84        15.32        13.61        33.90 
TCGA-06-1806 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 
       15.32         1.08        12.49         4.93        17.65        12.56 
TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 
       30.64         5.95        16.64         5.98         4.37         0.43 
TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 
       31.50        11.74         3.55         4.54         8.81         8.98 
TCGA-06-5415 TCGA-06-5416 TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 TCGA-06-5859 
        8.55         6.71         2.73         3.75         6.15         4.57 
TCGA-06-6388 TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 
        5.23         7.79         5.39         1.48       120.56         7.36 
TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 
        8.32        12.85         4.77         1.55         4.77         4.96 
TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK TCGA-06-A7TL 
        4.70         1.87         3.12         2.56         5.39         5.42 
TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 
       37.84         4.18       115.86         1.74         8.42        25.71 
TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 
       12.16         9.80        29.23        65.33         1.28         8.42 
TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 
       17.95        24.56        31.10        37.58        22.29         3.39 
TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0509 
       12.23        14.93        18.02        15.35        13.97        12.56 
TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 
       42.15        11.08        19.59        58.68        19.33        10.75 
TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 
        4.80         7.27        15.98        18.41         7.56        15.35 
TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 
       14.73        12.99        34.92        10.45         7.59        94.78 
TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 
        0.10        38.17        25.97        26.66        12.13         3.65 
TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 
       20.38        28.41        15.06        53.85        43.23         7.63 
TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 
        9.73        14.93        14.86        91.76        24.79        18.48 
TCGA-12-0821 TCGA-12-0822 TCGA-12-0826 TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 
       10.62        23.51        27.78        38.76         8.94        20.58 
TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 
      127.59         5.82         7.59        33.21        21.73        15.98 
TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 
       12.23        15.85         9.11        14.53         3.98         4.14 
TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 
       15.65        25.68        14.73         6.77        59.77        44.02 
TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 
       26.93        15.22        10.95        12.69        34.92        14.53 
TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0781 TCGA-14-0783 
       14.93         3.22         2.04        15.12         0.95         6.21 
TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 TCGA-14-0812 TCGA-14-0813 
       23.05         2.24        11.24        13.78         3.25         1.35 
TCGA-14-0817 TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 TCGA-14-0867 TCGA-14-0871 
        5.39         2.89        16.50        26.33         2.04        28.93 
TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 
       19.30         0.79         1.38         1.12         3.75        32.05 
TCGA-14-1450 TCGA-14-1451 TCGA-14-1452 TCGA-14-1453 TCGA-14-1454 TCGA-14-1455 
       58.78        23.11         7.10         1.15        30.18         0.92 
TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 
       40.96         6.67        12.43         0.99         1.97        17.79 
TCGA-14-1823 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 
       17.85         7.63         5.88         7.17        17.49         7.96 
TCGA-14-3477 TCGA-14-4157 TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 
        3.78         3.42        13.78        50.53        19.10        53.19 
TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 
       13.28         3.91        17.59        26.07        16.37         4.31 
TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 
       29.03         4.57        10.29        14.01         9.14        21.24 
TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 TCGA-19-0962 
       13.97         6.41        11.77        21.90         8.61         0.66 
TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 TCGA-19-1389 TCGA-19-1392 
       14.27         3.39        10.75         9.07         4.64         3.65 
TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 
        7.17        12.66         3.25         0.13         9.67         4.87 
TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 TCGA-19-2631 TCGA-19-4065 
        1.08         7.53         0.16         4.08         7.00         7.04 
TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 
        6.64        17.19         8.02        18.90         4.73        12.10 
TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I 
        1.78        22.49        14.07        16.80        14.96        17.79 
TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 
        3.98        28.54        10.03        13.87         9.73        31.33 
TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 
        7.13         9.37         9.40        14.86         5.49         8.88 
TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-26-A7UX TCGA-27-1830 
       18.97         1.58         7.92         2.33        19.33         5.06 
TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 
       16.60         9.86        24.23        40.54        21.30        30.05 
TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 
       14.04        11.51        24.76        10.39        10.39        16.08 
TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 
        7.59         2.86        14.40        15.78         0.20         2.53 
TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 TCGA-28-1755 
        9.21         8.35         7.63         8.48         1.22         1.55 
TCGA-28-1756 TCGA-28-1757 TCGA-28-2502 TCGA-28-2506 TCGA-28-2509 TCGA-28-2513 
        2.83         0.13         0.66         6.74         4.77         7.30 
TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 
        5.26        14.93        11.28        17.88        14.53        11.77 
TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 
       31.27        23.44        11.01        13.64         5.16        22.68 
TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 
       12.76         5.42        15.39        21.07         0.49         0.10 
TCGA-32-1978 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 
       15.85        19.50         1.18         4.67        12.69        14.86 
TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 TCGA-32-2616 
       16.93        12.23        20.78        15.02        15.95         7.36 
TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4210 TCGA-32-4211 
        8.84        22.78        25.18        21.14         3.72        12.59 
TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 
       19.86        10.85        19.23         0.85        13.35         8.94 
TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 TCGA-41-5651 TCGA-41-6646 
        9.53         0.99         4.44        11.84        15.12        12.46 
TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 
        4.14        14.76         3.45         4.34        14.33         8.22 
TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 
        7.50         4.80         4.54         3.09         3.65         9.17 
TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 
        2.53        10.78        16.70         3.29         2.70        11.38 
TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 
       17.06         8.35        20.98         4.83         5.03         0.23 
TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
        9.27         7.73         7.79         1.61        17.72        26.30 
TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC 
        5.92         6.28        20.55 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
              0.2               0.1 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            25.38            127.59 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            11.36             11.84 
[1] "0.2 - 25.4 (11.4)"  "0.1 - 127.6 (11.8)"
[1] "hr=" "1.3"
D43V2, continuous
D43V3, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     5   9
  1Q LOSS WILD-TYPE 219 337
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      5    9
  1Q LOSS WILD-TYPE  219  337
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE               5               219
  MALE                 9               337
[1] 2 2
[1] FALSE
D43V4, continuous
                   vv
clus                GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  1Q LOSS MUTATED                               0                   0
  1Q LOSS WILD-TYPE                            27                  18
                   vv
clus                UNTREATED PRIMARY (DE NOVO) GBM
  1Q LOSS MUTATED                                14
  1Q LOSS WILD-TYPE                             511
D43V5, multiclass
                                 clus
vv                                1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                 0                27
  TREATED PRIMARY GBM                           0                18
  UNTREATED PRIMARY (DE NOVO) GBM              14               511
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V6, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     8   6
  1Q LOSS WILD-TYPE 374 182
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      8    6
  1Q LOSS WILD-TYPE  374  182
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  NO                8               374
  YES               6               182
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1Q LOSS MUTATED       0                         0    12
  1Q LOSS WILD-TYPE    13                        49   473
D43V7, multiclass
                           clus
vv                          1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  ASIAN                                   0                13
  BLACK OR AFRICAN AMERICAN               0                49
  WHITE                                  12               473
[1] 3 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
  1Q LOSS MUTATED     0  11
  1Q LOSS WILD-TYPE  12 461
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      0   11
  1Q LOSS WILD-TYPE   12  461
                        clus
vv                       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                12
  NOT HISPANIC OR LATINO              11               461
[1] 2 2
[1] FALSE

Clustering(44) Variable = 2P LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                 0   1
  2P LOSS MUTATED     4  27
  2P LOSS WILD-TYPE 100 438
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               31               538 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               27               438 
$`2P LOSS MUTATED`
TCGA-02-0024 TCGA-02-0059 TCGA-02-0074 TCGA-02-0075 TCGA-06-0152 TCGA-06-0182 
       53.10         9.57        10.19        20.84        12.33         3.65 
TCGA-06-0188 TCGA-06-0414 TCGA-06-1087 TCGA-06-5416 TCGA-06-5856 TCGA-06-6389 
       44.58        35.11         4.04         6.71         3.75         7.79 
TCGA-06-6694 TCGA-06-A6S0 TCGA-12-0826 TCGA-12-1600 TCGA-12-3646 TCGA-14-0783 
        7.36         3.12        27.78        14.73        44.02         6.21 
TCGA-14-0812 TCGA-14-0867 TCGA-15-1447 TCGA-16-0850 TCGA-19-1388 TCGA-19-1390 
        3.25         2.04        53.19        16.37        12.95        25.38 
TCGA-19-1392 TCGA-19-2625 TCGA-19-5956 TCGA-28-2509 TCGA-28-5215 TCGA-32-2615 
        3.65         4.08        22.49         4.77        11.01        15.95 
TCGA-76-4934 
        2.53 

$`2P LOSS WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 
       11.77         4.73        18.35        23.18        10.59        35.41 
TCGA-02-0011 TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 
       20.71        82.59        20.61        87.06        77.65        20.12 
TCGA-02-0025 TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 
       42.74        24.59        12.16        90.58         2.83        14.14 
TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 
        3.62        10.72        10.52        18.31         6.87        14.73 
TCGA-02-0048 TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 TCGA-02-0055 TCGA-02-0057 
        3.22        15.09        12.59         6.54         2.50        19.86 
TCGA-02-0058 TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 TCGA-02-0069 TCGA-02-0070 
        8.35         6.02        19.73        26.43        28.70        25.05 
TCGA-02-0071 TCGA-02-0079 TCGA-02-0080 TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 
        5.49        27.25        89.72        22.72        12.62        51.32 
TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 TCGA-02-0104 
        8.81        57.76        16.96         3.48        27.02        65.00 
TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 TCGA-02-0113 TCGA-02-0114 TCGA-02-0115 
       11.67        17.65        23.18        92.65        99.98        15.65 
TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 TCGA-02-0266 TCGA-02-0269 TCGA-02-0271 
       48.95        16.54        16.93        17.72        10.75        14.47 
TCGA-02-0281 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 
        3.98        13.87        14.20        15.95        12.23         9.90 
TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 TCGA-02-0333 
        7.73        10.62         7.33        15.91        25.71         4.37 
TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 
       25.12        10.59        12.39        14.50        10.55        47.11 
TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 TCGA-02-2466 TCGA-02-2470 
       11.34         9.27        16.21         3.35        16.80        12.92 
TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 
       15.32        15.45        20.32         2.70         6.15        20.38 
TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 
       47.61         6.94         3.98        22.72        33.67        12.95 
TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 
       25.35        14.30        26.70        24.23        11.90         0.20 
TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 
       10.29         2.20        11.74         2.33        20.09        17.79 
TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0154 TCGA-06-0155 
       10.09         8.61        19.46        46.59        13.94        10.45 
TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 
        3.19        10.82         9.44        11.80         3.42        56.91 
TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 
       10.65         5.85        19.66         3.29        13.12         4.47 
TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 
        3.22         4.04        91.00         4.18        88.14        20.25 
TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 
       69.90        73.84        27.22        15.42        10.42        38.96 
TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 
        4.67         7.40         5.56         0.39         7.66         8.42 
TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 
        7.63         7.40        11.84         0.53        15.02        24.16 
TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 
        0.72        19.82        13.64        13.32        20.42        48.69 
TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 
       10.82         9.01         0.26        72.36         4.70         9.57 
TCGA-06-0413 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 
        3.16        12.62         5.75         5.75         9.80         2.10 
TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 
       23.57        14.20        26.40        46.88         7.86         2.70 
TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 
        2.70         0.92        43.46        46.19         5.65         7.17 
TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 
       40.41        16.57        20.78        26.76        23.93         6.84 
TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 
       26.79        11.84        15.32        13.61        33.90        15.32 
TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 
        1.08        12.49         4.93        17.65        12.56        30.64 
TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 
        5.95        16.64         5.98         4.37         0.43        31.50 
TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 
       11.74         3.55         8.35         4.54         8.81         8.98 
TCGA-06-5415 TCGA-06-5418 TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 TCGA-06-6390 
        8.55         2.73         6.15         4.57         5.23         5.39 
TCGA-06-6391 TCGA-06-6693 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 
        1.48       120.56         8.32        12.85         4.77         1.55 
TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S1 TCGA-06-A7TK 
        4.77         4.96         4.70         1.87         2.56         5.39 
TCGA-06-A7TL TCGA-08-0244 TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 
        5.42        22.68        37.84         4.18       115.86         1.74 
TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 
        8.42        25.71        12.16         9.80        29.23        65.33 
TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 
        1.28         8.42        17.95        24.56        31.10        37.58 
TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 
       22.29         3.39        12.23        14.93        18.02        15.35 
TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 
       13.97         0.72        12.56         4.27        42.15        11.08 
TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 
       19.59        58.68        19.33        10.75         4.80         7.27 
TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 
       15.98        18.41         7.56        15.35        14.73        12.99 
TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 
       34.92        10.45         7.59        94.78         0.10        38.17 
TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 
       25.97        26.66        12.13         3.65        20.38        28.41 
TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 
       15.06        53.85        43.23         7.63         9.73        14.93 
TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 
       14.86        91.76        24.79        18.48        10.62        23.51 
TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 
       38.76         8.94        20.58       127.59         5.82         7.59 
TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 
       33.21        21.73        15.98        12.23        15.85         9.11 
TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 TCGA-12-1598 TCGA-12-1599 TCGA-12-1602 
       14.53         3.98         4.14        15.65        25.68         6.77 
TCGA-12-3644 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 
       59.77        26.93        15.22        10.95        12.69        34.92 
TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 
       14.53        14.93         3.22         2.04        15.12        11.97 
TCGA-14-0781 TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 TCGA-14-0813 
        0.95        23.05         2.24        11.24        13.78         1.35 
TCGA-14-0817 TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 TCGA-14-0871 TCGA-14-1034 
        5.39         2.89        16.50        26.33        28.93        15.95 
TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 
       19.30         0.79         1.38         1.12         3.75        32.05 
TCGA-14-1450 TCGA-14-1451 TCGA-14-1452 TCGA-14-1453 TCGA-14-1454 TCGA-14-1455 
       58.78        23.11         7.10         1.15        30.18         0.92 
TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 
       40.96         6.67        12.43         0.99         1.97        17.79 
TCGA-14-1823 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 
       17.85         7.63         5.88         7.17        17.49         7.96 
TCGA-14-3477 TCGA-14-4157 TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-15-1449 
        3.78         3.42        13.78        50.53        19.10        13.28 
TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 
        3.91        17.59        26.07         4.31        29.03         4.57 
TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 
       10.29        14.01         9.14        21.24        13.97         6.41 
TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 
       11.77        21.90         8.61         0.66        14.27         3.39 
TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 TCGA-19-1389 TCGA-19-1786 TCGA-19-1787 
       10.75         9.07         5.95         4.64         7.17        12.66 
TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 
        3.25         0.13         9.67         4.87         1.08         7.53 
TCGA-19-2624 TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 
        0.16        24.23         7.00         7.04         6.64        17.19 
TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5958 
        8.02        18.90         4.73        12.10         1.78        14.07 
TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 
       16.80        14.96        17.79         3.98        28.54        10.03 
TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 
       13.87         9.73        31.33         7.13         9.37         9.40 
TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 
       14.86         5.49         8.88        18.97         1.58         7.92 
TCGA-26-6174 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 
        2.33        19.33         5.06        16.60         9.86        24.23 
TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 
       40.54        21.30        30.05        14.04        11.51        24.76 
TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 
       10.39        10.39        16.08         7.59         2.86        14.40 
TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 
       15.78         0.20         2.53         9.21         8.35         7.63 
TCGA-28-1752 TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 TCGA-28-2502 
        8.48         1.22         1.55         2.83         0.13         0.66 
TCGA-28-2506 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 
        6.74         7.30         5.26        14.93        11.28        17.88 
TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5216 TCGA-28-5218 
       14.53        11.77        31.27        23.44        13.64         5.16 
TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 
       22.68        12.76         5.42        15.39        21.07         0.49 
TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 
        0.10        15.85        19.50         1.18         4.67        12.69 
TCGA-32-1987 TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2616 
       14.86        16.93        12.23        20.78        15.02         7.36 
TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4210 TCGA-32-4211 
        8.84        22.78        25.18        21.14         3.72        12.59 
TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 
       19.86        10.85        19.23         0.85        13.35         8.94 
TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 
        9.53         0.99         4.44        11.84         0.20        15.12 
TCGA-41-6646 TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 
       12.46         4.14        14.76         3.45        20.91         4.34 
TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 
       14.33         8.22         7.50         4.80         4.54         3.09 
TCGA-76-4929 TCGA-76-4931 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 
        3.65         9.17        10.78        16.70         3.29         2.70 
TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 
       11.38        17.06         8.35        20.98         4.83         5.03 
TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 
        0.23         9.27         7.73         7.79         1.61        17.72 
TCGA-87-5896 TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC 
       26.30         5.92         6.28        20.55 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             2.04              0.10 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            53.19            127.59 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
           10.190            11.935 
[1] "2.0 - 53.2 (10.2)"  "0.1 - 127.6 (11.9)"
[1] "hr=" "1.1"
D44V2, continuous
D44V3, binary
                   cls
clus                  0   1
  2P LOSS MUTATED    17  14
  2P LOSS WILD-TYPE 207 332
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     17   14
  2P LOSS WILD-TYPE  207  332
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE              17               207
  MALE                14               332
[1] 2 2
[1] FALSE
D44V4, continuous
                   vv
clus                GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  2P LOSS MUTATED                               1                   1
  2P LOSS WILD-TYPE                            26                  17
                   vv
clus                UNTREATED PRIMARY (DE NOVO) GBM
  2P LOSS MUTATED                                29
  2P LOSS WILD-TYPE                             496
D44V5, multiclass
                                 clus
vv                                2P LOSS MUTATED 2P LOSS WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                 1                26
  TREATED PRIMARY GBM                           1                17
  UNTREATED PRIMARY (DE NOVO) GBM              29               496
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V6, binary
                   cls
clus                  0   1
  2P LOSS MUTATED    18  13
  2P LOSS WILD-TYPE 364 175
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     18   13
  2P LOSS WILD-TYPE  364  175
     clus
vv    2P LOSS MUTATED 2P LOSS WILD-TYPE
  NO               18               364
  YES              13               175
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2P LOSS MUTATED       0                         1    30
  2P LOSS WILD-TYPE    13                        48   455
D44V7, multiclass
                           clus
vv                          2P LOSS MUTATED 2P LOSS WILD-TYPE
  ASIAN                                   0                13
  BLACK OR AFRICAN AMERICAN               1                48
  WHITE                                  30               455
[1] 3 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
  2P LOSS MUTATED     0  25
  2P LOSS WILD-TYPE  12 447
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      0   25
  2P LOSS WILD-TYPE   12  447
                        clus
vv                       2P LOSS MUTATED 2P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                12
  NOT HISPANIC OR LATINO              25               447
[1] 2 2
[1] FALSE

Clustering(45) Variable = 2Q LOSS MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                 0   1
  2Q LOSS MUTATED     3  28
  2Q LOSS WILD-TYPE 101 437
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               31               538 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               28               437 
$`2Q LOSS MUTATED`
TCGA-02-0024 TCGA-02-0059 TCGA-02-0074 TCGA-02-0075 TCGA-06-0152 TCGA-06-0182 
       53.10         9.57        10.19        20.84        12.33         3.65 
TCGA-06-0188 TCGA-06-0414 TCGA-06-1087 TCGA-06-5416 TCGA-06-5856 TCGA-06-6694 
       44.58        35.11         4.04         6.71         3.75         7.36 
TCGA-06-A6S0 TCGA-12-0826 TCGA-12-1600 TCGA-12-3646 TCGA-14-0783 TCGA-14-0812 
        3.12        27.78        14.73        44.02         6.21         3.25 
TCGA-14-0867 TCGA-15-1444 TCGA-15-1447 TCGA-16-0850 TCGA-19-1388 TCGA-19-1390 
        2.04        50.53        53.19        16.37        12.95        25.38 
TCGA-19-1392 TCGA-19-2625 TCGA-19-5956 TCGA-28-2509 TCGA-28-5215 TCGA-32-2615 
        3.65         4.08        22.49         4.77        11.01        15.95 
TCGA-76-4934 
        2.53 

$`2Q LOSS WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 
       11.77         4.73        18.35        23.18        10.59        35.41 
TCGA-02-0011 TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 
       20.71        82.59        20.61        87.06        77.65        20.12 
TCGA-02-0025 TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 
       42.74        24.59        12.16        90.58         2.83        14.14 
TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 
        3.62        10.72        10.52        18.31         6.87        14.73 
TCGA-02-0048 TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 TCGA-02-0055 TCGA-02-0057 
        3.22        15.09        12.59         6.54         2.50        19.86 
TCGA-02-0058 TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 TCGA-02-0069 TCGA-02-0070 
        8.35         6.02        19.73        26.43        28.70        25.05 
TCGA-02-0071 TCGA-02-0079 TCGA-02-0080 TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 
        5.49        27.25        89.72        22.72        12.62        51.32 
TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 TCGA-02-0104 
        8.81        57.76        16.96         3.48        27.02        65.00 
TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 TCGA-02-0113 TCGA-02-0114 TCGA-02-0115 
       11.67        17.65        23.18        92.65        99.98        15.65 
TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 TCGA-02-0266 TCGA-02-0269 TCGA-02-0271 
       48.95        16.54        16.93        17.72        10.75        14.47 
TCGA-02-0281 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 
        3.98        13.87        14.20        15.95        12.23         9.90 
TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 TCGA-02-0333 
        7.73        10.62         7.33        15.91        25.71         4.37 
TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 
       25.12        10.59        12.39        14.50        10.55        47.11 
TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 TCGA-02-2466 TCGA-02-2470 
       11.34         9.27        16.21         3.35        16.80        12.92 
TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 
       15.32        15.45        20.32         2.70         6.15        20.38 
TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 
       47.61         6.94         3.98        22.72        33.67        12.95 
TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 
       25.35        14.30        26.70        24.23        11.90         0.20 
TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 
       10.29         2.20        11.74         2.33        20.09        17.79 
TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0154 TCGA-06-0155 
       10.09         8.61        19.46        46.59        13.94        10.45 
TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 
        3.19        10.82         9.44        11.80         3.42        56.91 
TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 
       10.65         5.85        19.66         3.29        13.12         4.47 
TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 
        3.22         4.04        91.00         4.18        88.14        20.25 
TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 
       69.90        73.84        27.22        15.42        10.42        38.96 
TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 
        4.67         7.40         5.56         0.39         7.66         8.42 
TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 
        7.63         7.40        11.84         0.53        15.02        24.16 
TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 
        0.72        19.82        13.64        13.32        20.42        48.69 
TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 
       10.82         9.01         0.26        72.36         4.70         9.57 
TCGA-06-0413 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 
        3.16        12.62         5.75         5.75         9.80         2.10 
TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 
       23.57        14.20        26.40        46.88         7.86         2.70 
TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 
        2.70         0.92        43.46        46.19         5.65         7.17 
TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 
       40.41        16.57        20.78        26.76        23.93         6.84 
TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 
       26.79        11.84        15.32        13.61        33.90        15.32 
TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 
        1.08        12.49         4.93        17.65        12.56        30.64 
TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 
        5.95        16.64         5.98         4.37         0.43        31.50 
TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 
       11.74         3.55         8.35         4.54         8.81         8.98 
TCGA-06-5415 TCGA-06-5418 TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 TCGA-06-6389 
        8.55         2.73         6.15         4.57         5.23         7.79 
TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 
        5.39         1.48       120.56         8.32        12.85         4.77 
TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S1 
        1.55         4.77         4.96         4.70         1.87         2.56 
TCGA-06-A7TK TCGA-06-A7TL TCGA-08-0244 TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 
        5.39         5.42        22.68        37.84         4.18       115.86 
TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 
        1.74         8.42        25.71        12.16         9.80        29.23 
TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 
       65.33         1.28         8.42        17.95        24.56        31.10 
TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 
       37.58        22.29         3.39        12.23        14.93        18.02 
TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 
       15.35        13.97         0.72        12.56         4.27        42.15 
TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 
       11.08        19.59        58.68        19.33        10.75         4.80 
TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 
        7.27        15.98        18.41         7.56        15.35        14.73 
TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 
       12.99        34.92        10.45         7.59        94.78         0.10 
TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 
       38.17        25.97        26.66        12.13         3.65        20.38 
TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 
       28.41        15.06        53.85        43.23         7.63         9.73 
TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 
       14.93        14.86        91.76        24.79        18.48        10.62 
TCGA-12-0822 TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 
       23.51        38.76         8.94        20.58       127.59         5.82 
TCGA-12-1090 TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 
        7.59        33.21        21.73        15.98        12.23        15.85 
TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 TCGA-12-1598 TCGA-12-1599 
        9.11        14.53         3.98         4.14        15.65        25.68 
TCGA-12-1602 TCGA-12-3644 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 
        6.77        59.77        26.93        15.22        10.95        12.69 
TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 
       34.92        14.53        14.93         3.22         2.04        15.12 
TCGA-14-0740 TCGA-14-0781 TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 
       11.97         0.95        23.05         2.24        11.24        13.78 
TCGA-14-0813 TCGA-14-0817 TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 TCGA-14-0871 
        1.35         5.39         2.89        16.50        26.33        28.93 
TCGA-14-1034 TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 
       15.95        19.30         0.79         1.38         1.12         3.75 
TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 TCGA-14-1452 TCGA-14-1453 TCGA-14-1454 
       32.05        58.78        23.11         7.10         1.15        30.18 
TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 
        0.92        40.96         6.67        12.43         0.99         1.97 
TCGA-14-1821 TCGA-14-1823 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 
       17.79        17.85         7.63         5.88         7.17        17.49 
TCGA-14-2555 TCGA-14-3477 TCGA-14-4157 TCGA-15-0742 TCGA-15-1446 TCGA-15-1449 
        7.96         3.78         3.42        13.78        19.10        13.28 
TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 
        3.91        17.59        26.07         4.31        29.03         4.57 
TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 
       10.29        14.01         9.14        21.24        13.97         6.41 
TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 
       11.77        21.90         8.61         0.66        14.27         3.39 
TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 TCGA-19-1389 TCGA-19-1786 TCGA-19-1787 
       10.75         9.07         5.95         4.64         7.17        12.66 
TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 
        3.25         0.13         9.67         4.87         1.08         7.53 
TCGA-19-2624 TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 
        0.16        24.23         7.00         7.04         6.64        17.19 
TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5958 
        8.02        18.90         4.73        12.10         1.78        14.07 
TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 
       16.80        14.96        17.79         3.98        28.54        10.03 
TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 
       13.87         9.73        31.33         7.13         9.37         9.40 
TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 
       14.86         5.49         8.88        18.97         1.58         7.92 
TCGA-26-6174 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 
        2.33        19.33         5.06        16.60         9.86        24.23 
TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 
       40.54        21.30        30.05        14.04        11.51        24.76 
TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 
       10.39        10.39        16.08         7.59         2.86        14.40 
TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 
       15.78         0.20         2.53         9.21         8.35         7.63 
TCGA-28-1752 TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 TCGA-28-2502 
        8.48         1.22         1.55         2.83         0.13         0.66 
TCGA-28-2506 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 
        6.74         7.30         5.26        14.93        11.28        17.88 
TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5216 TCGA-28-5218 
       14.53        11.77        31.27        23.44        13.64         5.16 
TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 
       22.68        12.76         5.42        15.39        21.07         0.49 
TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 
        0.10        15.85        19.50         1.18         4.67        12.69 
TCGA-32-1987 TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2616 
       14.86        16.93        12.23        20.78        15.02         7.36 
TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4210 TCGA-32-4211 
        8.84        22.78        25.18        21.14         3.72        12.59 
TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 
       19.86        10.85        19.23         0.85        13.35         8.94 
TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 
        9.53         0.99         4.44        11.84         0.20        15.12 
TCGA-41-6646 TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 
       12.46         4.14        14.76         3.45        20.91         4.34 
TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 
       14.33         8.22         7.50         4.80         4.54         3.09 
TCGA-76-4929 TCGA-76-4931 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 
        3.65         9.17        10.78        16.70         3.29         2.70 
TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 
       11.38        17.06         8.35        20.98         4.83         5.03 
TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 
        0.23         9.27         7.73         7.79         1.61        17.72 
TCGA-87-5896 TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC 
       26.30         5.92         6.28        20.55 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             2.04              0.10 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            53.19            127.59 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            11.01             11.87 
[1] "2.0 - 53.2 (11.0)"  "0.1 - 127.6 (11.9)"
[1] "hr=" "1"  
D45V2, continuous
D45V3, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED    16  15
  2Q LOSS WILD-TYPE 208 331
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     16   15
  2Q LOSS WILD-TYPE  208  331
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE              16               208
  MALE                15               331
[1] 2 2
[1] FALSE
D45V4, continuous
                   vv
clus                GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  2Q LOSS MUTATED                               2                   1
  2Q LOSS WILD-TYPE                            25                  17
                   vv
clus                UNTREATED PRIMARY (DE NOVO) GBM
  2Q LOSS MUTATED                                28
  2Q LOSS WILD-TYPE                             497
D45V5, multiclass
                                 clus
vv                                2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                 2                25
  TREATED PRIMARY GBM                           1                17
  UNTREATED PRIMARY (DE NOVO) GBM              28               497
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V6, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED    17  14
  2Q LOSS WILD-TYPE 365 174
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     17   14
  2Q LOSS WILD-TYPE  365  174
     clus
vv    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  NO               17               365
  YES              14               174
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2Q LOSS MUTATED       0                         1    30
  2Q LOSS WILD-TYPE    13                        48   455
D45V7, multiclass
                           clus
vv                          2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  ASIAN                                   0                13
  BLACK OR AFRICAN AMERICAN               1                48
  WHITE                                  30               455
[1] 3 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
  2Q LOSS MUTATED     0  25
  2Q LOSS WILD-TYPE  12 447
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      0   25
  2Q LOSS WILD-TYPE   12  447
                        clus
vv                       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                12
  NOT HISPANIC OR LATINO              25               447
[1] 2 2
[1] FALSE

Clustering(46) Variable = 3P LOSS MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                 0   1
  3P LOSS MUTATED     7  33
  3P LOSS WILD-TYPE  97 432
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               40               529 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               33               432 
$`3P LOSS MUTATED`
TCGA-02-0055 TCGA-02-0083 TCGA-02-0084 TCGA-02-0106 TCGA-02-0113 TCGA-02-0266 
        2.50        22.72        12.62        11.67        92.65        17.72 
TCGA-02-0330 TCGA-02-0432 TCGA-02-2486 TCGA-06-0128 TCGA-06-0152 TCGA-06-0216 
       15.91        47.11        20.32        22.72        12.33        24.16 
TCGA-06-0221 TCGA-06-0409 TCGA-06-0878 TCGA-06-1806 TCGA-06-5416 TCGA-06-5859 
       19.82        72.36         7.17        15.32         6.71         4.57 
TCGA-06-6390 TCGA-08-0246 TCGA-08-0386 TCGA-08-0390 TCGA-08-0516 TCGA-12-0776 
        5.39         4.18        18.02        13.97        19.59         9.73 
TCGA-12-0826 TCGA-12-3653 TCGA-14-0862 TCGA-14-0871 TCGA-14-1458 TCGA-14-1823 
       27.78        14.53         2.89        28.93         6.67        17.85 
TCGA-14-3477 TCGA-15-1447 TCGA-15-1449 TCGA-19-1388 TCGA-19-A6J4 TCGA-26-1439 
        3.78        53.19        13.28        12.95         3.98        13.87 
TCGA-28-1752 TCGA-32-1991 TCGA-32-2615 TCGA-76-4929 
        8.48        16.93        15.95         3.65 

$`3P LOSS WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 
       11.77         4.73        18.35        23.18        10.59        35.41 
TCGA-02-0011 TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 
       20.71        82.59        20.61        87.06        77.65        20.12 
TCGA-02-0024 TCGA-02-0025 TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 
       53.10        42.74        24.59        12.16        90.58         2.83 
TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 
       14.14         3.62        10.72        10.52        18.31         6.87 
TCGA-02-0047 TCGA-02-0048 TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 TCGA-02-0057 
       14.73         3.22        15.09        12.59         6.54        19.86 
TCGA-02-0058 TCGA-02-0059 TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 TCGA-02-0069 
        8.35         9.57         6.02        19.73        26.43        28.70 
TCGA-02-0070 TCGA-02-0071 TCGA-02-0074 TCGA-02-0075 TCGA-02-0079 TCGA-02-0080 
       25.05         5.49        10.19        20.84        27.25        89.72 
TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 
       51.32         8.81        57.76        16.96         3.48        27.02 
TCGA-02-0104 TCGA-02-0107 TCGA-02-0111 TCGA-02-0114 TCGA-02-0115 TCGA-02-0116 
       65.00        17.65        23.18        99.98        15.65        48.95 
TCGA-02-0258 TCGA-02-0260 TCGA-02-0269 TCGA-02-0271 TCGA-02-0281 TCGA-02-0285 
       16.54        16.93        10.75        14.47         3.98        13.87 
TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 
       14.20        15.95        12.23         9.90         7.73        10.62 
TCGA-02-0326 TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 
        7.33        25.71         4.37        25.12        10.59        12.39 
TCGA-02-0422 TCGA-02-0430 TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 
       14.50        10.55        11.34         9.27        16.21         3.35 
TCGA-02-2466 TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 TCGA-06-0119 TCGA-06-0122 
       16.80        12.92        15.32        15.45         2.70         6.15 
TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0129 TCGA-06-0130 
       20.38        47.61         6.94         3.98        33.67        12.95 
TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 
       25.35        14.30        26.70        24.23        11.90         0.20 
TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 
       10.29         2.20        11.74         2.33        20.09        17.79 
TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0154 TCGA-06-0155 
       10.09         8.61        19.46        46.59        13.94        10.45 
TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 
        3.19        10.82         9.44        11.80         3.42        56.91 
TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 
       10.65         5.85        19.66         3.29        13.12         4.47 
TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 
        3.22         4.04        91.00         4.18        88.14        20.25 
TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 
        3.65        69.90        73.84        27.22        44.58        15.42 
TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 
       10.42        38.96         4.67         7.40         5.56         0.39 
TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 
        7.66         8.42         7.63         7.40        11.84         0.53 
TCGA-06-0214 TCGA-06-0219 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 
       15.02         0.72        13.64        13.32        20.42        48.69 
TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 
       10.82         9.01         0.26         4.70         9.57         3.16 
TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 
       35.11        12.62         5.75         5.75         9.80         2.10 
TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 
       23.57        14.20        26.40        46.88         7.86         2.70 
TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 TCGA-06-0879 
        2.70         0.92        43.46        46.19         5.65        40.41 
TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 
       16.57        20.78        26.76        23.93         6.84         4.04 
TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-2557 
       26.79        11.84        15.32        13.61        33.90         1.08 
TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 
       12.49         4.93        17.65        12.56        30.64         5.95 
TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-5408 
       16.64         5.98         4.37         0.43        31.50        11.74 
TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 
        3.55         8.35         4.54         8.81         8.98         8.55 
TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 TCGA-06-6388 TCGA-06-6389 TCGA-06-6391 
        2.73         3.75         6.15         5.23         7.79         1.48 
TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 
      120.56         7.36         8.32        12.85         4.77         1.55 
TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 
        4.77         4.96         4.70         1.87         3.12         2.56 
TCGA-06-A7TK TCGA-06-A7TL TCGA-08-0244 TCGA-08-0245 TCGA-08-0344 TCGA-08-0345 
        5.39         5.42        22.68        37.84       115.86         1.74 
TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 
        8.42        25.71        12.16         9.80        29.23        65.33 
TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 
        1.28         8.42        17.95        24.56        31.10        37.58 
TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0389 TCGA-08-0392 
       22.29         3.39        12.23        14.93        15.35         0.72 
TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 TCGA-08-0517 TCGA-08-0518 
       12.56         4.27        42.15        11.08        58.68        19.33 
TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 
       10.75         4.80         7.27        15.98        18.41         7.56 
TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 
       15.35        14.73        12.99        34.92        10.45         7.59 
TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 
       94.78         0.10        38.17        25.97        26.66        12.13 
TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 
        3.65        20.38        28.41        15.06        53.85        43.23 
TCGA-12-0775 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 
        7.63        14.93        14.86        91.76        24.79        18.48 
TCGA-12-0821 TCGA-12-0822 TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 
       10.62        23.51        38.76         8.94        20.58       127.59 
TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 
        5.82         7.59        33.21        21.73        15.98        12.23 
TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 TCGA-12-1598 
       15.85         9.11        14.53         3.98         4.14        15.65 
TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 
       25.68        14.73         6.77        59.77        44.02        26.93 
TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-5295 TCGA-12-5299 
       15.22        10.95        12.69        34.92        14.93         3.22 
TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 
        2.04        15.12        11.97         0.95         6.21        23.05 
TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 TCGA-14-0812 TCGA-14-0813 TCGA-14-0817 
        2.24        11.24        13.78         3.25         1.35         5.39 
TCGA-14-0865 TCGA-14-0866 TCGA-14-0867 TCGA-14-1034 TCGA-14-1037 TCGA-14-1043 
       16.50        26.33         2.04        15.95        19.30         0.79 
TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 
        1.38         1.12         3.75        32.05        58.78        23.11 
TCGA-14-1452 TCGA-14-1453 TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1459 
        7.10         1.15        30.18         0.92        40.96        12.43 
TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 
        0.99         1.97        17.79         7.63         5.88         7.17 
TCGA-14-2554 TCGA-14-2555 TCGA-14-4157 TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 
       17.49         7.96         3.42        13.78        50.53        19.10 
TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 
        3.91        17.59        26.07        16.37         4.31        29.03 
TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 
        4.57        10.29        14.01         9.14        21.24        13.97 
TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 TCGA-19-0962 TCGA-19-0963 
        6.41        11.77        21.90         8.61         0.66        14.27 
TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 TCGA-19-1389 TCGA-19-1390 
        3.39        10.75         9.07         5.95         4.64        25.38 
TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 
        3.65         7.17        12.66         3.25         0.13         9.67 
TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 
        4.87         1.08         7.53         0.16         4.08        24.23 
TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 
        7.00         7.04         6.64        17.19         8.02        18.90 
TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 
        4.73        12.10         1.78        22.49        14.07        16.80 
TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1440 TCGA-26-1442 
       14.96        17.79        28.54        10.03         9.73        31.33 
TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 
        7.13         9.37         9.40        14.86         5.49         8.88 
TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-26-A7UX TCGA-27-1830 
       18.97         1.58         7.92         2.33        19.33         5.06 
TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 
       16.60         9.86        24.23        40.54        21.30        30.05 
TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 
       14.04        11.51        24.76        10.39        10.39        16.08 
TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 
        7.59         2.86        14.40        15.78         0.20         2.53 
TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 
        9.21         8.35         7.63         1.22         1.55         2.83 
TCGA-28-1757 TCGA-28-2502 TCGA-28-2506 TCGA-28-2509 TCGA-28-2513 TCGA-28-2514 
        0.13         0.66         6.74         4.77         7.30         5.26 
TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 
       14.93        11.28        17.88        14.53        11.77        31.27 
TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 
       23.44        11.01        13.64         5.16        22.68        12.76 
TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 TCGA-32-1978 
        5.42        15.39        21.07         0.49         0.10        15.85 
TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 TCGA-32-2491 
       19.50         1.18         4.67        12.69        14.86        12.23 
TCGA-32-2494 TCGA-32-2495 TCGA-32-2616 TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 
       20.78        15.02         7.36         8.84        22.78        25.18 
TCGA-32-4208 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 
       21.14         3.72        12.59        19.86        10.85        19.23 
TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 
        0.85        13.35         8.94         9.53         0.99         4.44 
TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9S TCGA-4W-AA9T 
       11.84         0.20        15.12        12.46         4.14        14.76 
TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 
        3.45        20.91         4.34        14.33         8.22         7.50 
TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4931 TCGA-76-4934 TCGA-76-4935 
        4.80         4.54         3.09         9.17         2.53        10.78 
TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 
       16.70         3.29         2.70        11.38        17.06         8.35 
TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 
       20.98         4.83         5.03         0.23         9.27         7.73 
TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R TCGA-RR-A6KA 
        7.79         1.61        17.72        26.30         5.92         6.28 
TCGA-RR-A6KC 
       20.55 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
              2.5               0.1 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            92.65            127.59 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            14.25             11.77 
[1] "2.5 - 92.7 (14.2)"  "0.1 - 127.6 (11.8)"
[1] "hr=" "1.1"
D46V2, continuous
D46V3, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    16  24
  3P LOSS WILD-TYPE 208 322
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     16   24
  3P LOSS WILD-TYPE  208  322
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE              16               208
  MALE                24               322
[1] 2 2
[1] FALSE
D46V4, continuous
                   vv
clus                GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  3P LOSS MUTATED                               2                   2
  3P LOSS WILD-TYPE                            25                  16
                   vv
clus                UNTREATED PRIMARY (DE NOVO) GBM
  3P LOSS MUTATED                                36
  3P LOSS WILD-TYPE                             489
D46V5, multiclass
                                 clus
vv                                3P LOSS MUTATED 3P LOSS WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                 2                25
  TREATED PRIMARY GBM                           2                16
  UNTREATED PRIMARY (DE NOVO) GBM              36               489
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V6, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    32   8
  3P LOSS WILD-TYPE 350 180
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     32    8
  3P LOSS WILD-TYPE  350  180
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  NO               32               350
  YES               8               180
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3P LOSS MUTATED       0                         4    35
  3P LOSS WILD-TYPE    13                        45   450
D46V7, multiclass
                           clus
vv                          3P LOSS MUTATED 3P LOSS WILD-TYPE
  ASIAN                                   0                13
  BLACK OR AFRICAN AMERICAN               4                45
  WHITE                                  35               450
[1] 3 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
  3P LOSS MUTATED     2  32
  3P LOSS WILD-TYPE  10 440
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      2   32
  3P LOSS WILD-TYPE   10  440
                        clus
vv                       3P LOSS MUTATED 3P LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                10
  NOT HISPANIC OR LATINO              32               440
[1] 2 2
[1] FALSE

Clustering(47) Variable = 3Q LOSS MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                 0   1
  3Q LOSS MUTATED     4  30
  3Q LOSS WILD-TYPE 100 435
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               34               535 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               30               435 
$`3Q LOSS MUTATED`
TCGA-02-0055 TCGA-02-0060 TCGA-02-0084 TCGA-02-0113 TCGA-02-0330 TCGA-06-0128 
        2.50         6.02        12.62        92.65        15.91        22.72 
TCGA-06-0152 TCGA-06-0214 TCGA-06-0216 TCGA-06-0221 TCGA-06-0409 TCGA-06-1806 
       12.33        15.02        24.16        19.82        72.36        15.32 
TCGA-06-5859 TCGA-06-6390 TCGA-08-0246 TCGA-08-0386 TCGA-08-0390 TCGA-08-0516 
        4.57         5.39         4.18        18.02        13.97        19.59 
TCGA-12-0691 TCGA-12-0826 TCGA-12-1099 TCGA-12-3653 TCGA-14-0812 TCGA-14-0871 
       12.13        27.78         4.14        14.53         3.25        28.93 
TCGA-14-1458 TCGA-14-1823 TCGA-15-1447 TCGA-15-1449 TCGA-19-1388 TCGA-19-A6J4 
        6.67        17.85        53.19        13.28        12.95         3.98 
TCGA-26-1439 TCGA-28-1752 TCGA-32-2615 TCGA-76-4929 
       13.87         8.48        15.95         3.65 

$`3Q LOSS WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 
       11.77         4.73        18.35        23.18        10.59        35.41 
TCGA-02-0011 TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 
       20.71        82.59        20.61        87.06        77.65        20.12 
TCGA-02-0024 TCGA-02-0025 TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 
       53.10        42.74        24.59        12.16        90.58         2.83 
TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 
       14.14         3.62        10.72        10.52        18.31         6.87 
TCGA-02-0047 TCGA-02-0048 TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 TCGA-02-0057 
       14.73         3.22        15.09        12.59         6.54        19.86 
TCGA-02-0058 TCGA-02-0059 TCGA-02-0064 TCGA-02-0068 TCGA-02-0069 TCGA-02-0070 
        8.35         9.57        19.73        26.43        28.70        25.05 
TCGA-02-0071 TCGA-02-0074 TCGA-02-0075 TCGA-02-0079 TCGA-02-0080 TCGA-02-0083 
        5.49        10.19        20.84        27.25        89.72        22.72 
TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 
       51.32         8.81        57.76        16.96         3.48        27.02 
TCGA-02-0104 TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 TCGA-02-0114 TCGA-02-0115 
       65.00        11.67        17.65        23.18        99.98        15.65 
TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 TCGA-02-0266 TCGA-02-0269 TCGA-02-0271 
       48.95        16.54        16.93        17.72        10.75        14.47 
TCGA-02-0281 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 
        3.98        13.87        14.20        15.95        12.23         9.90 
TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 
        7.73        10.62         7.33        25.71         4.37        25.12 
TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 
       10.59        12.39        14.50        10.55        47.11        11.34 
TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 TCGA-02-2466 TCGA-02-2470 TCGA-02-2483 
        9.27        16.21         3.35        16.80        12.92        15.32 
TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 
       15.45        20.32         2.70         6.15        20.38        47.61 
TCGA-06-0126 TCGA-06-0127 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 
        6.94         3.98        33.67        12.95        25.35        14.30 
TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 
       26.70        24.23        11.90         0.20        10.29         2.20 
TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 
       11.74         2.33        20.09        17.79        10.09         8.61 
TCGA-06-0150 TCGA-06-0151 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 
       19.46        46.59        13.94        10.45         3.19        10.82 
TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 
        9.44        11.80         3.42        56.91        10.65         5.85 
TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 
       19.66         3.29        13.12         4.47         3.22         4.04 
TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 
       91.00         4.18        88.14        20.25         3.65        69.90 
TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 
       73.84        27.22        44.58        15.42        10.42        38.96 
TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 
        4.67         7.40         5.56         0.39         7.66         8.42 
TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0219 TCGA-06-0237 
        7.63         7.40        11.84         0.53         0.72        13.64 
TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 
       13.32        20.42        48.69        10.82         9.01         0.26 
TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 
        4.70         9.57         3.16        35.11        12.62         5.75 
TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 
        5.75         9.80         2.10        23.57        14.20        26.40 
TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 
       46.88         7.86         2.70         2.70         0.92        43.46 
TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 
       46.19         5.65         7.17        40.41        16.57        20.78 
TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 
       26.76        23.93         6.84         4.04        26.79        11.84 
TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 
       15.32        13.61        33.90         1.08        12.49         4.93 
TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 
       17.65        12.56        30.64         5.95        16.64         5.98 
TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 
        4.37         0.43        31.50        11.74         3.55         8.35 
TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 TCGA-06-5418 
        4.54         8.81         8.98         8.55         6.71         2.73 
TCGA-06-5856 TCGA-06-5858 TCGA-06-6388 TCGA-06-6389 TCGA-06-6391 TCGA-06-6693 
        3.75         6.15         5.23         7.79         1.48       120.56 
TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 
        7.36         8.32        12.85         4.77         1.55         4.77 
TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK 
        4.96         4.70         1.87         3.12         2.56         5.39 
TCGA-06-A7TL TCGA-08-0244 TCGA-08-0245 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 
        5.42        22.68        37.84       115.86         1.74         8.42 
TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 
       25.71        12.16         9.80        29.23        65.33         1.28 
TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 
        8.42        17.95        24.56        31.10        37.58        22.29 
TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0389 TCGA-08-0392 TCGA-08-0509 
        3.39        12.23        14.93        15.35         0.72        12.56 
TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 
        4.27        42.15        11.08        58.68        19.33        10.75 
TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 
        4.80         7.27        15.98        18.41         7.56        15.35 
TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 
       14.73        12.99        34.92        10.45         7.59        94.78 
TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0692 TCGA-12-0703 
        0.10        38.17        25.97        26.66         3.65        20.38 
TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 
       28.41        15.06        53.85        43.23         7.63         9.73 
TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 
       14.93        14.86        91.76        24.79        18.48        10.62 
TCGA-12-0822 TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 
       23.51        38.76         8.94        20.58       127.59         5.82 
TCGA-12-1090 TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 
        7.59        33.21        21.73        15.98        12.23        15.85 
TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 
        9.11        14.53         3.98        15.65        25.68        14.73 
TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 
        6.77        59.77        44.02        26.93        15.22        10.95 
TCGA-12-3651 TCGA-12-3652 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 
       12.69        34.92        14.93         3.22         2.04        15.12 
TCGA-14-0740 TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 
       11.97         0.95         6.21        23.05         2.24        11.24 
TCGA-14-0790 TCGA-14-0813 TCGA-14-0817 TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 
       13.78         1.35         5.39         2.89        16.50        26.33 
TCGA-14-0867 TCGA-14-1034 TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 TCGA-14-1396 
        2.04        15.95        19.30         0.79         1.38         1.12 
TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 TCGA-14-1452 TCGA-14-1453 
        3.75        32.05        58.78        23.11         7.10         1.15 
TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 
       30.18         0.92        40.96        12.43         0.99         1.97 
TCGA-14-1821 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 
       17.79         7.63         5.88         7.17        17.49         7.96 
TCGA-14-3477 TCGA-14-4157 TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-16-0846 
        3.78         3.42        13.78        50.53        19.10         3.91 
TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 
       17.59        26.07        16.37         4.31        29.03         4.57 
TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 
       10.29        14.01         9.14        21.24        13.97         6.41 
TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 
       11.77        21.90         8.61         0.66        14.27         3.39 
TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 TCGA-19-1389 TCGA-19-1390 TCGA-19-1392 
       10.75         9.07         5.95         4.64        25.38         3.65 
TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 
        7.17        12.66         3.25         0.13         9.67         4.87 
TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 
        1.08         7.53         0.16         4.08        24.23         7.00 
TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 
        7.04         6.64        17.19         8.02        18.90         4.73 
TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 
       12.10         1.78        22.49        14.07        16.80        14.96 
TCGA-19-A60I TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 
       17.79        28.54        10.03         9.73        31.33         7.13 
TCGA-26-1799 TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 
        9.37         9.40        14.86         5.49         8.88        18.97 
TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 
        1.58         7.92         2.33        19.33         5.06        16.60 
TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 
        9.86        24.23        40.54        21.30        30.05        14.04 
TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 
       11.51        24.76        10.39        10.39        16.08         7.59 
TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 
        2.86        14.40        15.78         0.20         2.53         9.21 
TCGA-28-1750 TCGA-28-1751 TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 
        8.35         7.63         1.22         1.55         2.83         0.13 
TCGA-28-2502 TCGA-28-2506 TCGA-28-2509 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 
        0.66         6.74         4.77         7.30         5.26        14.93 
TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 
       11.28        17.88        14.53        11.77        31.27        23.44 
TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 
       11.01        13.64         5.16        22.68        12.76         5.42 
TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 
       15.39        21.07         0.49         0.10        15.85        19.50 
TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 TCGA-32-1991 TCGA-32-2491 
        1.18         4.67        12.69        14.86        16.93        12.23 
TCGA-32-2494 TCGA-32-2495 TCGA-32-2616 TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 
       20.78        15.02         7.36         8.84        22.78        25.18 
TCGA-32-4208 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 
       21.14         3.72        12.59        19.86        10.85        19.23 
TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 
        0.85        13.35         8.94         9.53         0.99         4.44 
TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9S TCGA-4W-AA9T 
       11.84         0.20        15.12        12.46         4.14        14.76 
TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 
        3.45        20.91         4.34        14.33         8.22         7.50 
TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4931 TCGA-76-4934 TCGA-76-4935 
        4.80         4.54         3.09         9.17         2.53        10.78 
TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 
       16.70         3.29         2.70        11.38        17.06         8.35 
TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 
       20.98         4.83         5.03         0.23         9.27         7.73 
TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R TCGA-RR-A6KA 
        7.79         1.61        17.72        26.30         5.92         6.28 
TCGA-RR-A6KC 
       20.55 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
              2.5               0.1 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            92.65            127.59 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            13.92             11.77 
[1] "2.5 - 92.7 (13.9)"  "0.1 - 127.6 (11.8)"
[1] "hr=" "1"  
D47V2, continuous
D47V3, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    15  19
  3Q LOSS WILD-TYPE 209 327
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     15   19
  3Q LOSS WILD-TYPE  209  327
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE              15               209
  MALE                19               327
[1] 2 2
[1] FALSE
D47V4, continuous
                   vv
clus                GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  3Q LOSS MUTATED                               2                   1
  3Q LOSS WILD-TYPE                            25                  17
                   vv
clus                UNTREATED PRIMARY (DE NOVO) GBM
  3Q LOSS MUTATED                                31
  3Q LOSS WILD-TYPE                             494
D47V5, multiclass
                                 clus
vv                                3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                 2                25
  TREATED PRIMARY GBM                           1                17
  UNTREATED PRIMARY (DE NOVO) GBM              31               494
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V6, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    25   9
  3Q LOSS WILD-TYPE 357 179
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     25    9
  3Q LOSS WILD-TYPE  357  179
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  NO               25               357
  YES               9               179
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3Q LOSS MUTATED       1                         3    30
  3Q LOSS WILD-TYPE    12                        46   455
D47V7, multiclass
                           clus
vv                          3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  ASIAN                                   1                12
  BLACK OR AFRICAN AMERICAN               3                46
  WHITE                                  30               455
[1] 3 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
  3Q LOSS MUTATED     1  27
  3Q LOSS WILD-TYPE  11 445
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      1   27
  3Q LOSS WILD-TYPE   11  445
                        clus
vv                       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                11
  NOT HISPANIC OR LATINO              27               445
[1] 2 2
[1] FALSE

Clustering(48) Variable = 4P LOSS MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                 0   1
  4P LOSS MUTATED     7  46
  4P LOSS WILD-TYPE  97 419
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               53               516 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               46               419 
$`4P LOSS MUTATED`
TCGA-02-0014 TCGA-02-0026 TCGA-02-0054 TCGA-02-0079 TCGA-02-2483 TCGA-02-2485 
       82.59        24.59         6.54        27.25        15.32        15.45 
TCGA-06-0138 TCGA-06-0152 TCGA-06-0166 TCGA-06-0173 TCGA-06-0175 TCGA-06-0177 
       24.23        12.33         5.85         4.47         4.04         4.18 
TCGA-06-0216 TCGA-06-0414 TCGA-06-0645 TCGA-06-0744 TCGA-06-1087 TCGA-06-1800 
       24.16        35.11         5.75        46.88         4.04        26.79 
TCGA-06-2557 TCGA-06-5416 TCGA-06-6693 TCGA-06-A6S0 TCGA-08-0351 TCGA-08-0386 
        1.08         6.71       120.56         3.12        65.33        18.02 
TCGA-08-0525 TCGA-12-0619 TCGA-12-0827 TCGA-12-1598 TCGA-12-3644 TCGA-12-3646 
       15.98        34.92        38.76        15.65        59.77        44.02 
TCGA-12-3653 TCGA-14-0867 TCGA-14-1454 TCGA-14-1458 TCGA-14-1823 TCGA-15-1449 
       14.53         2.04        30.18         6.67        17.85        13.28 
TCGA-16-0848 TCGA-16-0849 TCGA-19-1387 TCGA-19-2629 TCGA-19-4065 TCGA-27-1830 
       17.59        26.07         5.95        24.23         7.04         5.06 
TCGA-27-1837 TCGA-27-1838 TCGA-28-2514 TCGA-28-5207 TCGA-28-5214 TCGA-32-1973 
       14.04        11.51         5.26        11.28        23.44        21.07 
TCGA-32-1978 TCGA-32-2632 TCGA-76-4925 TCGA-76-4928 TCGA-76-4934 
       15.85         8.84         4.80         3.09         2.53 

$`4P LOSS WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 
       11.77         4.73        18.35        23.18        10.59        35.41 
TCGA-02-0011 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0024 
       20.71        20.61        87.06        77.65        20.12        53.10 
TCGA-02-0025 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 
       42.74        12.16        90.58         2.83        14.14         3.62 
TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 TCGA-02-0048 
       10.72        10.52        18.31         6.87        14.73         3.22 
TCGA-02-0051 TCGA-02-0052 TCGA-02-0055 TCGA-02-0057 TCGA-02-0058 TCGA-02-0059 
       15.09        12.59         2.50        19.86         8.35         9.57 
TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 TCGA-02-0069 TCGA-02-0070 TCGA-02-0071 
        6.02        19.73        26.43        28.70        25.05         5.49 
TCGA-02-0074 TCGA-02-0075 TCGA-02-0080 TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 
       10.19        20.84        89.72        22.72        12.62        51.32 
TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 TCGA-02-0104 
        8.81        57.76        16.96         3.48        27.02        65.00 
TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 TCGA-02-0113 TCGA-02-0114 TCGA-02-0115 
       11.67        17.65        23.18        92.65        99.98        15.65 
TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 TCGA-02-0266 TCGA-02-0269 TCGA-02-0271 
       48.95        16.54        16.93        17.72        10.75        14.47 
TCGA-02-0281 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 
        3.98        13.87        14.20        15.95        12.23         9.90 
TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 TCGA-02-0333 
        7.73        10.62         7.33        15.91        25.71         4.37 
TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 
       25.12        10.59        12.39        14.50        10.55        47.11 
TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 TCGA-02-2466 TCGA-02-2470 
       11.34         9.27        16.21         3.35        16.80        12.92 
TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 
       20.32         2.70         6.15        20.38        47.61         6.94 
TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 
        3.98        22.72        33.67        12.95        25.35        14.30 
TCGA-06-0137 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 
       26.70        11.90         0.20        10.29         2.20        11.74 
TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 
        2.33        20.09        17.79        10.09         8.61        19.46 
TCGA-06-0151 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 
       46.59        13.94        10.45         3.19        10.82         9.44 
TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0168 TCGA-06-0169 
       11.80         3.42        56.91        10.65        19.66         3.29 
TCGA-06-0171 TCGA-06-0174 TCGA-06-0176 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 
       13.12         3.22        91.00        88.14        20.25         3.65 
TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 
       69.90        73.84        27.22        44.58        15.42        10.42 
TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 
       38.96         4.67         7.40         5.56         0.39         7.66 
TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 
        8.42         7.63         7.40        11.84         0.53        15.02 
TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 
        0.72        19.82        13.64        13.32        20.42        48.69 
TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 
       10.82         9.01         0.26        72.36         4.70         9.57 
TCGA-06-0413 TCGA-06-0644 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 
        3.16        12.62         5.75         9.80         2.10        23.57 
TCGA-06-0686 TCGA-06-0743 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 
       14.20        26.40         7.86         2.70         2.70         0.92 
TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 
       43.46        46.19         5.65         7.17        40.41        16.57 
TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1801 TCGA-06-1802 
       20.78        26.76        23.93         6.84        11.84        15.32 
TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 
       13.61        33.90        15.32        12.49         4.93        17.65 
TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 
       12.56        30.64         5.95        16.64         5.98         4.37 
TCGA-06-2569 TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 
        0.43        31.50        11.74         3.55         8.35         4.54 
TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 
        8.81         8.98         8.55         2.73         3.75         6.15 
TCGA-06-5859 TCGA-06-6388 TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 TCGA-06-6694 
        4.57         5.23         7.79         5.39         1.48         7.36 
TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 
        8.32        12.85         4.77         1.55         4.77         4.96 
TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S1 TCGA-06-A7TK TCGA-06-A7TL TCGA-08-0244 
        4.70         1.87         2.56         5.39         5.42        22.68 
TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 
       37.84         4.18       115.86         1.74         8.42        25.71 
TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 
       12.16         9.80        29.23         1.28         8.42        17.95 
TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 
       24.56        31.10        37.58        22.29         3.39        12.23 
TCGA-08-0380 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 
       14.93        15.35        13.97         0.72        12.56         4.27 
TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 
       42.15        11.08        19.59        58.68        19.33        10.75 
TCGA-08-0521 TCGA-08-0524 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 
        4.80         7.27        18.41         7.56        15.35        14.73 
TCGA-12-0618 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 
       12.99        10.45         7.59        94.78         0.10        38.17 
TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 
       25.97        26.66        12.13         3.65        20.38        28.41 
TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 
       15.06        53.85        43.23         7.63         9.73        14.93 
TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 
       14.86        91.76        24.79        18.48        10.62        23.51 
TCGA-12-0826 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 
       27.78         8.94        20.58       127.59         5.82         7.59 
TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 
       33.21        21.73        15.98        12.23        15.85         9.11 
TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 
       14.53         3.98         4.14        25.68        14.73         6.77 
TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-5295 
       26.93        15.22        10.95        12.69        34.92        14.93 
TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 TCGA-14-0783 
        3.22         2.04        15.12        11.97         0.95         6.21 
TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 TCGA-14-0812 TCGA-14-0813 
       23.05         2.24        11.24        13.78         3.25         1.35 
TCGA-14-0817 TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 TCGA-14-0871 TCGA-14-1034 
        5.39         2.89        16.50        26.33        28.93        15.95 
TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 
       19.30         0.79         1.38         1.12         3.75        32.05 
TCGA-14-1450 TCGA-14-1451 TCGA-14-1452 TCGA-14-1453 TCGA-14-1455 TCGA-14-1456 
       58.78        23.11         7.10         1.15         0.92        40.96 
TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 TCGA-14-1825 TCGA-14-1827 
       12.43         0.99         1.97        17.79         7.63         5.88 
TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-3477 TCGA-14-4157 TCGA-15-0742 
        7.17        17.49         7.96         3.78         3.42        13.78 
TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 TCGA-16-0846 TCGA-16-0850 TCGA-16-0861 
       50.53        19.10        53.19         3.91        16.37         4.31 
TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 
       29.03         4.57        10.29        14.01         9.14        21.24 
TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 TCGA-19-0962 
       13.97         6.41        11.77        21.90         8.61         0.66 
TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 TCGA-19-1388 TCGA-19-1389 
       14.27         3.39        10.75         9.07        12.95         4.64 
TCGA-19-1390 TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 
       25.38         3.65         7.17        12.66         3.25         0.13 
TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 
        9.67         4.87         1.08         7.53         0.16         4.08 
TCGA-19-2631 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 
        7.00         6.64        17.19         8.02        18.90         4.73 
TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 
       12.10         1.78        22.49        14.07        16.80        14.96 
TCGA-19-A60I TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 
       17.79         3.98        28.54        10.03        13.87         9.73 
TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 
       31.33         7.13         9.37         9.40        14.86         5.49 
TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-26-A7UX 
        8.88        18.97         1.58         7.92         2.33        19.33 
TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 
       16.60         9.86        24.23        40.54        21.30        30.05 
TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 
       24.76        10.39        10.39        16.08         7.59         2.86 
TCGA-27-2527 TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 
       14.40        15.78         0.20         2.53         9.21         8.35 
TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 
        7.63         8.48         1.22         1.55         2.83         0.13 
TCGA-28-2502 TCGA-28-2506 TCGA-28-2509 TCGA-28-2513 TCGA-28-5204 TCGA-28-5208 
        0.66         6.74         4.77         7.30        14.93        17.88 
TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 
       14.53        11.77        31.27        11.01        13.64         5.16 
TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1976 TCGA-32-1977 
       22.68        12.76         5.42        15.39         0.49         0.10 
TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 TCGA-32-1991 
       19.50         1.18         4.67        12.69        14.86        16.93 
TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 TCGA-32-2616 TCGA-32-2634 
       12.23        20.78        15.02        15.95         7.36        22.78 
TCGA-32-2638 TCGA-32-4208 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 
       25.18        21.14         3.72        12.59        19.86        10.85 
TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 
       19.23         0.85        13.35         8.94         9.53         0.99 
TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9S 
        4.44        11.84         0.20        15.12        12.46         4.14 
TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 
       14.76         3.45        20.91         4.34        14.33         8.22 
TCGA-74-6584 TCGA-76-4926 TCGA-76-4929 TCGA-76-4931 TCGA-76-4935 TCGA-76-6191 
        7.50         4.54         3.65         9.17        10.78        16.70 
TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 
        3.29         2.70        11.38        17.06         8.35        20.98 
TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 
        4.83         5.03         0.23         9.27         7.73         7.79 
TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC 
        1.61        17.72        26.30         5.92         6.28        20.55 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             1.08              0.10 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
           120.56            127.59 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            15.32             11.77 
[1] "1.1 - 120.6 (15.3)" "0.1 - 127.6 (11.8)"
[1] "hr=" "1.2"
D48V2, continuous
D48V3, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    16  37
  4P LOSS WILD-TYPE 208 309
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     16   37
  4P LOSS WILD-TYPE  208  309
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE              16               208
  MALE                37               309
[1] 2 2
[1] FALSE
D48V4, continuous
                   vv
clus                GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  4P LOSS MUTATED                               1                   0
  4P LOSS WILD-TYPE                            26                  18
                   vv
clus                UNTREATED PRIMARY (DE NOVO) GBM
  4P LOSS MUTATED                                52
  4P LOSS WILD-TYPE                             473
D48V5, multiclass
                                 clus
vv                                4P LOSS MUTATED 4P LOSS WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                 1                26
  TREATED PRIMARY GBM                           0                18
  UNTREATED PRIMARY (DE NOVO) GBM              52               473
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V6, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    38  15
  4P LOSS WILD-TYPE 344 173
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     38   15
  4P LOSS WILD-TYPE  344  173
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  NO               38               344
  YES              15               173
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4P LOSS MUTATED       2                         3    47
  4P LOSS WILD-TYPE    11                        46   438
D48V7, multiclass
                           clus
vv                          4P LOSS MUTATED 4P LOSS WILD-TYPE
  ASIAN                                   2                11
  BLACK OR AFRICAN AMERICAN               3                46
  WHITE                                  47               438
[1] 3 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
  4P LOSS MUTATED     2  42
  4P LOSS WILD-TYPE  10 430
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      2   42
  4P LOSS WILD-TYPE   10  430
                        clus
vv                       4P LOSS MUTATED 4P LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                10
  NOT HISPANIC OR LATINO              42               430
[1] 2 2
[1] FALSE

Clustering(49) Variable = 4Q LOSS MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                 0   1
  4Q LOSS MUTATED    13  41
  4Q LOSS WILD-TYPE  91 424
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               54               515 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               41               424 
$`4Q LOSS MUTATED`
TCGA-02-0024 TCGA-02-0026 TCGA-02-0054 TCGA-02-0079 TCGA-02-2483 TCGA-02-2485 
       53.10        24.59         6.54        27.25        15.32        15.45 
TCGA-06-0138 TCGA-06-0152 TCGA-06-0166 TCGA-06-0177 TCGA-06-0216 TCGA-06-0414 
       24.23        12.33         5.85         4.18        24.16        35.11 
TCGA-06-0645 TCGA-06-0744 TCGA-06-1087 TCGA-06-1800 TCGA-06-1805 TCGA-06-2557 
        5.75        46.88         4.04        26.79        33.90         1.08 
TCGA-06-2569 TCGA-06-5416 TCGA-06-6389 TCGA-06-6693 TCGA-06-A5U0 TCGA-08-0386 
        0.43         6.71         7.79       120.56         4.70        18.02 
TCGA-12-0619 TCGA-12-0827 TCGA-12-1598 TCGA-12-3644 TCGA-12-3646 TCGA-12-3653 
       34.92        38.76        15.65        59.77        44.02        14.53 
TCGA-14-0740 TCGA-14-0867 TCGA-14-1453 TCGA-14-1454 TCGA-14-1458 TCGA-14-1823 
       11.97         2.04         1.15        30.18         6.67        17.85 
TCGA-15-1447 TCGA-15-1449 TCGA-16-0848 TCGA-19-1387 TCGA-19-2629 TCGA-19-4065 
       53.19        13.28        17.59         5.95        24.23         7.04 
TCGA-19-A6J5 TCGA-26-1442 TCGA-27-1830 TCGA-27-1838 TCGA-28-2514 TCGA-28-5207 
       28.54        31.33         5.06        11.51         5.26        11.28 
TCGA-28-5214 TCGA-32-1973 TCGA-32-2632 TCGA-76-4925 TCGA-76-4934 TCGA-76-6285 
       23.44        21.07         8.84         4.80         2.53         8.35 

$`4Q LOSS WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 
       11.77         4.73        18.35        23.18        10.59        35.41 
TCGA-02-0011 TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 
       20.71        82.59        20.61        87.06        77.65        20.12 
TCGA-02-0025 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 
       42.74        12.16        90.58         2.83        14.14         3.62 
TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 TCGA-02-0048 
       10.72        10.52        18.31         6.87        14.73         3.22 
TCGA-02-0051 TCGA-02-0052 TCGA-02-0055 TCGA-02-0057 TCGA-02-0058 TCGA-02-0059 
       15.09        12.59         2.50        19.86         8.35         9.57 
TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 TCGA-02-0069 TCGA-02-0070 TCGA-02-0071 
        6.02        19.73        26.43        28.70        25.05         5.49 
TCGA-02-0074 TCGA-02-0075 TCGA-02-0080 TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 
       10.19        20.84        89.72        22.72        12.62        51.32 
TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 TCGA-02-0104 
        8.81        57.76        16.96         3.48        27.02        65.00 
TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 TCGA-02-0113 TCGA-02-0114 TCGA-02-0115 
       11.67        17.65        23.18        92.65        99.98        15.65 
TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 TCGA-02-0266 TCGA-02-0269 TCGA-02-0271 
       48.95        16.54        16.93        17.72        10.75        14.47 
TCGA-02-0281 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 
        3.98        13.87        14.20        15.95        12.23         9.90 
TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 TCGA-02-0333 
        7.73        10.62         7.33        15.91        25.71         4.37 
TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 
       25.12        10.59        12.39        14.50        10.55        47.11 
TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 TCGA-02-2466 TCGA-02-2470 
       11.34         9.27        16.21         3.35        16.80        12.92 
TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 
       20.32         2.70         6.15        20.38        47.61         6.94 
TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 
        3.98        22.72        33.67        12.95        25.35        14.30 
TCGA-06-0137 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 
       26.70        11.90         0.20        10.29         2.20        11.74 
TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 
        2.33        20.09        17.79        10.09         8.61        19.46 
TCGA-06-0151 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 
       46.59        13.94        10.45         3.19        10.82         9.44 
TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0168 TCGA-06-0169 
       11.80         3.42        56.91        10.65        19.66         3.29 
TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0178 
       13.12         4.47         3.22         4.04        91.00        88.14 
TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 
       20.25         3.65        69.90        73.84        27.22        44.58 
TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 
       15.42        10.42        38.96         4.67         7.40         5.56 
TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 
        0.39         7.66         8.42         7.63         7.40        11.84 
TCGA-06-0213 TCGA-06-0214 TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 
        0.53        15.02         0.72        19.82        13.64        13.32 
TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 
       20.42        48.69        10.82         9.01         0.26        72.36 
TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0644 TCGA-06-0646 TCGA-06-0648 
        4.70         9.57         3.16        12.62         5.75         9.80 
TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0745 TCGA-06-0747 
        2.10        23.57        14.20        26.40         7.86         2.70 
TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 
        2.70         0.92        43.46        46.19         5.65         7.17 
TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 
       40.41        16.57        20.78        26.76        23.93         6.84 
TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1806 TCGA-06-2558 TCGA-06-2559 
       11.84        15.32        13.61        15.32        12.49         4.93 
TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 
       17.65        12.56        30.64         5.95        16.64         5.98 
TCGA-06-2567 TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 
        4.37        31.50        11.74         3.55         8.35         4.54 
TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 
        8.81         8.98         8.55         2.73         3.75         6.15 
TCGA-06-5859 TCGA-06-6388 TCGA-06-6390 TCGA-06-6391 TCGA-06-6694 TCGA-06-6695 
        4.57         5.23         5.39         1.48         7.36         8.32 
TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U1 
       12.85         4.77         1.55         4.77         4.96         1.87 
TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK TCGA-06-A7TL TCGA-08-0244 TCGA-08-0245 
        3.12         2.56         5.39         5.42        22.68        37.84 
TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 
        4.18       115.86         1.74         8.42        25.71        12.16 
TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 
        9.80        29.23        65.33         1.28         8.42        17.95 
TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 
       24.56        31.10        37.58        22.29         3.39        12.23 
TCGA-08-0380 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 
       14.93        15.35        13.97         0.72        12.56         4.27 
TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 
       42.15        11.08        19.59        58.68        19.33        10.75 
TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 
        4.80         7.27        15.98        18.41         7.56        15.35 
TCGA-12-0616 TCGA-12-0618 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 
       14.73        12.99        10.45         7.59        94.78         0.10 
TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 
       38.17        25.97        26.66        12.13         3.65        20.38 
TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 
       28.41        15.06        53.85        43.23         7.63         9.73 
TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 
       14.93        14.86        91.76        24.79        18.48        10.62 
TCGA-12-0822 TCGA-12-0826 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 
       23.51        27.78         8.94        20.58       127.59         5.82 
TCGA-12-1090 TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 
        7.59        33.21        21.73        15.98        12.23        15.85 
TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 TCGA-12-1599 TCGA-12-1600 
        9.11        14.53         3.98         4.14        25.68        14.73 
TCGA-12-1602 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 
        6.77        26.93        15.22        10.95        12.69        34.92 
TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0781 TCGA-14-0783 
       14.93         3.22         2.04        15.12         0.95         6.21 
TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 TCGA-14-0812 TCGA-14-0813 
       23.05         2.24        11.24        13.78         3.25         1.35 
TCGA-14-0817 TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 TCGA-14-0871 TCGA-14-1034 
        5.39         2.89        16.50        26.33        28.93        15.95 
TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 
       19.30         0.79         1.38         1.12         3.75        32.05 
TCGA-14-1450 TCGA-14-1451 TCGA-14-1452 TCGA-14-1455 TCGA-14-1456 TCGA-14-1459 
       58.78        23.11         7.10         0.92        40.96        12.43 
TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 
        0.99         1.97        17.79         7.63         5.88         7.17 
TCGA-14-2554 TCGA-14-2555 TCGA-14-3477 TCGA-14-4157 TCGA-15-0742 TCGA-15-1444 
       17.49         7.96         3.78         3.42        13.78        50.53 
TCGA-15-1446 TCGA-16-0846 TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 
       19.10         3.91        26.07        16.37         4.31        29.03 
TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 
        4.57        10.29        14.01         9.14        21.24        13.97 
TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 TCGA-19-0962 TCGA-19-0963 
        6.41        11.77        21.90         8.61         0.66        14.27 
TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 TCGA-19-1388 TCGA-19-1389 TCGA-19-1390 
        3.39        10.75         9.07        12.95         4.64        25.38 
TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 
        3.65         7.17        12.66         3.25         0.13         9.67 
TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 TCGA-19-2631 
        4.87         1.08         7.53         0.16         4.08         7.00 
TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 
        6.64        17.19         8.02        18.90         4.73        12.10 
TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I 
        1.78        22.49        14.07        16.80        14.96        17.79 
TCGA-19-A6J4 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1443 TCGA-26-1799 
        3.98        10.03        13.87         9.73         7.13         9.37 
TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 
        9.40        14.86         5.49         8.88        18.97         1.58 
TCGA-26-6173 TCGA-26-6174 TCGA-26-A7UX TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 
        7.92         2.33        19.33        16.60         9.86        24.23 
TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-2518 TCGA-27-2519 
       40.54        21.30        30.05        14.04        24.76        10.39 
TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 
       10.39        16.08         7.59         2.86        14.40        15.78 
TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 TCGA-28-1752 
        0.20         2.53         9.21         8.35         7.63         8.48 
TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 TCGA-28-2502 TCGA-28-2506 
        1.22         1.55         2.83         0.13         0.66         6.74 
TCGA-28-2509 TCGA-28-2513 TCGA-28-5204 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 
        4.77         7.30        14.93        17.88        14.53        11.77 
TCGA-28-5213 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 
       31.27        11.01        13.64         5.16        22.68        12.76 
TCGA-28-6450 TCGA-32-1970 TCGA-32-1976 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 
        5.42        15.39         0.49         0.10        15.85        19.50 
TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 TCGA-32-1991 TCGA-32-2491 
        1.18         4.67        12.69        14.86        16.93        12.23 
TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 TCGA-32-2616 TCGA-32-2634 TCGA-32-2638 
       20.78        15.02        15.95         7.36        22.78        25.18 
TCGA-32-4208 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 
       21.14         3.72        12.59        19.86        10.85        19.23 
TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 
        0.85        13.35         8.94         9.53         0.99         4.44 
TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9S TCGA-4W-AA9T 
       11.84         0.20        15.12        12.46         4.14        14.76 
TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 
        3.45        20.91         4.34        14.33         8.22         7.50 
TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-4935 TCGA-76-6191 
        4.54         3.09         3.65         9.17        10.78        16.70 
TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 TCGA-76-6286 TCGA-76-6656 
        3.29         2.70        11.38        17.06        20.98         4.83 
TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 
        5.03         0.23         9.27         7.73         7.79         1.61 
TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC 
       17.72        26.30         5.92         6.28        20.55 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             0.43              0.10 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           120.56            127.59 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           14.925            11.770 
[1] "0.4 - 120.6 (14.9)" "0.1 - 127.6 (11.8)"
[1] "hr=" "1.4"
D49V2, continuous
D49V3, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED    20  34
  4Q LOSS WILD-TYPE 204 312
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     20   34
  4Q LOSS WILD-TYPE  204  312
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE              20               204
  MALE                34               312
[1] 2 2
[1] FALSE
D49V4, continuous
                   vv
clus                GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  4Q LOSS MUTATED                               2                   1
  4Q LOSS WILD-TYPE                            25                  17
                   vv
clus                UNTREATED PRIMARY (DE NOVO) GBM
  4Q LOSS MUTATED                                51
  4Q LOSS WILD-TYPE                             474
D49V5, multiclass
                                 clus
vv                                4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                 2                25
  TREATED PRIMARY GBM                           1                17
  UNTREATED PRIMARY (DE NOVO) GBM              51               474
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V6, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED    38  16
  4Q LOSS WILD-TYPE 344 172
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     38   16
  4Q LOSS WILD-TYPE  344  172
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  NO               38               344
  YES              16               172
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4Q LOSS MUTATED       2                         5    47
  4Q LOSS WILD-TYPE    11                        44   438
D49V7, multiclass
                           clus
vv                          4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  ASIAN                                   2                11
  BLACK OR AFRICAN AMERICAN               5                44
  WHITE                                  47               438
[1] 3 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
  4Q LOSS MUTATED     2  40
  4Q LOSS WILD-TYPE  10 432
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      2   40
  4Q LOSS WILD-TYPE   10  432
                        clus
vv                       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                10
  NOT HISPANIC OR LATINO              40               432
[1] 2 2
[1] FALSE

Clustering(50) Variable = 5P LOSS MUTATION ANALYSIS
D50V1, survival
                   sevent
clus2                 0   1
  5P LOSS MUTATED     8  34
  5P LOSS WILD-TYPE  96 431
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               42               527 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               34               431 
$`5P LOSS MUTATED`
TCGA-02-0025 TCGA-02-0052 TCGA-02-0069 TCGA-02-0084 TCGA-02-0115 TCGA-02-0339 
       42.74        12.59        28.70        12.62        15.65        12.39 
TCGA-02-2483 TCGA-06-0128 TCGA-06-0188 TCGA-06-0414 TCGA-06-0644 TCGA-06-0686 
       15.32        22.72        44.58        35.11        12.62        14.20 
TCGA-06-1087 TCGA-06-6389 TCGA-08-0245 TCGA-08-0344 TCGA-08-0386 TCGA-08-0516 
        4.04         7.79        37.84       115.86        18.02        19.59 
TCGA-08-0517 TCGA-12-0818 TCGA-12-3652 TCGA-12-3653 TCGA-14-0740 TCGA-14-0817 
       58.68        91.76        34.92        14.53        11.97         5.39 
TCGA-14-0865 TCGA-14-0867 TCGA-14-0871 TCGA-14-1453 TCGA-14-1821 TCGA-14-3477 
       16.50         2.04        28.93         1.15        17.79         3.78 
TCGA-16-0850 TCGA-19-1387 TCGA-19-4065 TCGA-19-5954 TCGA-26-5133 TCGA-27-1834 
       16.37         5.95         7.04        12.10        14.86        40.54 
TCGA-27-2521 TCGA-28-1755 TCGA-28-5215 TCGA-41-5651 TCGA-76-4925 TCGA-76-4929 
       10.39         1.55        11.01        15.12         4.80         3.65 

$`5P LOSS WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 
       11.77         4.73        18.35        23.18        10.59        35.41 
TCGA-02-0011 TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 
       20.71        82.59        20.61        87.06        77.65        20.12 
TCGA-02-0024 TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 
       53.10        24.59        12.16        90.58         2.83        14.14 
TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 
        3.62        10.72        10.52        18.31         6.87        14.73 
TCGA-02-0048 TCGA-02-0051 TCGA-02-0054 TCGA-02-0055 TCGA-02-0057 TCGA-02-0058 
        3.22        15.09         6.54         2.50        19.86         8.35 
TCGA-02-0059 TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 TCGA-02-0070 TCGA-02-0071 
        9.57         6.02        19.73        26.43        25.05         5.49 
TCGA-02-0074 TCGA-02-0075 TCGA-02-0079 TCGA-02-0080 TCGA-02-0083 TCGA-02-0085 
       10.19        20.84        27.25        89.72        22.72        51.32 
TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 TCGA-02-0104 
        8.81        57.76        16.96         3.48        27.02        65.00 
TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 TCGA-02-0113 TCGA-02-0114 TCGA-02-0116 
       11.67        17.65        23.18        92.65        99.98        48.95 
TCGA-02-0258 TCGA-02-0260 TCGA-02-0266 TCGA-02-0269 TCGA-02-0271 TCGA-02-0281 
       16.54        16.93        17.72        10.75        14.47         3.98 
TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 
       13.87        14.20        15.95        12.23         9.90         7.73 
TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 
       10.62         7.33        15.91        25.71         4.37        25.12 
TCGA-02-0338 TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 
       10.59        14.50        10.55        47.11        11.34         9.27 
TCGA-02-0451 TCGA-02-0456 TCGA-02-2466 TCGA-02-2470 TCGA-02-2485 TCGA-02-2486 
       16.21         3.35        16.80        12.92        15.45        20.32 
TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 
        2.70         6.15        20.38        47.61         6.94         3.98 
TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 
       33.67        12.95        25.35        14.30        26.70        24.23 
TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 
       11.90         0.20        10.29         2.20        11.74         2.33 
TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 
       20.09        17.79        10.09         8.61        19.46        46.59 
TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 
       12.33        13.94        10.45         3.19        10.82         9.44 
TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 
       11.80         3.42        56.91        10.65         5.85        19.66 
TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 
        3.29        13.12         4.47         3.22         4.04        91.00 
TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 
        4.18        88.14        20.25         3.65        69.90        73.84 
TCGA-06-0187 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 
       27.22        15.42        10.42        38.96         4.67         7.40 
TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 
        5.56         0.39         7.66         8.42         7.63         7.40 
TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 
       11.84         0.53        15.02        24.16         0.72        19.82 
TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 
       13.64        13.32        20.42        48.69        10.82         9.01 
TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0645 
        0.26        72.36         4.70         9.57         3.16         5.75 
TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0743 TCGA-06-0744 
        5.75         9.80         2.10        23.57        26.40        46.88 
TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 
        7.86         2.70         2.70         0.92        43.46        46.19 
TCGA-06-0877 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 
        5.65         7.17        40.41        16.57        20.78        26.76 
TCGA-06-1084 TCGA-06-1086 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 
       23.93         6.84        26.79        11.84        15.32        13.61 
TCGA-06-1805 TCGA-06-1806 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 
       33.90        15.32         1.08        12.49         4.93        17.65 
TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 
       12.56        30.64         5.95        16.64         5.98         4.37 
TCGA-06-2569 TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 
        0.43        31.50        11.74         3.55         8.35         4.54 
TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 TCGA-06-5418 TCGA-06-5856 
        8.81         8.98         8.55         6.71         2.73         3.75 
TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 
        6.15         4.57         5.23         5.39         1.48       120.56 
TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 
        7.36         8.32        12.85         4.77         1.55         4.77 
TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK 
        4.96         4.70         1.87         3.12         2.56         5.39 
TCGA-06-A7TL TCGA-08-0244 TCGA-08-0246 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 
        5.42        22.68         4.18         1.74         8.42        25.71 
TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 
       12.16         9.80        29.23        65.33         1.28         8.42 
TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 
       17.95        24.56        31.10        37.58        22.29         3.39 
TCGA-08-0375 TCGA-08-0380 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 
       12.23        14.93        15.35        13.97         0.72        12.56 
TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 
        4.27        42.15        11.08        19.33        10.75         4.80 
TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 
        7.27        15.98        18.41         7.56        15.35        14.73 
TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 
       12.99        34.92        10.45         7.59        94.78         0.10 
TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 
       38.17        25.97        26.66        12.13         3.65        20.38 
TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 
       28.41        15.06        53.85        43.23         7.63         9.73 
TCGA-12-0778 TCGA-12-0780 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 
       14.93        14.86        24.79        18.48        10.62        23.51 
TCGA-12-0826 TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 
       27.78        38.76         8.94        20.58       127.59         5.82 
TCGA-12-1090 TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 
        7.59        33.21        21.73        15.98        12.23        15.85 
TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 TCGA-12-1598 TCGA-12-1599 
        9.11        14.53         3.98         4.14        15.65        25.68 
TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 
       14.73         6.77        59.77        44.02        26.93        15.22 
TCGA-12-3650 TCGA-12-3651 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 
       10.95        12.69        14.93         3.22         2.04        15.12 
TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 
        0.95         6.21        23.05         2.24        11.24        13.78 
TCGA-14-0812 TCGA-14-0813 TCGA-14-0862 TCGA-14-0866 TCGA-14-1034 TCGA-14-1037 
        3.25         1.35         2.89        26.33        15.95        19.30 
TCGA-14-1043 TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 
        0.79         1.38         1.12         3.75        32.05        58.78 
TCGA-14-1451 TCGA-14-1452 TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 
       23.11         7.10        30.18         0.92        40.96         6.67 
TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1823 TCGA-14-1825 TCGA-14-1827 
       12.43         0.99         1.97        17.85         7.63         5.88 
TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-4157 TCGA-15-0742 TCGA-15-1444 
        7.17        17.49         7.96         3.42        13.78        50.53 
TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 
       19.10        53.19        13.28         3.91        17.59        26.07 
TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 
        4.31        29.03         4.57        10.29        14.01         9.14 
TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 
       21.24        13.97         6.41        11.77        21.90         8.61 
TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 TCGA-19-1388 
        0.66        14.27         3.39        10.75         9.07        12.95 
TCGA-19-1389 TCGA-19-1390 TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 
        4.64        25.38         3.65         7.17        12.66         3.25 
TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 
        0.13         9.67         4.87         1.08         7.53         0.16 
TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 
        4.08        24.23         7.00         6.64        17.19         8.02 
TCGA-19-5952 TCGA-19-5953 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 
       18.90         4.73         1.78        22.49        14.07        16.80 
TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 
       14.96        17.79         3.98        28.54        10.03        13.87 
TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5134 
        9.73        31.33         7.13         9.37         9.40         5.49 
TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-26-A7UX 
        8.88        18.97         1.58         7.92         2.33        19.33 
TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1835 TCGA-27-1836 
        5.06        16.60         9.86        24.23        21.30        30.05 
TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2523 TCGA-27-2524 
       14.04        11.51        24.76        10.39        16.08         7.59 
TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 
        2.86        14.40        15.78         0.20         2.53         9.21 
TCGA-28-1750 TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 TCGA-28-1756 TCGA-28-1757 
        8.35         7.63         8.48         1.22         2.83         0.13 
TCGA-28-2502 TCGA-28-2506 TCGA-28-2509 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 
        0.66         6.74         4.77         7.30         5.26        14.93 
TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 
       11.28        17.88        14.53        11.77        31.27        23.44 
TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 
       13.64         5.16        22.68        12.76         5.42        15.39 
TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 TCGA-32-1980 
       21.07         0.49         0.10        15.85        19.50         1.18 
TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 
        4.67        12.69        14.86        16.93        12.23        20.78 
TCGA-32-2495 TCGA-32-2615 TCGA-32-2616 TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 
       15.02        15.95         7.36         8.84        22.78        25.18 
TCGA-32-4208 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 
       21.14         3.72        12.59        19.86        10.85        19.23 
TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 
        0.85        13.35         8.94         9.53         0.99         4.44 
TCGA-41-3915 TCGA-41-4097 TCGA-41-6646 TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 
       11.84         0.20        12.46         4.14        14.76         3.45 
TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 TCGA-76-4926 
       20.91         4.34        14.33         8.22         7.50         4.54 
TCGA-76-4928 TCGA-76-4931 TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 
        3.09         9.17         2.53        10.78        16.70         3.29 
TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 
        2.70        11.38        17.06         8.35        20.98         4.83 
TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 
        5.03         0.23         9.27         7.73         7.79         1.61 
TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC 
       17.72        26.30         5.92         6.28        20.55 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             1.15              0.10 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
           115.86            127.59 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
           14.695            11.740 
[1] "1.1 - 115.9 (14.7)" "0.1 - 127.6 (11.7)"
[1] "hr=" "1.3"
D50V2, continuous
D50V3, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    16  26
  5P LOSS WILD-TYPE 208 320
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     16   26
  5P LOSS WILD-TYPE  208  320
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE              16               208
  MALE                26               320
[1] 2 2
[1] FALSE
D50V4, continuous
                   vv
clus                GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  5P LOSS MUTATED                               0                   1
  5P LOSS WILD-TYPE                            27                  17
                   vv
clus                UNTREATED PRIMARY (DE NOVO) GBM
  5P LOSS MUTATED                                41
  5P LOSS WILD-TYPE                             484
D50V5, multiclass
                                 clus
vv                                5P LOSS MUTATED 5P LOSS WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                 0                27
  TREATED PRIMARY GBM                           1                17
  UNTREATED PRIMARY (DE NOVO) GBM              41               484
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V6, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    35   7
  5P LOSS WILD-TYPE 347 181
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     35    7
  5P LOSS WILD-TYPE  347  181
     clus
vv    5P LOSS MUTATED 5P LOSS WILD-TYPE
  NO               35               347
  YES               7               181
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5P LOSS MUTATED       3                         4    35
  5P LOSS WILD-TYPE    10                        45   450
D50V7, multiclass
                           clus
vv                          5P LOSS MUTATED 5P LOSS WILD-TYPE
  ASIAN                                   3                10
  BLACK OR AFRICAN AMERICAN               4                45
  WHITE                                  35               450
[1] 3 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
  5P LOSS MUTATED     2  32
  5P LOSS WILD-TYPE  10 440
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      2   32
  5P LOSS WILD-TYPE   10  440
                        clus
vv                       5P LOSS MUTATED 5P LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                10
  NOT HISPANIC OR LATINO              32               440
[1] 2 2
[1] FALSE

Clustering(51) Variable = 5Q LOSS MUTATION ANALYSIS
D51V1, survival
                   sevent
clus2                 0   1
  5Q LOSS MUTATED    10  33
  5Q LOSS WILD-TYPE  94 432
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               43               526 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               33               432 
$`5Q LOSS MUTATED`
TCGA-02-0011 TCGA-02-0025 TCGA-02-0051 TCGA-02-0052 TCGA-02-0069 TCGA-02-0084 
       20.71        42.74        15.09        12.59        28.70        12.62 
TCGA-02-2483 TCGA-06-0128 TCGA-06-0188 TCGA-06-0237 TCGA-06-0414 TCGA-06-0644 
       15.32        22.72        44.58        13.64        35.11        12.62 
TCGA-06-0686 TCGA-06-1087 TCGA-06-2569 TCGA-06-6389 TCGA-08-0344 TCGA-08-0350 
       14.20         4.04         0.43         7.79       115.86        29.23 
TCGA-08-0386 TCGA-08-0516 TCGA-12-0818 TCGA-12-3652 TCGA-12-3653 TCGA-14-0740 
       18.02        19.59        91.76        34.92        14.53        11.97 
TCGA-14-0817 TCGA-14-0865 TCGA-14-0867 TCGA-14-0871 TCGA-14-1453 TCGA-14-1821 
        5.39        16.50         2.04        28.93         1.15        17.79 
TCGA-14-3477 TCGA-16-0850 TCGA-19-0960 TCGA-19-1387 TCGA-19-4065 TCGA-19-5954 
        3.78        16.37         8.61         5.95         7.04        12.10 
TCGA-26-5133 TCGA-27-1834 TCGA-27-2521 TCGA-28-5215 TCGA-41-5651 TCGA-76-4925 
       14.86        40.54        10.39        11.01        15.12         4.80 
TCGA-76-4929 
        3.65 

$`5Q LOSS WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 
       11.77         4.73        18.35        23.18        10.59        35.41 
TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0024 
       82.59        20.61        87.06        77.65        20.12        53.10 
TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 
       24.59        12.16        90.58         2.83        14.14         3.62 
TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 TCGA-02-0048 
       10.72        10.52        18.31         6.87        14.73         3.22 
TCGA-02-0054 TCGA-02-0055 TCGA-02-0057 TCGA-02-0058 TCGA-02-0059 TCGA-02-0060 
        6.54         2.50        19.86         8.35         9.57         6.02 
TCGA-02-0064 TCGA-02-0068 TCGA-02-0070 TCGA-02-0071 TCGA-02-0074 TCGA-02-0075 
       19.73        26.43        25.05         5.49        10.19        20.84 
TCGA-02-0079 TCGA-02-0080 TCGA-02-0083 TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 
       27.25        89.72        22.72        51.32         8.81        57.76 
TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 TCGA-02-0104 TCGA-02-0106 TCGA-02-0107 
       16.96         3.48        27.02        65.00        11.67        17.65 
TCGA-02-0111 TCGA-02-0113 TCGA-02-0114 TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 
       23.18        92.65        99.98        15.65        48.95        16.54 
TCGA-02-0260 TCGA-02-0266 TCGA-02-0269 TCGA-02-0271 TCGA-02-0281 TCGA-02-0285 
       16.93        17.72        10.75        14.47         3.98        13.87 
TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 
       14.20        15.95        12.23         9.90         7.73        10.62 
TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 
        7.33        15.91        25.71         4.37        25.12        10.59 
TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 
       12.39        14.50        10.55        47.11        11.34         9.27 
TCGA-02-0451 TCGA-02-0456 TCGA-02-2466 TCGA-02-2470 TCGA-02-2485 TCGA-02-2486 
       16.21         3.35        16.80        12.92        15.45        20.32 
TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 
        2.70         6.15        20.38        47.61         6.94         3.98 
TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 
       33.67        12.95        25.35        14.30        26.70        24.23 
TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 
       11.90         0.20        10.29         2.20        11.74         2.33 
TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 
       20.09        17.79        10.09         8.61        19.46        46.59 
TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 
       12.33        13.94        10.45         3.19        10.82         9.44 
TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 
       11.80         3.42        56.91        10.65         5.85        19.66 
TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 
        3.29        13.12         4.47         3.22         4.04        91.00 
TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 
        4.18        88.14        20.25         3.65        69.90        73.84 
TCGA-06-0187 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 
       27.22        15.42        10.42        38.96         4.67         7.40 
TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 
        5.56         0.39         7.66         8.42         7.63         7.40 
TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 
       11.84         0.53        15.02        24.16         0.72        19.82 
TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 
       13.32        20.42        48.69        10.82         9.01         0.26 
TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0645 TCGA-06-0646 
       72.36         4.70         9.57         3.16         5.75         5.75 
TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 
        9.80         2.10        23.57        26.40        46.88         7.86 
TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 
        2.70         2.70         0.92        43.46        46.19         5.65 
TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 
        7.17        40.41        16.57        20.78        26.76        23.93 
TCGA-06-1086 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 
        6.84        26.79        11.84        15.32        13.61        33.90 
TCGA-06-1806 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 
       15.32         1.08        12.49         4.93        17.65        12.56 
TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2570 
       30.64         5.95        16.64         5.98         4.37        31.50 
TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 
       11.74         3.55         8.35         4.54         8.81         8.98 
TCGA-06-5415 TCGA-06-5416 TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 TCGA-06-5859 
        8.55         6.71         2.73         3.75         6.15         4.57 
TCGA-06-6388 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 
        5.23         5.39         1.48       120.56         7.36         8.32 
TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 
       12.85         4.77         1.55         4.77         4.96         4.70 
TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK TCGA-06-A7TL TCGA-08-0244 
        1.87         3.12         2.56         5.39         5.42        22.68 
TCGA-08-0245 TCGA-08-0246 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 
       37.84         4.18         1.74         8.42        25.71        12.16 
TCGA-08-0349 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 
        9.80        65.33         1.28         8.42        17.95        24.56 
TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 
       31.10        37.58        22.29         3.39        12.23        14.93 
TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 
       15.35        13.97         0.72        12.56         4.27        42.15 
TCGA-08-0514 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 
       11.08        58.68        19.33        10.75         4.80         7.27 
TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 
       15.98        18.41         7.56        15.35        14.73        12.99 
TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 
       34.92        10.45         7.59        94.78         0.10        38.17 
TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 
       25.97        26.66        12.13         3.65        20.38        28.41 
TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 
       15.06        53.85        43.23         7.63         9.73        14.93 
TCGA-12-0780 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 TCGA-12-0826 
       14.86        24.79        18.48        10.62        23.51        27.78 
TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 
       38.76         8.94        20.58       127.59         5.82         7.59 
TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 
       33.21        21.73        15.98        12.23        15.85         9.11 
TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 
       14.53         3.98         4.14        15.65        25.68        14.73 
TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 
        6.77        59.77        44.02        26.93        15.22        10.95 
TCGA-12-3651 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0781 
       12.69        14.93         3.22         2.04        15.12         0.95 
TCGA-14-0783 TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 TCGA-14-0812 
        6.21        23.05         2.24        11.24        13.78         3.25 
TCGA-14-0813 TCGA-14-0862 TCGA-14-0866 TCGA-14-1034 TCGA-14-1037 TCGA-14-1043 
        1.35         2.89        26.33        15.95        19.30         0.79 
TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 
        1.38         1.12         3.75        32.05        58.78        23.11 
TCGA-14-1452 TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 
        7.10        30.18         0.92        40.96         6.67        12.43 
TCGA-14-1794 TCGA-14-1795 TCGA-14-1823 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 
        0.99         1.97        17.85         7.63         5.88         7.17 
TCGA-14-2554 TCGA-14-2555 TCGA-14-4157 TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 
       17.49         7.96         3.42        13.78        50.53        19.10 
TCGA-15-1447 TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 TCGA-16-0861 
       53.19        13.28         3.91        17.59        26.07         4.31 
TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 
       29.03         4.57        10.29        14.01         9.14        21.24 
TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 TCGA-19-0962 TCGA-19-0963 
       13.97         6.41        11.77        21.90         0.66        14.27 
TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 TCGA-19-1388 TCGA-19-1389 TCGA-19-1390 
        3.39        10.75         9.07        12.95         4.64        25.38 
TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 
        3.65         7.17        12.66         3.25         0.13         9.67 
TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 
        4.87         1.08         7.53         0.16         4.08        24.23 
TCGA-19-2631 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 
        7.00         6.64        17.19         8.02        18.90         4.73 
TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I 
        1.78        22.49        14.07        16.80        14.96        17.79 
TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 
        3.98        28.54        10.03        13.87         9.73        31.33 
TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 
        7.13         9.37         9.40         5.49         8.88        18.97 
TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 
        1.58         7.92         2.33        19.33         5.06        16.60 
TCGA-27-1832 TCGA-27-1833 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 
        9.86        24.23        21.30        30.05        14.04        11.51 
TCGA-27-2518 TCGA-27-2519 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 
       24.76        10.39        16.08         7.59         2.86        14.40 
TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 
       15.78         0.20         2.53         9.21         8.35         7.63 
TCGA-28-1752 TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 TCGA-28-2502 
        8.48         1.22         1.55         2.83         0.13         0.66 
TCGA-28-2506 TCGA-28-2509 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 
        6.74         4.77         7.30         5.26        14.93        11.28 
TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5216 
       17.88        14.53        11.77        31.27        23.44        13.64 
TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 
        5.16        22.68        12.76         5.42        15.39        21.07 
TCGA-32-1976 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 
        0.49         0.10        15.85        19.50         1.18         4.67 
TCGA-32-1986 TCGA-32-1987 TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 
       12.69        14.86        16.93        12.23        20.78        15.02 
TCGA-32-2615 TCGA-32-2616 TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 
       15.95         7.36         8.84        22.78        25.18        21.14 
TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 
        3.72        12.59        19.86        10.85        19.23         0.85 
TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 
       13.35         8.94         9.53         0.99         4.44        11.84 
TCGA-41-4097 TCGA-41-6646 TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 
        0.20        12.46         4.14        14.76         3.45        20.91 
TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 TCGA-76-4926 TCGA-76-4928 
        4.34        14.33         8.22         7.50         4.54         3.09 
TCGA-76-4931 TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 
        9.17         2.53        10.78        16.70         3.29         2.70 
TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 
       11.38        17.06         8.35        20.98         4.83         5.03 
TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 
        0.23         9.27         7.73         7.79         1.61        17.72 
TCGA-87-5896 TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC 
       26.30         5.92         6.28        20.55 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             0.43              0.10 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
           115.86            127.59 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            14.53             11.74 
[1] "0.4 - 115.9 (14.5)" "0.1 - 127.6 (11.7)"
[1] "hr=" "1.3"
D51V2, continuous
D51V3, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    17  26
  5Q LOSS WILD-TYPE 207 320
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     17   26
  5Q LOSS WILD-TYPE  207  320
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE              17               207
  MALE                26               320
[1] 2 2
[1] FALSE
D51V4, continuous
                   vv
clus                GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  5Q LOSS MUTATED                               0                   0
  5Q LOSS WILD-TYPE                            27                  18
                   vv
clus                UNTREATED PRIMARY (DE NOVO) GBM
  5Q LOSS MUTATED                                43
  5Q LOSS WILD-TYPE                             482
D51V5, multiclass
                                 clus
vv                                5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                 0                27
  TREATED PRIMARY GBM                           0                18
  UNTREATED PRIMARY (DE NOVO) GBM              43               482
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V6, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    34   9
  5Q LOSS WILD-TYPE 348 179
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     34    9
  5Q LOSS WILD-TYPE  348  179
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  NO               34               348
  YES               9               179
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5Q LOSS MUTATED       2                         4    37
  5Q LOSS WILD-TYPE    11                        45   448
D51V7, multiclass
                           clus
vv                          5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  ASIAN                                   2                11
  BLACK OR AFRICAN AMERICAN               4                45
  WHITE                                  37               448
[1] 3 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
  5Q LOSS MUTATED     3  32
  5Q LOSS WILD-TYPE   9 440
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      3   32
  5Q LOSS WILD-TYPE    9  440
                        clus
vv                       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                 9
  NOT HISPANIC OR LATINO              32               440
[1] 2 2
[1] FALSE

Clustering(52) Variable = 6P LOSS MUTATION ANALYSIS
D52V1, survival
                   sevent
clus2                 0   1
  6P LOSS MUTATED     9  77
  6P LOSS WILD-TYPE  95 388
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               86               483 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               77               388 
$`6P LOSS MUTATED`
TCGA-02-0023 TCGA-02-0026 TCGA-02-0039 TCGA-02-0048 TCGA-02-0051 TCGA-02-0074 
       20.12        24.59        10.52         3.22        15.09        10.19 
TCGA-02-0080 TCGA-02-0086 TCGA-02-0106 TCGA-02-0113 TCGA-02-0115 TCGA-02-0281 
       89.72         8.81        11.67        92.65        15.65         3.98 
TCGA-02-0317 TCGA-02-0324 TCGA-02-0325 TCGA-02-2466 TCGA-02-2483 TCGA-06-0129 
       12.23         7.73        10.62        16.80        15.32        33.67 
TCGA-06-0130 TCGA-06-0138 TCGA-06-0141 TCGA-06-0162 TCGA-06-0166 TCGA-06-0184 
       12.95        24.23        10.29         3.42         5.85        69.90 
TCGA-06-0192 TCGA-06-0209 TCGA-06-0216 TCGA-06-0402 TCGA-06-0644 TCGA-06-0649 
       38.96         7.63        24.16         0.26        12.62         2.10 
TCGA-06-1806 TCGA-06-2561 TCGA-06-5410 TCGA-06-5416 TCGA-06-5856 TCGA-06-6390 
       15.32        17.65         3.55         6.71         3.75         5.39 
TCGA-06-6694 TCGA-08-0246 TCGA-08-0353 TCGA-08-0392 TCGA-08-0510 TCGA-08-0512 
        7.36         4.18         8.42         0.72         4.27        42.15 
TCGA-12-0616 TCGA-12-0691 TCGA-12-0692 TCGA-12-0822 TCGA-12-1098 TCGA-12-1099 
       14.73        12.13         3.65        23.51         3.98         4.14 
TCGA-12-1602 TCGA-12-3646 TCGA-12-3653 TCGA-14-0736 TCGA-14-0817 TCGA-14-0865 
        6.77        44.02        14.53        15.12         5.39        16.50 
TCGA-14-1453 TCGA-14-1823 TCGA-16-0846 TCGA-19-0962 TCGA-19-1392 TCGA-19-2629 
        1.15        17.85         3.91         0.66         3.65        24.23 
TCGA-19-4065 TCGA-19-5947 TCGA-19-5960 TCGA-19-A6J4 TCGA-26-1439 TCGA-27-1832 
        7.04         6.64        14.96         3.98        13.87         9.86 
TCGA-27-2524 TCGA-28-1750 TCGA-28-2506 TCGA-28-2509 TCGA-28-2514 TCGA-28-5220 
        7.59         8.35         6.74         4.77         5.26        12.76 
TCGA-32-1976 TCGA-32-1980 TCGA-32-2495 TCGA-32-2615 TCGA-32-4210 TCGA-32-4211 
        0.49         1.18        15.02        15.95         3.72        12.59 
TCGA-32-4719 TCGA-41-4097 TCGA-41-5651 TCGA-74-6573 TCGA-74-6575 TCGA-76-4928 
       10.85         0.20        15.12         3.45        20.91         3.09 
TCGA-76-4931 TCGA-OX-A56R 
        9.17         5.92 

$`6P LOSS WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 
       11.77         4.73        18.35        23.18        10.59        35.41 
TCGA-02-0011 TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0024 
       20.71        82.59        20.61        87.06        77.65        53.10 
TCGA-02-0025 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 
       42.74        12.16        90.58         2.83        14.14         3.62 
TCGA-02-0038 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 TCGA-02-0052 TCGA-02-0054 
       10.72        18.31         6.87        14.73        12.59         6.54 
TCGA-02-0055 TCGA-02-0057 TCGA-02-0058 TCGA-02-0059 TCGA-02-0060 TCGA-02-0064 
        2.50        19.86         8.35         9.57         6.02        19.73 
TCGA-02-0068 TCGA-02-0069 TCGA-02-0070 TCGA-02-0071 TCGA-02-0075 TCGA-02-0079 
       26.43        28.70        25.05         5.49        20.84        27.25 
TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 
       22.72        12.62        51.32        57.76        16.96         3.48 
TCGA-02-0102 TCGA-02-0104 TCGA-02-0107 TCGA-02-0111 TCGA-02-0114 TCGA-02-0116 
       27.02        65.00        17.65        23.18        99.98        48.95 
TCGA-02-0258 TCGA-02-0260 TCGA-02-0266 TCGA-02-0269 TCGA-02-0271 TCGA-02-0285 
       16.54        16.93        17.72        10.75        14.47        13.87 
TCGA-02-0289 TCGA-02-0290 TCGA-02-0321 TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 
       14.20        15.95         9.90         7.33        15.91        25.71 
TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 
        4.37        25.12        10.59        12.39        14.50        10.55 
TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 TCGA-02-2470 
       47.11        11.34         9.27        16.21         3.35        12.92 
TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 
       15.45        20.32         2.70         6.15        20.38        47.61 
TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 
        6.94         3.98        22.72        25.35        14.30        26.70 
TCGA-06-0139 TCGA-06-0140 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 
       11.90         0.20         2.20        11.74         2.33        20.09 
TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 
       17.79        10.09         8.61        19.46        46.59        12.33 
TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 
       13.94        10.45         3.19        10.82         9.44        11.80 
TCGA-06-0164 TCGA-06-0165 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 
       56.91        10.65        19.66         3.29        13.12         4.47 
TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 
        3.22         4.04        91.00         4.18        88.14        20.25 
TCGA-06-0182 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 
        3.65        73.84        27.22        44.58        15.42        10.42 
TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 
        4.67         7.40         5.56         0.39         7.66         8.42 
TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0219 TCGA-06-0221 
        7.40        11.84         0.53        15.02         0.72        19.82 
TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 
       13.64        13.32        20.42        48.69        10.82         9.01 
TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0645 
       72.36         4.70         9.57         3.16        35.11         5.75 
TCGA-06-0646 TCGA-06-0648 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 
        5.75         9.80        23.57        14.20        26.40        46.88 
TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 
        7.86         2.70         2.70         0.92        43.46        46.19 
TCGA-06-0877 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 
        5.65         7.17        40.41        16.57        20.78        26.76 
TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 
       23.93         6.84         4.04        26.79        11.84        15.32 
TCGA-06-1804 TCGA-06-1805 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2562 
       13.61        33.90         1.08        12.49         4.93        12.56 
TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 
       30.64         5.95        16.64         5.98         4.37         0.43 
TCGA-06-2570 TCGA-06-5408 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 
       31.50        11.74         8.35         4.54         8.81         8.98 
TCGA-06-5415 TCGA-06-5418 TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 TCGA-06-6389 
        8.55         2.73         6.15         4.57         5.23         7.79 
TCGA-06-6391 TCGA-06-6693 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 
        1.48       120.56         8.32        12.85         4.77         1.55 
TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 
        4.77         4.96         4.70         1.87         3.12         2.56 
TCGA-06-A7TK TCGA-06-A7TL TCGA-08-0244 TCGA-08-0245 TCGA-08-0344 TCGA-08-0345 
        5.39         5.42        22.68        37.84       115.86         1.74 
TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 
        8.42        25.71        12.16         9.80        29.23        65.33 
TCGA-08-0352 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 
        1.28        17.95        24.56        31.10        37.58        22.29 
TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 
        3.39        12.23        14.93        18.02        15.35        13.97 
TCGA-08-0509 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 
       12.56        11.08        19.59        58.68        19.33        10.75 
TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 
        4.80         7.27        15.98        18.41         7.56        15.35 
TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 
       12.99        34.92        10.45         7.59        94.78         0.10 
TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 
       38.17        25.97        26.66        20.38        28.41        15.06 
TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 
       53.85        43.23         7.63         9.73        14.93        14.86 
TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0826 TCGA-12-0827 
       91.76        24.79        18.48        10.62        27.78        38.76 
TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 
        8.94        20.58       127.59         5.82         7.59        33.21 
TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 
       21.73        15.98        12.23        15.85         9.11        14.53 
TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 TCGA-12-3644 TCGA-12-3648 TCGA-12-3649 
       15.65        25.68        14.73        59.77        26.93        15.22 
TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 
       10.95        12.69        34.92        14.93         3.22         2.04 
TCGA-14-0740 TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 
       11.97         0.95         6.21        23.05         2.24        11.24 
TCGA-14-0790 TCGA-14-0812 TCGA-14-0813 TCGA-14-0862 TCGA-14-0866 TCGA-14-0867 
       13.78         3.25         1.35         2.89        26.33         2.04 
TCGA-14-0871 TCGA-14-1034 TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 TCGA-14-1396 
       28.93        15.95        19.30         0.79         1.38         1.12 
TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 TCGA-14-1452 TCGA-14-1454 
        3.75        32.05        58.78        23.11         7.10        30.18 
TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 
        0.92        40.96         6.67        12.43         0.99         1.97 
TCGA-14-1821 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 
       17.79         7.63         5.88         7.17        17.49         7.96 
TCGA-14-3477 TCGA-14-4157 TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 
        3.78         3.42        13.78        50.53        19.10        53.19 
TCGA-15-1449 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 
       13.28        17.59        26.07        16.37         4.31        29.03 
TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 
        4.57        10.29        14.01         9.14        21.24        13.97 
TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 TCGA-19-0963 TCGA-19-0964 
        6.41        11.77        21.90         8.61        14.27         3.39 
TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 TCGA-19-1388 TCGA-19-1389 TCGA-19-1390 
       10.75         9.07         5.95        12.95         4.64        25.38 
TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 
        7.17        12.66         3.25         0.13         9.67         4.87 
TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 TCGA-19-2631 TCGA-19-5950 
        1.08         7.53         0.16         4.08         7.00        17.19 
TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 
        8.02        18.90         4.73        12.10         1.78        22.49 
TCGA-19-5958 TCGA-19-5959 TCGA-19-A60I TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1440 
       14.07        16.80        17.79        28.54        10.03         9.73 
TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 
       31.33         7.13         9.37         9.40        14.86         5.49 
TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-26-A7UX 
        8.88        18.97         1.58         7.92         2.33        19.33 
TCGA-27-1830 TCGA-27-1831 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 
        5.06        16.60        24.23        40.54        21.30        30.05 
TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 
       14.04        11.51        24.76        10.39        10.39        16.08 
TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 
        2.86        14.40        15.78         0.20         2.53         9.21 
TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 
        7.63         8.48         1.22         1.55         2.83         0.13 
TCGA-28-2502 TCGA-28-2513 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 
        0.66         7.30        14.93        11.28        17.88        14.53 
TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 
       11.77        31.27        23.44        11.01        13.64         5.16 
TCGA-28-5219 TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 TCGA-32-1977 TCGA-32-1978 
       22.68         5.42        15.39        21.07         0.10        15.85 
TCGA-32-1979 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 TCGA-32-1991 TCGA-32-2491 
       19.50         4.67        12.69        14.86        16.93        12.23 
TCGA-32-2494 TCGA-32-2616 TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 
       20.78         7.36         8.84        22.78        25.18        21.14 
TCGA-32-4213 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 
       19.86        19.23         0.85        13.35         8.94         9.53 
TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 TCGA-41-6646 TCGA-4W-AA9S TCGA-4W-AA9T 
        0.99         4.44        11.84        12.46         4.14        14.76 
TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 
        4.34        14.33         8.22         7.50         4.80         4.54 
TCGA-76-4929 TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 
        3.65         2.53        10.78        16.70         3.29         2.70 
TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 
       11.38        17.06         8.35        20.98         4.83         5.03 
TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 
        0.23         9.27         7.73         7.79         1.61        17.72 
TCGA-87-5896 TCGA-RR-A6KA TCGA-RR-A6KC 
       26.30         6.28        20.55 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
              0.2               0.1 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            92.65            127.59 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            9.515            12.230 
[1] "0.2 - 92.7 (9.5)"   "0.1 - 127.6 (12.2)"
[1] "hr=" "1.4"
D52V2, continuous
D52V3, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    35  51
  6P LOSS WILD-TYPE 189 295
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     35   51
  6P LOSS WILD-TYPE  189  295
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE              35               189
  MALE                51               295
[1] 2 2
[1] FALSE
D52V4, continuous
                   vv
clus                GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  6P LOSS MUTATED                               3                   4
  6P LOSS WILD-TYPE                            24                  14
                   vv
clus                UNTREATED PRIMARY (DE NOVO) GBM
  6P LOSS MUTATED                                79
  6P LOSS WILD-TYPE                             446
D52V5, multiclass
                                 clus
vv                                6P LOSS MUTATED 6P LOSS WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                 3                24
  TREATED PRIMARY GBM                           4                14
  UNTREATED PRIMARY (DE NOVO) GBM              79               446
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V6, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    56  30
  6P LOSS WILD-TYPE 326 158
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     56   30
  6P LOSS WILD-TYPE  326  158
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  NO               56               326
  YES              30               158
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6P LOSS MUTATED       4                         7    71
  6P LOSS WILD-TYPE     9                        42   414
D52V7, multiclass
                           clus
vv                          6P LOSS MUTATED 6P LOSS WILD-TYPE
  ASIAN                                   4                 9
  BLACK OR AFRICAN AMERICAN               7                42
  WHITE                                  71               414
[1] 3 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
  6P LOSS MUTATED     1  74
  6P LOSS WILD-TYPE  11 398
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      1   74
  6P LOSS WILD-TYPE   11  398
                        clus
vv                       6P LOSS MUTATED 6P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                11
  NOT HISPANIC OR LATINO              74               398
[1] 2 2
[1] FALSE

Clustering(53) Variable = 6Q LOSS MUTATION ANALYSIS
D53V1, survival
                   sevent
clus2                 0   1
  6Q LOSS MUTATED    18 106
  6Q LOSS WILD-TYPE  86 359
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              124               445 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              106               359 
$`6Q LOSS MUTATED`
TCGA-02-0007 TCGA-02-0023 TCGA-02-0026 TCGA-02-0039 TCGA-02-0048 TCGA-02-0051 
       23.18        20.12        24.59        10.52         3.22        15.09 
TCGA-02-0060 TCGA-02-0074 TCGA-02-0080 TCGA-02-0086 TCGA-02-0106 TCGA-02-0113 
        6.02        10.19        89.72         8.81        11.67        92.65 
TCGA-02-0115 TCGA-02-0258 TCGA-02-0281 TCGA-02-0317 TCGA-02-0324 TCGA-02-0325 
       15.65        16.54         3.98        12.23         7.73        10.62 
TCGA-02-0330 TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 TCGA-02-2466 TCGA-02-2483 
       15.91        14.50        10.55        47.11        16.80        15.32 
TCGA-06-0129 TCGA-06-0130 TCGA-06-0138 TCGA-06-0141 TCGA-06-0162 TCGA-06-0166 
       33.67        12.95        24.23        10.29         3.42         5.85 
TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0192 TCGA-06-0209 TCGA-06-0214 
       69.90        73.84        27.22        38.96         7.63        15.02 
TCGA-06-0216 TCGA-06-0402 TCGA-06-0644 TCGA-06-0649 TCGA-06-0750 TCGA-06-1806 
       24.16         0.26        12.62         2.10         0.92        15.32 
TCGA-06-2561 TCGA-06-5408 TCGA-06-5410 TCGA-06-5413 TCGA-06-5416 TCGA-06-5856 
       17.65        11.74         3.55         8.81         6.71         3.75 
TCGA-06-6390 TCGA-06-6694 TCGA-06-A6S1 TCGA-08-0246 TCGA-08-0353 TCGA-08-0358 
        5.39         7.36         2.56         4.18         8.42        22.29 
TCGA-08-0380 TCGA-08-0392 TCGA-08-0510 TCGA-08-0512 TCGA-08-0517 TCGA-08-0525 
       14.93         0.72         4.27        42.15        58.68        15.98 
TCGA-12-0615 TCGA-12-0616 TCGA-12-0654 TCGA-12-0656 TCGA-12-0691 TCGA-12-0692 
       15.35        14.73         7.59        94.78        12.13         3.65 
TCGA-12-0772 TCGA-12-0822 TCGA-12-1095 TCGA-12-1099 TCGA-12-1602 TCGA-12-3646 
       53.85        23.51        15.85         4.14         6.77        44.02 
TCGA-12-3653 TCGA-12-5299 TCGA-14-0736 TCGA-14-0817 TCGA-14-0865 TCGA-14-1037 
       14.53         3.22        15.12         5.39        16.50        19.30 
TCGA-14-1453 TCGA-14-1823 TCGA-14-4157 TCGA-15-0742 TCGA-16-0846 TCGA-16-0861 
        1.15        17.85         3.42        13.78         3.91         4.31 
TCGA-16-1045 TCGA-16-1063 TCGA-19-0962 TCGA-19-1392 TCGA-19-2629 TCGA-19-4065 
       29.03        13.97         0.66         3.65        24.23         7.04 
TCGA-19-5947 TCGA-19-5952 TCGA-19-5960 TCGA-19-A6J4 TCGA-26-1439 TCGA-26-1443 
        6.64        18.90        14.96         3.98        13.87         7.13 
TCGA-27-1832 TCGA-27-2524 TCGA-28-1750 TCGA-28-2506 TCGA-28-2509 TCGA-28-2514 
        9.86         7.59         8.35         6.74         4.77         5.26 
TCGA-28-5204 TCGA-28-5209 TCGA-28-5213 TCGA-28-5220 TCGA-32-1976 TCGA-32-1980 
       14.93        14.53        31.27        12.76         0.49         1.18 
TCGA-32-2495 TCGA-32-2615 TCGA-32-4208 TCGA-32-4210 TCGA-32-4211 TCGA-32-4719 
       15.02        15.95        21.14         3.72        12.59        10.85 
TCGA-41-3392 TCGA-41-4097 TCGA-41-5651 TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 
        0.99         0.20        15.12        14.76         3.45        20.91 
TCGA-76-4928 TCGA-76-4931 TCGA-76-6285 TCGA-OX-A56R 
        3.09         9.17         8.35         5.92 

$`6Q LOSS WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0009 TCGA-02-0010 TCGA-02-0011 
       11.77         4.73        18.35        10.59        35.41        20.71 
TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0024 TCGA-02-0025 
       82.59        20.61        87.06        77.65        53.10        42.74 
TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 
       12.16        90.58         2.83        14.14         3.62        10.72 
TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 TCGA-02-0052 TCGA-02-0054 TCGA-02-0055 
       18.31         6.87        14.73        12.59         6.54         2.50 
TCGA-02-0057 TCGA-02-0058 TCGA-02-0059 TCGA-02-0064 TCGA-02-0068 TCGA-02-0069 
       19.86         8.35         9.57        19.73        26.43        28.70 
TCGA-02-0070 TCGA-02-0071 TCGA-02-0075 TCGA-02-0079 TCGA-02-0083 TCGA-02-0084 
       25.05         5.49        20.84        27.25        22.72        12.62 
TCGA-02-0085 TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 TCGA-02-0104 
       51.32        57.76        16.96         3.48        27.02        65.00 
TCGA-02-0107 TCGA-02-0111 TCGA-02-0114 TCGA-02-0116 TCGA-02-0260 TCGA-02-0266 
       17.65        23.18        99.98        48.95        16.93        17.72 
TCGA-02-0269 TCGA-02-0271 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 TCGA-02-0321 
       10.75        14.47        13.87        14.20        15.95         9.90 
TCGA-02-0326 TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 
        7.33        25.71         4.37        25.12        10.59        12.39 
TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 TCGA-02-2470 TCGA-02-2485 
       11.34         9.27        16.21         3.35        12.92        15.45 
TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 
       20.32         2.70         6.15        20.38        47.61         6.94 
TCGA-06-0127 TCGA-06-0128 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0139 
        3.98        22.72        25.35        14.30        26.70        11.90 
TCGA-06-0140 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 
        0.20         2.20        11.74         2.33        20.09        17.79 
TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 
       10.09         8.61        19.46        46.59        12.33        13.94 
TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0164 
       10.45         3.19        10.82         9.44        11.80        56.91 
TCGA-06-0165 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 
       10.65        19.66         3.29        13.12         4.47         3.22 
TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 
        4.04        91.00         4.18        88.14        20.25         3.65 
TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 
       44.58        15.42        10.42         4.67         7.40         5.56 
TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 
        0.39         7.66         8.42         7.40        11.84         0.53 
TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 
        0.72        19.82        13.64        13.32        20.42        48.69 
TCGA-06-0394 TCGA-06-0397 TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 
       10.82         9.01        72.36         4.70         9.57         3.16 
TCGA-06-0414 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0650 TCGA-06-0686 
       35.11         5.75         5.75         9.80        23.57        14.20 
TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0875 
       26.40        46.88         7.86         2.70         2.70        43.46 
TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 
       46.19         5.65         7.17        40.41        16.57        20.78 
TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 
       26.76        23.93         6.84         4.04        26.79        11.84 
TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 
       15.32        13.61        33.90         1.08        12.49         4.93 
TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 
       12.56        30.64         5.95        16.64         5.98         4.37 
TCGA-06-2569 TCGA-06-2570 TCGA-06-5411 TCGA-06-5412 TCGA-06-5414 TCGA-06-5415 
        0.43        31.50         8.35         4.54         8.98         8.55 
TCGA-06-5418 TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 TCGA-06-6389 TCGA-06-6391 
        2.73         6.15         4.57         5.23         7.79         1.48 
TCGA-06-6693 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 
      120.56         8.32        12.85         4.77         1.55         4.77 
TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A7TK TCGA-06-A7TL 
        4.96         4.70         1.87         3.12         5.39         5.42 
TCGA-08-0244 TCGA-08-0245 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 
       22.68        37.84       115.86         1.74         8.42        25.71 
TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0354 
       12.16         9.80        29.23        65.33         1.28        17.95 
TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0359 TCGA-08-0375 TCGA-08-0386 
       24.56        31.10        37.58         3.39        12.23        18.02 
TCGA-08-0389 TCGA-08-0390 TCGA-08-0509 TCGA-08-0514 TCGA-08-0516 TCGA-08-0518 
       15.35        13.97        12.56        11.08        19.59        19.33 
TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0529 TCGA-08-0531 TCGA-12-0618 
       10.75         4.80         7.27        18.41         7.56        12.99 
TCGA-12-0619 TCGA-12-0620 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 
       34.92        10.45         0.10        38.17        25.97        26.66 
TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 
       20.38        28.41        15.06        43.23         7.63         9.73 
TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 
       14.93        14.86        91.76        24.79        18.48        10.62 
TCGA-12-0826 TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 
       27.78        38.76         8.94        20.58       127.59         5.82 
TCGA-12-1090 TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1096 
        7.59        33.21        21.73        15.98        12.23         9.11 
TCGA-12-1097 TCGA-12-1098 TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 TCGA-12-3644 
       14.53         3.98        15.65        25.68        14.73        59.77 
TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-5295 
       26.93        15.22        10.95        12.69        34.92        14.93 
TCGA-12-5301 TCGA-14-0740 TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 TCGA-14-0787 
        2.04        11.97         0.95         6.21        23.05         2.24 
TCGA-14-0789 TCGA-14-0790 TCGA-14-0812 TCGA-14-0813 TCGA-14-0862 TCGA-14-0866 
       11.24        13.78         3.25         1.35         2.89        26.33 
TCGA-14-0867 TCGA-14-0871 TCGA-14-1034 TCGA-14-1043 TCGA-14-1395 TCGA-14-1396 
        2.04        28.93        15.95         0.79         1.38         1.12 
TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 TCGA-14-1452 TCGA-14-1454 
        3.75        32.05        58.78        23.11         7.10        30.18 
TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 
        0.92        40.96         6.67        12.43         0.99         1.97 
TCGA-14-1821 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 
       17.79         7.63         5.88         7.17        17.49         7.96 
TCGA-14-3477 TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 TCGA-16-0848 
        3.78        50.53        19.10        53.19        13.28        17.59 
TCGA-16-0849 TCGA-16-0850 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 
       26.07        16.37         4.57        10.29        14.01         9.14 
TCGA-16-1062 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 TCGA-19-0963 
       21.24         6.41        11.77        21.90         8.61        14.27 
TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 TCGA-19-1388 TCGA-19-1389 
        3.39        10.75         9.07         5.95        12.95         4.64 
TCGA-19-1390 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 
       25.38         7.17        12.66         3.25         0.13         9.67 
TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 TCGA-19-2631 
        4.87         1.08         7.53         0.16         4.08         7.00 
TCGA-19-5950 TCGA-19-5951 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 
       17.19         8.02         4.73        12.10         1.78        22.49 
TCGA-19-5958 TCGA-19-5959 TCGA-19-A60I TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1440 
       14.07        16.80        17.79        28.54        10.03         9.73 
TCGA-26-1442 TCGA-26-1799 TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 
       31.33         9.37         9.40        14.86         5.49         8.88 
TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-26-A7UX TCGA-27-1830 
       18.97         1.58         7.92         2.33        19.33         5.06 
TCGA-27-1831 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 
       16.60        24.23        40.54        21.30        30.05        14.04 
TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 TCGA-27-2526 
       11.51        24.76        10.39        10.39        16.08         2.86 
TCGA-27-2527 TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 TCGA-28-1751 
       14.40        15.78         0.20         2.53         9.21         7.63 
TCGA-28-1752 TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 TCGA-28-2502 
        8.48         1.22         1.55         2.83         0.13         0.66 
TCGA-28-2513 TCGA-28-5207 TCGA-28-5208 TCGA-28-5211 TCGA-28-5214 TCGA-28-5215 
        7.30        11.28        17.88        11.77        23.44        11.01 
TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 
       13.64         5.16        22.68         5.42        15.39        21.07 
TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 
        0.10        15.85        19.50         4.67        12.69        14.86 
TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 TCGA-32-2616 TCGA-32-2632 TCGA-32-2634 
       16.93        12.23        20.78         7.36         8.84        22.78 
TCGA-32-2638 TCGA-32-4213 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 
       25.18        19.86        19.23         0.85        13.35         8.94 
TCGA-41-2575 TCGA-41-3393 TCGA-41-3915 TCGA-41-6646 TCGA-4W-AA9S TCGA-74-6577 
        9.53         4.44        11.84        12.46         4.14         4.34 
TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 TCGA-76-4929 
       14.33         8.22         7.50         4.80         4.54         3.65 
TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 
        2.53        10.78        16.70         3.29         2.70        11.38 
TCGA-76-6282 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 
       17.06        20.98         4.83         5.03         0.23         9.27 
TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-RR-A6KA 
        7.73         7.79         1.61        17.72        26.30         6.28 
TCGA-RR-A6KC 
       20.55 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              0.2               0.1 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            94.78            127.59 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           11.935            11.840 
[1] "0.2 - 94.8 (11.9)"  "0.1 - 127.6 (11.8)"
[1] "hr=" "1.1"
D53V2, continuous
D53V3, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    54  70
  6Q LOSS WILD-TYPE 170 276
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     54   70
  6Q LOSS WILD-TYPE  170  276
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE              54               170
  MALE                70               276
[1] 2 2
[1] FALSE
D53V4, continuous
                   vv
clus                GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  6Q LOSS MUTATED                               5                   5
  6Q LOSS WILD-TYPE                            22                  13
                   vv
clus                UNTREATED PRIMARY (DE NOVO) GBM
  6Q LOSS MUTATED                               114
  6Q LOSS WILD-TYPE                             411
D53V5, multiclass
                                 clus
vv                                6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                 5                22
  TREATED PRIMARY GBM                           5                13
  UNTREATED PRIMARY (DE NOVO) GBM             114               411
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V6, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    84  40
  6Q LOSS WILD-TYPE 298 148
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     84   40
  6Q LOSS WILD-TYPE  298  148
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  NO               84               298
  YES              40               148
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6Q LOSS MUTATED       5                        12   101
  6Q LOSS WILD-TYPE     8                        37   384
D53V7, multiclass
                           clus
vv                          6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  ASIAN                                   5                 8
  BLACK OR AFRICAN AMERICAN              12                37
  WHITE                                 101               384
[1] 3 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
  6Q LOSS MUTATED     1 104
  6Q LOSS WILD-TYPE  11 368
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      1  104
  6Q LOSS WILD-TYPE   11  368
                        clus
vv                       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                11
  NOT HISPANIC OR LATINO             104               368
[1] 2 2
[1] FALSE

Clustering(54) Variable = 7P LOSS MUTATION ANALYSIS
D54V1, survival
                   sevent
clus2                 0   1
  7P LOSS MUTATED     2   6
  7P LOSS WILD-TYPE 102 459
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                8               561 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                6               459 
$`7P LOSS MUTATED`
TCGA-02-0015 TCGA-02-0026 TCGA-02-0432 TCGA-06-0221 TCGA-06-0410 TCGA-08-0516 
       20.61        24.59        47.11        19.82         4.70        19.59 
TCGA-14-3477 TCGA-19-0960 
        3.78         8.61 

$`7P LOSS WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 
       11.77         4.73        18.35        23.18        10.59        35.41 
TCGA-02-0011 TCGA-02-0014 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0024 
       20.71        82.59        87.06        77.65        20.12        53.10 
TCGA-02-0025 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 
       42.74        12.16        90.58         2.83        14.14         3.62 
TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 TCGA-02-0048 
       10.72        10.52        18.31         6.87        14.73         3.22 
TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 TCGA-02-0055 TCGA-02-0057 TCGA-02-0058 
       15.09        12.59         6.54         2.50        19.86         8.35 
TCGA-02-0059 TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 TCGA-02-0069 TCGA-02-0070 
        9.57         6.02        19.73        26.43        28.70        25.05 
TCGA-02-0071 TCGA-02-0074 TCGA-02-0075 TCGA-02-0079 TCGA-02-0080 TCGA-02-0083 
        5.49        10.19        20.84        27.25        89.72        22.72 
TCGA-02-0084 TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 
       12.62        51.32         8.81        57.76        16.96         3.48 
TCGA-02-0102 TCGA-02-0104 TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 TCGA-02-0113 
       27.02        65.00        11.67        17.65        23.18        92.65 
TCGA-02-0114 TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 TCGA-02-0266 
       99.98        15.65        48.95        16.54        16.93        17.72 
TCGA-02-0269 TCGA-02-0271 TCGA-02-0281 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 
       10.75        14.47         3.98        13.87        14.20        15.95 
TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 
       12.23         9.90         7.73        10.62         7.33        15.91 
TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 
       25.71         4.37        25.12        10.59        12.39        14.50 
TCGA-02-0430 TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 TCGA-02-2466 
       10.55        11.34         9.27        16.21         3.35        16.80 
TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 
       12.92        15.32        15.45        20.32         2.70         6.15 
TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 
       20.38        47.61         6.94         3.98        22.72        33.67 
TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 
       12.95        25.35        14.30        26.70        24.23        11.90 
TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 
        0.20        10.29         2.20        11.74         2.33        20.09 
TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 
       17.79        10.09         8.61        19.46        46.59        12.33 
TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 
       13.94        10.45         3.19        10.82         9.44        11.80 
TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 
        3.42        56.91        10.65         5.85        19.66         3.29 
TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 
       13.12         4.47         3.22         4.04        91.00         4.18 
TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 
       88.14        20.25         3.65        69.90        73.84        27.22 
TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 
       44.58        15.42        10.42        38.96         4.67         7.40 
TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 
        5.56         0.39         7.66         8.42         7.63         7.40 
TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0237 
       11.84         0.53        15.02        24.16         0.72        13.64 
TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 
       13.32        20.42        48.69        10.82         9.01         0.26 
TCGA-06-0409 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 
       72.36         9.57         3.16        35.11        12.62         5.75 
TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 
        5.75         9.80         2.10        23.57        14.20        26.40 
TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 
       46.88         7.86         2.70         2.70         0.92        43.46 
TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 
       46.19         5.65         7.17        40.41        16.57        20.78 
TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 
       26.76        23.93         6.84         4.04        26.79        11.84 
TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 TCGA-06-2557 TCGA-06-2558 
       15.32        13.61        33.90        15.32         1.08        12.49 
TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 
        4.93        17.65        12.56        30.64         5.95        16.64 
TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 
        5.98         4.37         0.43        31.50        11.74         3.55 
TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 
        8.35         4.54         8.81         8.98         8.55         6.71 
TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 TCGA-06-6389 
        2.73         3.75         6.15         4.57         5.23         7.79 
TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 
        5.39         1.48       120.56         7.36         8.32        12.85 
TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A5U1 
        4.77         1.55         4.77         4.96         4.70         1.87 
TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK TCGA-06-A7TL TCGA-08-0244 TCGA-08-0245 
        3.12         2.56         5.39         5.42        22.68        37.84 
TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 
        4.18       115.86         1.74         8.42        25.71        12.16 
TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 
        9.80        29.23        65.33         1.28         8.42        17.95 
TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 
       24.56        31.10        37.58        22.29         3.39        12.23 
TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 
       14.93        18.02        15.35        13.97         0.72        12.56 
TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 
        4.27        42.15        11.08        58.68        19.33        10.75 
TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 
        4.80         7.27        15.98        18.41         7.56        15.35 
TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 
       14.73        12.99        34.92        10.45         7.59        94.78 
TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 
        0.10        38.17        25.97        26.66        12.13         3.65 
TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 
       20.38        28.41        15.06        53.85        43.23         7.63 
TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 
        9.73        14.93        14.86        91.76        24.79        18.48 
TCGA-12-0821 TCGA-12-0822 TCGA-12-0826 TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 
       10.62        23.51        27.78        38.76         8.94        20.58 
TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 
      127.59         5.82         7.59        33.21        21.73        15.98 
TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 
       12.23        15.85         9.11        14.53         3.98         4.14 
TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 
       15.65        25.68        14.73         6.77        59.77        44.02 
TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 
       26.93        15.22        10.95        12.69        34.92        14.53 
TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 
       14.93         3.22         2.04        15.12        11.97         0.95 
TCGA-14-0783 TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 TCGA-14-0812 
        6.21        23.05         2.24        11.24        13.78         3.25 
TCGA-14-0813 TCGA-14-0817 TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 TCGA-14-0867 
        1.35         5.39         2.89        16.50        26.33         2.04 
TCGA-14-0871 TCGA-14-1034 TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 TCGA-14-1396 
       28.93        15.95        19.30         0.79         1.38         1.12 
TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 TCGA-14-1452 TCGA-14-1453 
        3.75        32.05        58.78        23.11         7.10         1.15 
TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 TCGA-14-1794 
       30.18         0.92        40.96         6.67        12.43         0.99 
TCGA-14-1795 TCGA-14-1821 TCGA-14-1823 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 
        1.97        17.79        17.85         7.63         5.88         7.17 
TCGA-14-2554 TCGA-14-2555 TCGA-14-4157 TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 
       17.49         7.96         3.42        13.78        50.53        19.10 
TCGA-15-1447 TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 
       53.19        13.28         3.91        17.59        26.07        16.37 
TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 
        4.31        29.03         4.57        10.29        14.01         9.14 
TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 TCGA-19-0962 
       21.24        13.97         6.41        11.77        21.90         0.66 
TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 TCGA-19-1388 
       14.27         3.39        10.75         9.07         5.95        12.95 
TCGA-19-1389 TCGA-19-1390 TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 
        4.64        25.38         3.65         7.17        12.66         3.25 
TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 
        0.13         9.67         4.87         1.08         7.53         0.16 
TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 
        4.08        24.23         7.00         7.04         6.64        17.19 
TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 
        8.02        18.90         4.73        12.10         1.78        22.49 
TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J4 TCGA-19-A6J5 
       14.07        16.80        14.96        17.79         3.98        28.54 
TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 
       10.03        13.87         9.73        31.33         7.13         9.37 
TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 
        9.40        14.86         5.49         8.88        18.97         1.58 
TCGA-26-6173 TCGA-26-6174 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 
        7.92         2.33        19.33         5.06        16.60         9.86 
TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 
       24.23        40.54        21.30        30.05        14.04        11.51 
TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 
       24.76        10.39        10.39        16.08         7.59         2.86 
TCGA-27-2527 TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 
       14.40        15.78         0.20         2.53         9.21         8.35 
TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 
        7.63         8.48         1.22         1.55         2.83         0.13 
TCGA-28-2502 TCGA-28-2506 TCGA-28-2509 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 
        0.66         6.74         4.77         7.30         5.26        14.93 
TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 
       11.28        17.88        14.53        11.77        31.27        23.44 
TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 
       11.01        13.64         5.16        22.68        12.76         5.42 
TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 
       15.39        21.07         0.49         0.10        15.85        19.50 
TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 TCGA-32-1991 TCGA-32-2491 
        1.18         4.67        12.69        14.86        16.93        12.23 
TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 TCGA-32-2616 TCGA-32-2632 TCGA-32-2634 
       20.78        15.02        15.95         7.36         8.84        22.78 
TCGA-32-2638 TCGA-32-4208 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 
       25.18        21.14         3.72        12.59        19.86        10.85 
TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 
       19.23         0.85        13.35         8.94         9.53         0.99 
TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9S 
        4.44        11.84         0.20        15.12        12.46         4.14 
TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 
       14.76         3.45        20.91         4.34        14.33         8.22 
TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 
        7.50         4.80         4.54         3.09         3.65         9.17 
TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 
        2.53        10.78        16.70         3.29         2.70        11.38 
TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 
       17.06         8.35        20.98         4.83         5.03         0.23 
TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
        9.27         7.73         7.79         1.61        17.72        26.30 
TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC 
        5.92         6.28        20.55 

  7P LOSS MUTATED 7P LOSS WILD-TYPE 
             3.78              0.10 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
            47.11            127.59 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
           19.705            11.840 
[1] "3.8 - 47.1 (19.7)"  "0.1 - 127.6 (11.8)"
[1] "hr=" "1.4"
D54V2, continuous
D54V3, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     3   5
  7P LOSS WILD-TYPE 221 341
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      3    5
  7P LOSS WILD-TYPE  221  341
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  FEMALE               3               221
  MALE                 5               341
[1] 2 2
[1] FALSE
D54V4, continuous
                   vv
clus                GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  7P LOSS MUTATED                               0                   0
  7P LOSS WILD-TYPE                            27                  18
                   vv
clus                UNTREATED PRIMARY (DE NOVO) GBM
  7P LOSS MUTATED                                 8
  7P LOSS WILD-TYPE                             517
D54V5, multiclass
                                 clus
vv                                7P LOSS MUTATED 7P LOSS WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                 0                27
  TREATED PRIMARY GBM                           0                18
  UNTREATED PRIMARY (DE NOVO) GBM               8               517
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V6, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     7   1
  7P LOSS WILD-TYPE 375 187
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      7    1
  7P LOSS WILD-TYPE  375  187
     clus
vv    7P LOSS MUTATED 7P LOSS WILD-TYPE
  NO                7               375
  YES               1               187
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7P LOSS MUTATED       0                         1     7
  7P LOSS WILD-TYPE    13                        48   478
D54V7, multiclass
                           clus
vv                          7P LOSS MUTATED 7P LOSS WILD-TYPE
  ASIAN                                   0                13
  BLACK OR AFRICAN AMERICAN               1                48
  WHITE                                   7               478
[1] 3 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
  7P LOSS MUTATED     0   8
  7P LOSS WILD-TYPE  12 464
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      0    8
  7P LOSS WILD-TYPE   12  464
                        clus
vv                       7P LOSS MUTATED 7P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                12
  NOT HISPANIC OR LATINO               8               464
[1] 2 2
[1] FALSE

Clustering(55) Variable = 7Q LOSS MUTATION ANALYSIS
D55V1, survival
                   sevent
clus2                 0   1
  7Q LOSS MUTATED     1   5
  7Q LOSS WILD-TYPE 103 460
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                6               563 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                5               460 
$`7Q LOSS MUTATED`
TCGA-02-0015 TCGA-02-0432 TCGA-06-0221 TCGA-06-0410 TCGA-08-0516 TCGA-14-3477 
       20.61        47.11        19.82         4.70        19.59         3.78 

$`7Q LOSS WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 
       11.77         4.73        18.35        23.18        10.59        35.41 
TCGA-02-0011 TCGA-02-0014 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0024 
       20.71        82.59        87.06        77.65        20.12        53.10 
TCGA-02-0025 TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 
       42.74        24.59        12.16        90.58         2.83        14.14 
TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 
        3.62        10.72        10.52        18.31         6.87        14.73 
TCGA-02-0048 TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 TCGA-02-0055 TCGA-02-0057 
        3.22        15.09        12.59         6.54         2.50        19.86 
TCGA-02-0058 TCGA-02-0059 TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 TCGA-02-0069 
        8.35         9.57         6.02        19.73        26.43        28.70 
TCGA-02-0070 TCGA-02-0071 TCGA-02-0074 TCGA-02-0075 TCGA-02-0079 TCGA-02-0080 
       25.05         5.49        10.19        20.84        27.25        89.72 
TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 
       22.72        12.62        51.32         8.81        57.76        16.96 
TCGA-02-0099 TCGA-02-0102 TCGA-02-0104 TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 
        3.48        27.02        65.00        11.67        17.65        23.18 
TCGA-02-0113 TCGA-02-0114 TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 
       92.65        99.98        15.65        48.95        16.54        16.93 
TCGA-02-0266 TCGA-02-0269 TCGA-02-0271 TCGA-02-0281 TCGA-02-0285 TCGA-02-0289 
       17.72        10.75        14.47         3.98        13.87        14.20 
TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 
       15.95        12.23         9.90         7.73        10.62         7.33 
TCGA-02-0330 TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 
       15.91        25.71         4.37        25.12        10.59        12.39 
TCGA-02-0422 TCGA-02-0430 TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 
       14.50        10.55        11.34         9.27        16.21         3.35 
TCGA-02-2466 TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 
       16.80        12.92        15.32        15.45        20.32         2.70 
TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 
        6.15        20.38        47.61         6.94         3.98        22.72 
TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 
       33.67        12.95        25.35        14.30        26.70        24.23 
TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 
       11.90         0.20        10.29         2.20        11.74         2.33 
TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 
       20.09        17.79        10.09         8.61        19.46        46.59 
TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 
       12.33        13.94        10.45         3.19        10.82         9.44 
TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 
       11.80         3.42        56.91        10.65         5.85        19.66 
TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 
        3.29        13.12         4.47         3.22         4.04        91.00 
TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 
        4.18        88.14        20.25         3.65        69.90        73.84 
TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 
       27.22        44.58        15.42        10.42        38.96         4.67 
TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 
        7.40         5.56         0.39         7.66         8.42         7.63 
TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 
        7.40        11.84         0.53        15.02        24.16         0.72 
TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 
       13.64        13.32        20.42        48.69        10.82         9.01 
TCGA-06-0402 TCGA-06-0409 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 
        0.26        72.36         9.57         3.16        35.11        12.62 
TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 
        5.75         5.75         9.80         2.10        23.57        14.20 
TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 
       26.40        46.88         7.86         2.70         2.70         0.92 
TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 
       43.46        46.19         5.65         7.17        40.41        16.57 
TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 
       20.78        26.76        23.93         6.84         4.04        26.79 
TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 TCGA-06-2557 
       11.84        15.32        13.61        33.90        15.32         1.08 
TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 
       12.49         4.93        17.65        12.56        30.64         5.95 
TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-5408 
       16.64         5.98         4.37         0.43        31.50        11.74 
TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 
        3.55         8.35         4.54         8.81         8.98         8.55 
TCGA-06-5416 TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 
        6.71         2.73         3.75         6.15         4.57         5.23 
TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 
        7.79         5.39         1.48       120.56         7.36         8.32 
TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 
       12.85         4.77         1.55         4.77         4.96         4.70 
TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK TCGA-06-A7TL TCGA-08-0244 
        1.87         3.12         2.56         5.39         5.42        22.68 
TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 
       37.84         4.18       115.86         1.74         8.42        25.71 
TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 
       12.16         9.80        29.23        65.33         1.28         8.42 
TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 
       17.95        24.56        31.10        37.58        22.29         3.39 
TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 
       12.23        14.93        18.02        15.35        13.97         0.72 
TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 TCGA-08-0517 TCGA-08-0518 
       12.56         4.27        42.15        11.08        58.68        19.33 
TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 
       10.75         4.80         7.27        15.98        18.41         7.56 
TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 
       15.35        14.73        12.99        34.92        10.45         7.59 
TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 
       94.78         0.10        38.17        25.97        26.66        12.13 
TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 
        3.65        20.38        28.41        15.06        53.85        43.23 
TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 
        7.63         9.73        14.93        14.86        91.76        24.79 
TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 TCGA-12-0826 TCGA-12-0827 TCGA-12-0828 
       18.48        10.62        23.51        27.78        38.76         8.94 
TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 TCGA-12-1092 
       20.58       127.59         5.82         7.59        33.21        21.73 
TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 
       15.98        12.23        15.85         9.11        14.53         3.98 
TCGA-12-1099 TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 
        4.14        15.65        25.68        14.73         6.77        59.77 
TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 
       44.02        26.93        15.22        10.95        12.69        34.92 
TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 
       14.53        14.93         3.22         2.04        15.12        11.97 
TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 
        0.95         6.21        23.05         2.24        11.24        13.78 
TCGA-14-0812 TCGA-14-0813 TCGA-14-0817 TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 
        3.25         1.35         5.39         2.89        16.50        26.33 
TCGA-14-0867 TCGA-14-0871 TCGA-14-1034 TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 
        2.04        28.93        15.95        19.30         0.79         1.38 
TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 TCGA-14-1452 
        1.12         3.75        32.05        58.78        23.11         7.10 
TCGA-14-1453 TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 
        1.15        30.18         0.92        40.96         6.67        12.43 
TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 TCGA-14-1823 TCGA-14-1825 TCGA-14-1827 
        0.99         1.97        17.79        17.85         7.63         5.88 
TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-4157 TCGA-15-0742 TCGA-15-1444 
        7.17        17.49         7.96         3.42        13.78        50.53 
TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 
       19.10        53.19        13.28         3.91        17.59        26.07 
TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 
       16.37         4.31        29.03         4.57        10.29        14.01 
TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 
        9.14        21.24        13.97         6.41        11.77        21.90 
TCGA-19-0960 TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 
        8.61         0.66        14.27         3.39        10.75         9.07 
TCGA-19-1387 TCGA-19-1388 TCGA-19-1389 TCGA-19-1390 TCGA-19-1392 TCGA-19-1786 
        5.95        12.95         4.64        25.38         3.65         7.17 
TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 
       12.66         3.25         0.13         9.67         4.87         1.08 
TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 
        7.53         0.16         4.08        24.23         7.00         7.04 
TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 
        6.64        17.19         8.02        18.90         4.73        12.10 
TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I 
        1.78        22.49        14.07        16.80        14.96        17.79 
TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 
        3.98        28.54        10.03        13.87         9.73        31.33 
TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 
        7.13         9.37         9.40        14.86         5.49         8.88 
TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-26-A7UX TCGA-27-1830 
       18.97         1.58         7.92         2.33        19.33         5.06 
TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 
       16.60         9.86        24.23        40.54        21.30        30.05 
TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 
       14.04        11.51        24.76        10.39        10.39        16.08 
TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 
        7.59         2.86        14.40        15.78         0.20         2.53 
TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 TCGA-28-1755 
        9.21         8.35         7.63         8.48         1.22         1.55 
TCGA-28-1756 TCGA-28-1757 TCGA-28-2502 TCGA-28-2506 TCGA-28-2509 TCGA-28-2513 
        2.83         0.13         0.66         6.74         4.77         7.30 
TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 
        5.26        14.93        11.28        17.88        14.53        11.77 
TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 
       31.27        23.44        11.01        13.64         5.16        22.68 
TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 
       12.76         5.42        15.39        21.07         0.49         0.10 
TCGA-32-1978 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 
       15.85        19.50         1.18         4.67        12.69        14.86 
TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 TCGA-32-2616 
       16.93        12.23        20.78        15.02        15.95         7.36 
TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4210 TCGA-32-4211 
        8.84        22.78        25.18        21.14         3.72        12.59 
TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 
       19.86        10.85        19.23         0.85        13.35         8.94 
TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 
        9.53         0.99         4.44        11.84         0.20        15.12 
TCGA-41-6646 TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 
       12.46         4.14        14.76         3.45        20.91         4.34 
TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 
       14.33         8.22         7.50         4.80         4.54         3.09 
TCGA-76-4929 TCGA-76-4931 TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 
        3.65         9.17         2.53        10.78        16.70         3.29 
TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 
        2.70        11.38        17.06         8.35        20.98         4.83 
TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 
        5.03         0.23         9.27         7.73         7.79         1.61 
TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC 
       17.72        26.30         5.92         6.28        20.55 

  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
             3.78              0.10 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            47.11            127.59 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
           19.705            11.840 
[1] "3.8 - 47.1 (19.7)"  "0.1 - 127.6 (11.8)"
[1] "hr=" "1.3"
D55V2, continuous
D55V3, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     2   4
  7Q LOSS WILD-TYPE 222 342
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      2    4
  7Q LOSS WILD-TYPE  222  342
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  FEMALE               2               222
  MALE                 4               342
[1] 2 2
[1] FALSE
D55V4, continuous
                   vv
clus                GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  7Q LOSS MUTATED                               0                   0
  7Q LOSS WILD-TYPE                            27                  18
                   vv
clus                UNTREATED PRIMARY (DE NOVO) GBM
  7Q LOSS MUTATED                                 6
  7Q LOSS WILD-TYPE                             519
D55V5, multiclass
                                 clus
vv                                7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                 0                27
  TREATED PRIMARY GBM                           0                18
  UNTREATED PRIMARY (DE NOVO) GBM               6               519
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V6, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     5   1
  7Q LOSS WILD-TYPE 377 187
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      5    1
  7Q LOSS WILD-TYPE  377  187
     clus
vv    7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  NO                5               377
  YES               1               187
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7Q LOSS MUTATED       0                         1     5
  7Q LOSS WILD-TYPE    13                        48   480
D55V7, multiclass
                           clus
vv                          7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  ASIAN                                   0                13
  BLACK OR AFRICAN AMERICAN               1                48
  WHITE                                   5               480
[1] 3 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
  7Q LOSS MUTATED     0   6
  7Q LOSS WILD-TYPE  12 466
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      0    6
  7Q LOSS WILD-TYPE   12  466
                        clus
vv                       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                12
  NOT HISPANIC OR LATINO               6               466
[1] 2 2
[1] FALSE

Clustering(56) Variable = 8P LOSS MUTATION ANALYSIS
D56V1, survival
                   sevent
clus2                 0   1
  8P LOSS MUTATED    12  46
  8P LOSS WILD-TYPE  92 419
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               58               511 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               46               419 
$`8P LOSS MUTATED`
TCGA-02-0001 TCGA-02-0025 TCGA-02-0059 TCGA-02-0060 TCGA-02-0086 TCGA-02-0106 
       11.77        42.74         9.57         6.02         8.81        11.67 
TCGA-02-0111 TCGA-02-0115 TCGA-02-0281 TCGA-02-0324 TCGA-02-0430 TCGA-02-2486 
       23.18        15.65         3.98         7.73        10.55        20.32 
TCGA-06-0159 TCGA-06-0171 TCGA-06-0195 TCGA-06-0216 TCGA-06-0410 TCGA-06-0743 
        9.44        13.12         7.40        24.16         4.70        26.40 
TCGA-06-2570 TCGA-06-5408 TCGA-06-5411 TCGA-06-5413 TCGA-06-6693 TCGA-08-0246 
       31.50        11.74         8.35         8.81       120.56         4.18 
TCGA-08-0392 TCGA-08-0510 TCGA-08-0525 TCGA-12-0776 TCGA-12-0826 TCGA-12-0827 
        0.72         4.27        15.98         9.73        27.78        38.76 
TCGA-12-1098 TCGA-12-1598 TCGA-14-0736 TCGA-14-0862 TCGA-14-1034 TCGA-14-1450 
        3.98        15.65        15.12         2.89        15.95        58.78 
TCGA-14-1794 TCGA-14-1823 TCGA-15-1447 TCGA-16-0846 TCGA-16-1063 TCGA-19-0960 
        0.99        17.85        53.19         3.91        13.97         8.61 
TCGA-19-1385 TCGA-19-1786 TCGA-26-1439 TCGA-26-5136 TCGA-27-2524 TCGA-28-1750 
       10.75         7.17        13.87        18.97         7.59         8.35 
TCGA-28-2502 TCGA-28-2509 TCGA-28-2514 TCGA-28-5204 TCGA-32-4208 TCGA-32-4210 
        0.66         4.77         5.26        14.93        21.14         3.72 
TCGA-32-4719 TCGA-41-3915 TCGA-74-6584 TCGA-76-4934 
       10.85        11.84         7.50         2.53 

$`8P LOSS WILD-TYPE`
TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 TCGA-02-0011 
        4.73        18.35        23.18        10.59        35.41        20.71 
TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0024 
       82.59        20.61        87.06        77.65        20.12        53.10 
TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 
       24.59        12.16        90.58         2.83        14.14         3.62 
TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 TCGA-02-0048 
       10.72        10.52        18.31         6.87        14.73         3.22 
TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 TCGA-02-0055 TCGA-02-0057 TCGA-02-0058 
       15.09        12.59         6.54         2.50        19.86         8.35 
TCGA-02-0064 TCGA-02-0068 TCGA-02-0069 TCGA-02-0070 TCGA-02-0071 TCGA-02-0074 
       19.73        26.43        28.70        25.05         5.49        10.19 
TCGA-02-0075 TCGA-02-0079 TCGA-02-0080 TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 
       20.84        27.25        89.72        22.72        12.62        51.32 
TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 TCGA-02-0104 TCGA-02-0107 
       57.76        16.96         3.48        27.02        65.00        17.65 
TCGA-02-0113 TCGA-02-0114 TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 TCGA-02-0266 
       92.65        99.98        48.95        16.54        16.93        17.72 
TCGA-02-0269 TCGA-02-0271 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 
       10.75        14.47        13.87        14.20        15.95        12.23 
TCGA-02-0321 TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 TCGA-02-0333 
        9.90        10.62         7.33        15.91        25.71         4.37 
TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 TCGA-02-0432 TCGA-02-0440 
       25.12        10.59        12.39        14.50        47.11        11.34 
TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 TCGA-02-2466 TCGA-02-2470 TCGA-02-2483 
        9.27        16.21         3.35        16.80        12.92        15.32 
TCGA-02-2485 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 
       15.45         2.70         6.15        20.38        47.61         6.94 
TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 
        3.98        22.72        33.67        12.95        25.35        14.30 
TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 
       26.70        24.23        11.90         0.20        10.29         2.20 
TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 
       11.74         2.33        20.09        17.79        10.09         8.61 
TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 
       19.46        46.59        12.33        13.94        10.45         3.19 
TCGA-06-0158 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 
       10.82        11.80         3.42        56.91        10.65         5.85 
TCGA-06-0168 TCGA-06-0169 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 
       19.66         3.29         4.47         3.22         4.04        91.00 
TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 
        4.18        88.14        20.25         3.65        69.90        73.84 
TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 
       27.22        44.58        15.42        10.42        38.96         4.67 
TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 
        5.56         0.39         7.66         8.42         7.63         7.40 
TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 
       11.84         0.53        15.02         0.72        19.82        13.64 
TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 
       13.32        20.42        48.69        10.82         9.01         0.26 
TCGA-06-0409 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 
       72.36         9.57         3.16        35.11        12.62         5.75 
TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0744 
        5.75         9.80         2.10        23.57        14.20        46.88 
TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 
        7.86         2.70         2.70         0.92        43.46        46.19 
TCGA-06-0877 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 
        5.65         7.17        40.41        16.57        20.78        26.76 
TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 
       23.93         6.84         4.04        26.79        11.84        15.32 
TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 
       13.61        33.90        15.32         1.08        12.49         4.93 
TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 
       17.65        12.56        30.64         5.95        16.64         5.98 
TCGA-06-2567 TCGA-06-2569 TCGA-06-5410 TCGA-06-5412 TCGA-06-5414 TCGA-06-5415 
        4.37         0.43         3.55         4.54         8.98         8.55 
TCGA-06-5416 TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 
        6.71         2.73         3.75         6.15         4.57         5.23 
TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 
        7.79         5.39         1.48         7.36         8.32        12.85 
TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A5U1 
        4.77         1.55         4.77         4.96         4.70         1.87 
TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK TCGA-06-A7TL TCGA-08-0244 TCGA-08-0245 
        3.12         2.56         5.39         5.42        22.68        37.84 
TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 
      115.86         1.74         8.42        25.71        12.16         9.80 
TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 
       29.23        65.33         1.28         8.42        17.95        24.56 
TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 
       31.10        37.58        22.29         3.39        12.23        14.93 
TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0509 TCGA-08-0512 TCGA-08-0514 
       18.02        15.35        13.97        12.56        42.15        11.08 
TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 
       19.59        58.68        19.33        10.75         4.80         7.27 
TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 
       18.41         7.56        15.35        14.73        12.99        34.92 
TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 
       10.45         7.59        94.78         0.10        38.17        25.97 
TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 
       26.66        12.13         3.65        20.38        28.41        15.06 
TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 
       53.85        43.23         7.63        14.93        14.86        91.76 
TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 TCGA-12-0828 TCGA-12-0829 
       24.79        18.48        10.62        23.51         8.94        20.58 
TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 
      127.59         5.82         7.59        33.21        21.73        15.98 
TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1099 TCGA-12-1599 
       12.23        15.85         9.11        14.53         4.14        25.68 
TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 
       14.73         6.77        59.77        44.02        26.93        15.22 
TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 
       10.95        12.69        34.92        14.53        14.93         3.22 
TCGA-12-5301 TCGA-14-0740 TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 TCGA-14-0787 
        2.04        11.97         0.95         6.21        23.05         2.24 
TCGA-14-0789 TCGA-14-0790 TCGA-14-0812 TCGA-14-0813 TCGA-14-0817 TCGA-14-0865 
       11.24        13.78         3.25         1.35         5.39        16.50 
TCGA-14-0866 TCGA-14-0867 TCGA-14-0871 TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 
       26.33         2.04        28.93        19.30         0.79         1.38 
TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 TCGA-14-1451 TCGA-14-1452 TCGA-14-1453 
        1.12         3.75        32.05        23.11         7.10         1.15 
TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 TCGA-14-1795 
       30.18         0.92        40.96         6.67        12.43         1.97 
TCGA-14-1821 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 
       17.79         7.63         5.88         7.17        17.49         7.96 
TCGA-14-3477 TCGA-14-4157 TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-15-1449 
        3.78         3.42        13.78        50.53        19.10        13.28 
TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 
       17.59        26.07        16.37         4.31        29.03         4.57 
TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1460 TCGA-19-0955 
       10.29        14.01         9.14        21.24         6.41        11.77 
TCGA-19-0957 TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 TCGA-19-1386 TCGA-19-1387 
       21.90         0.66        14.27         3.39         9.07         5.95 
TCGA-19-1388 TCGA-19-1389 TCGA-19-1390 TCGA-19-1392 TCGA-19-1787 TCGA-19-1789 
       12.95         4.64        25.38         3.65        12.66         3.25 
TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 
        0.13         9.67         4.87         1.08         7.53         0.16 
TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 
        4.08        24.23         7.00         7.04         6.64        17.19 
TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 
        8.02        18.90         4.73        12.10         1.78        22.49 
TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J4 TCGA-19-A6J5 
       14.07        16.80        14.96        17.79         3.98        28.54 
TCGA-26-1438 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 
       10.03         9.73        31.33         7.13         9.37         9.40 
TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 
       14.86         5.49         8.88         1.58         7.92         2.33 
TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 
       19.33         5.06        16.60         9.86        24.23        40.54 
TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 
       21.30        30.05        14.04        11.51        24.76        10.39 
TCGA-27-2521 TCGA-27-2523 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1746 
       10.39        16.08         2.86        14.40        15.78         0.20 
TCGA-28-1747 TCGA-28-1749 TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 TCGA-28-1755 
        2.53         9.21         7.63         8.48         1.22         1.55 
TCGA-28-1756 TCGA-28-1757 TCGA-28-2506 TCGA-28-2513 TCGA-28-5207 TCGA-28-5208 
        2.83         0.13         6.74         7.30        11.28        17.88 
TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 
       14.53        11.77        31.27        23.44        11.01        13.64 
TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 
        5.16        22.68        12.76         5.42        15.39        21.07 
TCGA-32-1976 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 
        0.49         0.10        15.85        19.50         1.18         4.67 
TCGA-32-1986 TCGA-32-1987 TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 
       12.69        14.86        16.93        12.23        20.78        15.02 
TCGA-32-2615 TCGA-32-2616 TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 TCGA-32-4211 
       15.95         7.36         8.84        22.78        25.18        12.59 
TCGA-32-4213 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 
       19.86        19.23         0.85        13.35         8.94         9.53 
TCGA-41-3392 TCGA-41-3393 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9S 
        0.99         4.44         0.20        15.12        12.46         4.14 
TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 
       14.76         3.45        20.91         4.34        14.33         8.22 
TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-4935 
        4.80         4.54         3.09         3.65         9.17        10.78 
TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 
       16.70         3.29         2.70        11.38        17.06         8.35 
TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 
       20.98         4.83         5.03         0.23         9.27         7.73 
TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R TCGA-RR-A6KA 
        7.79         1.61        17.72        26.30         5.92         6.28 
TCGA-RR-A6KC 
       20.55 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             0.66              0.10 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           120.56            127.59 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            10.65             12.16 
[1] "0.7 - 120.6 (10.7)" "0.1 - 127.6 (12.2)"
[1] "hr=" "1"  
D56V2, continuous
D56V3, binary
                   cls
clus                  0   1
  8P LOSS MUTATED    28  30
  8P LOSS WILD-TYPE 196 316
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     28   30
  8P LOSS WILD-TYPE  196  316
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE              28               196
  MALE                30               316
[1] 2 2
[1] FALSE
D56V4, continuous
                   vv
clus                GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  8P LOSS MUTATED                               1                   1
  8P LOSS WILD-TYPE                            26                  17
                   vv
clus                UNTREATED PRIMARY (DE NOVO) GBM
  8P LOSS MUTATED                                56
  8P LOSS WILD-TYPE                             469
D56V5, multiclass
                                 clus
vv                                8P LOSS MUTATED 8P LOSS WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                 1                26
  TREATED PRIMARY GBM                           1                17
  UNTREATED PRIMARY (DE NOVO) GBM              56               469
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V6, binary
                   cls
clus                  0   1
  8P LOSS MUTATED    42  16
  8P LOSS WILD-TYPE 340 172
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     42   16
  8P LOSS WILD-TYPE  340  172
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  NO               42               340
  YES              16               172
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8P LOSS MUTATED       5                         2    46
  8P LOSS WILD-TYPE     8                        47   439
D56V7, multiclass
                           clus
vv                          8P LOSS MUTATED 8P LOSS WILD-TYPE
  ASIAN                                   5                 8
  BLACK OR AFRICAN AMERICAN               2                47
  WHITE                                  46               439
[1] 3 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
  8P LOSS MUTATED     0  48
  8P LOSS WILD-TYPE  12 424
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      0   48
  8P LOSS WILD-TYPE   12  424
                        clus
vv                       8P LOSS MUTATED 8P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                12
  NOT HISPANIC OR LATINO              48               424
[1] 2 2
[1] FALSE

Clustering(57) Variable = 8Q LOSS MUTATION ANALYSIS
D57V1, survival
                   sevent
clus2                 0   1
  8Q LOSS MUTATED     7  35
  8Q LOSS WILD-TYPE  97 430
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               42               527 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               35               430 
$`8Q LOSS MUTATED`
TCGA-02-0001 TCGA-02-0025 TCGA-02-0059 TCGA-02-0086 TCGA-02-0115 TCGA-02-0281 
       11.77        42.74         9.57         8.81        15.65         3.98 
TCGA-02-0324 TCGA-02-2486 TCGA-06-0159 TCGA-06-0171 TCGA-06-0195 TCGA-06-0216 
        7.73        20.32         9.44        13.12         7.40        24.16 
TCGA-06-0410 TCGA-06-0743 TCGA-06-5408 TCGA-06-5411 TCGA-06-5413 TCGA-08-0246 
        4.70        26.40        11.74         8.35         8.81         4.18 
TCGA-08-0392 TCGA-08-0510 TCGA-08-0525 TCGA-12-0776 TCGA-12-0826 TCGA-12-1598 
        0.72         4.27        15.98         9.73        27.78        15.65 
TCGA-14-0736 TCGA-14-1034 TCGA-14-1450 TCGA-14-1794 TCGA-14-1823 TCGA-16-0846 
       15.12        15.95        58.78         0.99        17.85         3.91 
TCGA-26-1439 TCGA-26-5136 TCGA-27-2524 TCGA-28-1750 TCGA-28-2502 TCGA-28-2509 
       13.87        18.97         7.59         8.35         0.66         4.77 
TCGA-28-2514 TCGA-32-4210 TCGA-32-4719 TCGA-41-3915 TCGA-74-6584 TCGA-76-4934 
        5.26         3.72        10.85        11.84         7.50         2.53 

$`8Q LOSS WILD-TYPE`
TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 TCGA-02-0011 
        4.73        18.35        23.18        10.59        35.41        20.71 
TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0024 
       82.59        20.61        87.06        77.65        20.12        53.10 
TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 
       24.59        12.16        90.58         2.83        14.14         3.62 
TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 TCGA-02-0048 
       10.72        10.52        18.31         6.87        14.73         3.22 
TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 TCGA-02-0055 TCGA-02-0057 TCGA-02-0058 
       15.09        12.59         6.54         2.50        19.86         8.35 
TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 TCGA-02-0069 TCGA-02-0070 TCGA-02-0071 
        6.02        19.73        26.43        28.70        25.05         5.49 
TCGA-02-0074 TCGA-02-0075 TCGA-02-0079 TCGA-02-0080 TCGA-02-0083 TCGA-02-0084 
       10.19        20.84        27.25        89.72        22.72        12.62 
TCGA-02-0085 TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 TCGA-02-0104 
       51.32        57.76        16.96         3.48        27.02        65.00 
TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 TCGA-02-0113 TCGA-02-0114 TCGA-02-0116 
       11.67        17.65        23.18        92.65        99.98        48.95 
TCGA-02-0258 TCGA-02-0260 TCGA-02-0266 TCGA-02-0269 TCGA-02-0271 TCGA-02-0285 
       16.54        16.93        17.72        10.75        14.47        13.87 
TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 TCGA-02-0325 TCGA-02-0326 
       14.20        15.95        12.23         9.90        10.62         7.33 
TCGA-02-0330 TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 
       15.91        25.71         4.37        25.12        10.59        12.39 
TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 
       14.50        10.55        47.11        11.34         9.27        16.21 
TCGA-02-0456 TCGA-02-2466 TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 TCGA-06-0119 
        3.35        16.80        12.92        15.32        15.45         2.70 
TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 
        6.15        20.38        47.61         6.94         3.98        22.72 
TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 
       33.67        12.95        25.35        14.30        26.70        24.23 
TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 
       11.90         0.20        10.29         2.20        11.74         2.33 
TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 
       20.09        17.79        10.09         8.61        19.46        46.59 
TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0160 
       12.33        13.94        10.45         3.19        10.82        11.80 
TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 
        3.42        56.91        10.65         5.85        19.66         3.29 
TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 
        4.47         3.22         4.04        91.00         4.18        88.14 
TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 
       20.25         3.65        69.90        73.84        27.22        44.58 
TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0197 TCGA-06-0201 
       15.42        10.42        38.96         4.67         5.56         0.39 
TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 
        7.66         8.42         7.63         7.40        11.84         0.53 
TCGA-06-0214 TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 
       15.02         0.72        19.82        13.64        13.32        20.42 
TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0412 
       48.69        10.82         9.01         0.26        72.36         9.57 
TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 
        3.16        35.11        12.62         5.75         5.75         9.80 
TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 
        2.10        23.57        14.20        46.88         7.86         2.70 
TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 
        2.70         0.92        43.46        46.19         5.65         7.17 
TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 
       40.41        16.57        20.78        26.76        23.93         6.84 
TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 
        4.04        26.79        11.84        15.32        13.61        33.90 
TCGA-06-1806 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 
       15.32         1.08        12.49         4.93        17.65        12.56 
TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 
       30.64         5.95        16.64         5.98         4.37         0.43 
TCGA-06-2570 TCGA-06-5410 TCGA-06-5412 TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 
       31.50         3.55         4.54         8.98         8.55         6.71 
TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 TCGA-06-6389 
        2.73         3.75         6.15         4.57         5.23         7.79 
TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 
        5.39         1.48       120.56         7.36         8.32        12.85 
TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A5U1 
        4.77         1.55         4.77         4.96         4.70         1.87 
TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK TCGA-06-A7TL TCGA-08-0244 TCGA-08-0245 
        3.12         2.56         5.39         5.42        22.68        37.84 
TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 
      115.86         1.74         8.42        25.71        12.16         9.80 
TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 
       29.23        65.33         1.28         8.42        17.95        24.56 
TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 
       31.10        37.58        22.29         3.39        12.23        14.93 
TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0509 TCGA-08-0512 TCGA-08-0514 
       18.02        15.35        13.97        12.56        42.15        11.08 
TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 
       19.59        58.68        19.33        10.75         4.80         7.27 
TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 
       18.41         7.56        15.35        14.73        12.99        34.92 
TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 
       10.45         7.59        94.78         0.10        38.17        25.97 
TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 
       26.66        12.13         3.65        20.38        28.41        15.06 
TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 
       53.85        43.23         7.63        14.93        14.86        91.76 
TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 TCGA-12-0827 TCGA-12-0828 
       24.79        18.48        10.62        23.51        38.76         8.94 
TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 TCGA-12-1092 
       20.58       127.59         5.82         7.59        33.21        21.73 
TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 
       15.98        12.23        15.85         9.11        14.53         3.98 
TCGA-12-1099 TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 
        4.14        25.68        14.73         6.77        59.77        44.02 
TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 
       26.93        15.22        10.95        12.69        34.92        14.53 
TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0740 TCGA-14-0781 TCGA-14-0783 
       14.93         3.22         2.04        11.97         0.95         6.21 
TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 TCGA-14-0812 TCGA-14-0813 
       23.05         2.24        11.24        13.78         3.25         1.35 
TCGA-14-0817 TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 TCGA-14-0867 TCGA-14-0871 
        5.39         2.89        16.50        26.33         2.04        28.93 
TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 
       19.30         0.79         1.38         1.12         3.75        32.05 
TCGA-14-1451 TCGA-14-1452 TCGA-14-1453 TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 
       23.11         7.10         1.15        30.18         0.92        40.96 
TCGA-14-1458 TCGA-14-1459 TCGA-14-1795 TCGA-14-1821 TCGA-14-1825 TCGA-14-1827 
        6.67        12.43         1.97        17.79         7.63         5.88 
TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-3477 TCGA-14-4157 TCGA-15-0742 
        7.17        17.49         7.96         3.78         3.42        13.78 
TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 TCGA-16-0848 TCGA-16-0849 
       50.53        19.10        53.19        13.28        17.59        26.07 
TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 
       16.37         4.31        29.03         4.57        10.29        14.01 
TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 
        9.14        21.24        13.97         6.41        11.77        21.90 
TCGA-19-0960 TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 
        8.61         0.66        14.27         3.39        10.75         9.07 
TCGA-19-1387 TCGA-19-1388 TCGA-19-1389 TCGA-19-1390 TCGA-19-1392 TCGA-19-1786 
        5.95        12.95         4.64        25.38         3.65         7.17 
TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 
       12.66         3.25         0.13         9.67         4.87         1.08 
TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 
        7.53         0.16         4.08        24.23         7.00         7.04 
TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 
        6.64        17.19         8.02        18.90         4.73        12.10 
TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I 
        1.78        22.49        14.07        16.80        14.96        17.79 
TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 
        3.98        28.54        10.03         9.73        31.33         7.13 
TCGA-26-1799 TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 TCGA-26-5139 
        9.37         9.40        14.86         5.49         8.88         1.58 
TCGA-26-6173 TCGA-26-6174 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 
        7.92         2.33        19.33         5.06        16.60         9.86 
TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 
       24.23        40.54        21.30        30.05        14.04        11.51 
TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 TCGA-27-2526 TCGA-27-2527 
       24.76        10.39        10.39        16.08         2.86        14.40 
TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 TCGA-28-1751 TCGA-28-1752 
       15.78         0.20         2.53         9.21         7.63         8.48 
TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 TCGA-28-2506 TCGA-28-2513 
        1.22         1.55         2.83         0.13         6.74         7.30 
TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 
       14.93        11.28        17.88        14.53        11.77        31.27 
TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 
       23.44        11.01        13.64         5.16        22.68        12.76 
TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 TCGA-32-1978 
        5.42        15.39        21.07         0.49         0.10        15.85 
TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 TCGA-32-1991 
       19.50         1.18         4.67        12.69        14.86        16.93 
TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 TCGA-32-2616 TCGA-32-2632 
       12.23        20.78        15.02        15.95         7.36         8.84 
TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4211 TCGA-32-4213 TCGA-32-5222 
       22.78        25.18        21.14        12.59        19.86        19.23 
TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 
        0.85        13.35         8.94         9.53         0.99         4.44 
TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 
        0.20        15.12        12.46         4.14        14.76         3.45 
TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-76-4925 TCGA-76-4926 
       20.91         4.34        14.33         8.22         4.80         4.54 
TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 
        3.09         3.65         9.17        10.78        16.70         3.29 
TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 
        2.70        11.38        17.06         8.35        20.98         4.83 
TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 
        5.03         0.23         9.27         7.73         7.79         1.61 
TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC 
       17.72        26.30         5.92         6.28        20.55 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             0.66              0.10 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            58.78            127.59 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            9.505            12.160 
[1] "0.7 - 58.8 (9.5)"   "0.1 - 127.6 (12.2)"
[1] "hr=" "1.4"
D57V2, continuous
D57V3, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    19  23
  8Q LOSS WILD-TYPE 205 323
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     19   23
  8Q LOSS WILD-TYPE  205  323
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE              19               205
  MALE                23               323
[1] 2 2
[1] FALSE
D57V4, continuous
                   vv
clus                GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  8Q LOSS MUTATED                               1                   1
  8Q LOSS WILD-TYPE                            26                  17
                   vv
clus                UNTREATED PRIMARY (DE NOVO) GBM
  8Q LOSS MUTATED                                40
  8Q LOSS WILD-TYPE                             485
D57V5, multiclass
                                 clus
vv                                8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                 1                26
  TREATED PRIMARY GBM                           1                17
  UNTREATED PRIMARY (DE NOVO) GBM              40               485
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V6, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    29  13
  8Q LOSS WILD-TYPE 353 175
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     29   13
  8Q LOSS WILD-TYPE  353  175
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  NO               29               353
  YES              13               175
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8Q LOSS MUTATED       2                         2    33
  8Q LOSS WILD-TYPE    11                        47   452
D57V7, multiclass
                           clus
vv                          8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  ASIAN                                   2                11
  BLACK OR AFRICAN AMERICAN               2                47
  WHITE                                  33               452
[1] 3 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
  8Q LOSS MUTATED     0  35
  8Q LOSS WILD-TYPE  12 437
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      0   35
  8Q LOSS WILD-TYPE   12  437
                        clus
vv                       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                12
  NOT HISPANIC OR LATINO              35               437
[1] 2 2
[1] FALSE

Clustering(58) Variable = 9P LOSS MUTATION ANALYSIS
D58V1, survival
                   sevent
clus2                 0   1
  9P LOSS MUTATED    34 163
  9P LOSS WILD-TYPE  70 302
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              197               372 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              163               302 
$`9P LOSS MUTATED`
TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0027 TCGA-02-0048 TCGA-02-0054 
       82.59        20.61        87.06        12.16         3.22         6.54 
TCGA-02-0057 TCGA-02-0058 TCGA-02-0064 TCGA-02-0086 TCGA-02-0099 TCGA-02-0104 
       19.86         8.35        19.73         8.81         3.48        65.00 
TCGA-02-0106 TCGA-02-0107 TCGA-02-0114 TCGA-02-0115 TCGA-02-0258 TCGA-02-0269 
       11.67        17.65        99.98        15.65        16.54        10.75 
TCGA-02-0285 TCGA-02-0290 TCGA-02-0330 TCGA-02-0333 TCGA-02-0339 TCGA-02-0432 
       13.87        15.95        15.91         4.37        12.39        47.11 
TCGA-02-2466 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0128 TCGA-06-0132 
       16.80         2.70         6.15        20.38        22.72        25.35 
TCGA-06-0141 TCGA-06-0145 TCGA-06-0150 TCGA-06-0154 TCGA-06-0158 TCGA-06-0162 
       10.29         2.33        19.46        13.94        10.82         3.42 
TCGA-06-0164 TCGA-06-0166 TCGA-06-0171 TCGA-06-0173 TCGA-06-0175 TCGA-06-0177 
       56.91         5.85        13.12         4.47         4.04         4.18 
TCGA-06-0185 TCGA-06-0188 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 
       73.84        44.58         8.42         7.63         7.40        11.84 
TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0394 TCGA-06-0409 TCGA-06-0412 
        0.72        19.82        13.64        10.82        72.36         9.57 
TCGA-06-0649 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0750 
        2.10        26.40        46.88         7.86         2.70         0.92 
TCGA-06-0875 TCGA-06-0876 TCGA-06-0879 TCGA-06-0882 TCGA-06-1084 TCGA-06-1086 
       43.46        46.19        40.41        20.78        23.93         6.84 
TCGA-06-1800 TCGA-06-1802 TCGA-06-1806 TCGA-06-2557 TCGA-06-2561 TCGA-06-2562 
       26.79        15.32        15.32         1.08        17.65        12.56 
TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-5412 TCGA-06-5415 TCGA-06-5418 
       16.64         5.98         4.37         4.54         8.55         2.73 
TCGA-06-5856 TCGA-06-5859 TCGA-06-6389 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 
        3.75         4.57         7.79       120.56         7.36         8.32 
TCGA-06-6697 TCGA-06-6699 TCGA-06-A5U0 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-08-0246 
       12.85         1.55         4.70         3.12         2.56         4.18 
TCGA-08-0348 TCGA-08-0353 TCGA-08-0355 TCGA-08-0358 TCGA-08-0375 TCGA-08-0390 
       12.16         8.42        24.56        22.29        12.23        13.97 
TCGA-08-0510 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0525 TCGA-12-0615 
        4.27        11.08        19.59        58.68        15.98        15.35 
TCGA-12-0654 TCGA-12-0656 TCGA-12-0670 TCGA-12-0707 TCGA-12-0778 TCGA-12-0818 
        7.59        94.78        25.97        28.41        14.93        91.76 
TCGA-12-0821 TCGA-12-0826 TCGA-12-0827 TCGA-12-1088 TCGA-12-1089 TCGA-12-1092 
       10.62        27.78        38.76       127.59         5.82        21.73 
TCGA-12-1093 TCGA-12-1095 TCGA-12-1097 TCGA-12-1599 TCGA-12-1602 TCGA-12-3651 
       15.98        15.85        14.53        25.68         6.77        12.69 
TCGA-12-3652 TCGA-12-3653 TCGA-14-0736 TCGA-14-0740 TCGA-14-0783 TCGA-14-0786 
       34.92        14.53        15.12        11.97         6.21        23.05 
TCGA-14-0787 TCGA-14-0813 TCGA-14-0862 TCGA-14-1037 TCGA-14-1395 TCGA-14-1396 
        2.24         1.35         2.89        19.30         1.38         1.12 
TCGA-14-1402 TCGA-14-1453 TCGA-14-1458 TCGA-15-1444 TCGA-15-1447 TCGA-16-0846 
       32.05         1.15         6.67        50.53        53.19         3.91 
TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1056 TCGA-16-1063 TCGA-19-0955 
        4.31        29.03         4.57        14.01        13.97        11.77 
TCGA-19-0960 TCGA-19-0963 TCGA-19-1388 TCGA-19-1786 TCGA-19-2619 TCGA-19-2620 
        8.61        14.27        12.95         7.17         9.67         4.87 
TCGA-19-2625 TCGA-19-2629 TCGA-19-5947 TCGA-19-5950 TCGA-19-5952 TCGA-19-5955 
        4.08        24.23         6.64        17.19        18.90         1.78 
TCGA-19-5958 TCGA-19-5959 TCGA-19-A6J4 TCGA-26-1439 TCGA-26-1442 TCGA-26-6174 
       14.07        16.80         3.98        13.87        31.33         2.33 
TCGA-27-1833 TCGA-27-2521 TCGA-27-2526 TCGA-28-1750 TCGA-28-1756 TCGA-28-1757 
       24.23        10.39         2.86         8.35         2.83         0.13 
TCGA-28-2502 TCGA-28-2506 TCGA-28-2513 TCGA-28-5208 TCGA-28-5209 TCGA-28-5213 
        0.66         6.74         7.30        17.88        14.53        31.27 
TCGA-28-5220 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-1991 TCGA-32-4208 
       12.76        15.39        21.07         0.49        16.93        21.14 
TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-41-2572 TCGA-41-2573 TCGA-41-3392 
       12.59        19.86        10.85        13.35         8.94         0.99 
TCGA-41-3393 TCGA-41-4097 TCGA-74-6575 TCGA-74-6584 TCGA-76-4928 TCGA-76-4931 
        4.44         0.20        20.91         7.50         3.09         9.17 
TCGA-76-4935 TCGA-76-6282 TCGA-76-6657 TCGA-76-6664 TCGA-OX-A56R 
       10.78        17.06         5.03         7.79         5.92 

$`9P LOSS WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 
       11.77         4.73        18.35        23.18        10.59        35.41 
TCGA-02-0011 TCGA-02-0021 TCGA-02-0023 TCGA-02-0024 TCGA-02-0025 TCGA-02-0026 
       20.71        77.65        20.12        53.10        42.74        24.59 
TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 
       90.58         2.83        14.14         3.62        10.72        10.52 
TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 TCGA-02-0051 TCGA-02-0052 TCGA-02-0055 
       18.31         6.87        14.73        15.09        12.59         2.50 
TCGA-02-0059 TCGA-02-0060 TCGA-02-0068 TCGA-02-0069 TCGA-02-0070 TCGA-02-0071 
        9.57         6.02        26.43        28.70        25.05         5.49 
TCGA-02-0074 TCGA-02-0075 TCGA-02-0079 TCGA-02-0080 TCGA-02-0083 TCGA-02-0084 
       10.19        20.84        27.25        89.72        22.72        12.62 
TCGA-02-0085 TCGA-02-0087 TCGA-02-0089 TCGA-02-0102 TCGA-02-0111 TCGA-02-0113 
       51.32        57.76        16.96        27.02        23.18        92.65 
TCGA-02-0116 TCGA-02-0260 TCGA-02-0266 TCGA-02-0271 TCGA-02-0281 TCGA-02-0289 
       48.95        16.93        17.72        14.47         3.98        14.20 
TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 TCGA-02-0332 
       12.23         9.90         7.73        10.62         7.33        25.71 
TCGA-02-0337 TCGA-02-0338 TCGA-02-0422 TCGA-02-0430 TCGA-02-0440 TCGA-02-0446 
       25.12        10.59        14.50        10.55        11.34         9.27 
TCGA-02-0451 TCGA-02-0456 TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 
       16.21         3.35        12.92        15.32        15.45        20.32 
TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0129 TCGA-06-0130 TCGA-06-0133 
       47.61         6.94         3.98        33.67        12.95        14.30 
TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0142 TCGA-06-0143 
       26.70        24.23        11.90         0.20         2.20        11.74 
TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0151 TCGA-06-0152 
       20.09        17.79        10.09         8.61        46.59        12.33 
TCGA-06-0155 TCGA-06-0157 TCGA-06-0159 TCGA-06-0160 TCGA-06-0165 TCGA-06-0168 
       10.45         3.19         9.44        11.80        10.65        19.66 
TCGA-06-0169 TCGA-06-0174 TCGA-06-0176 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 
        3.29         3.22        91.00        88.14        20.25         3.65 
TCGA-06-0184 TCGA-06-0187 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 
       69.90        27.22        15.42        10.42        38.96         4.67 
TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0213 TCGA-06-0214 
        7.40         5.56         0.39         7.66         0.53        15.02 
TCGA-06-0216 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0397 TCGA-06-0402 
       24.16        13.32        20.42        48.69         9.01         0.26 
TCGA-06-0410 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 
        4.70         3.16        35.11        12.62         5.75         5.75 
TCGA-06-0648 TCGA-06-0650 TCGA-06-0686 TCGA-06-0749 TCGA-06-0877 TCGA-06-0878 
        9.80        23.57        14.20         2.70         5.65         7.17 
TCGA-06-0881 TCGA-06-0939 TCGA-06-1087 TCGA-06-1801 TCGA-06-1804 TCGA-06-1805 
       16.57        26.76         4.04        11.84        13.61        33.90 
TCGA-06-2558 TCGA-06-2559 TCGA-06-2563 TCGA-06-2564 TCGA-06-2569 TCGA-06-2570 
       12.49         4.93        30.64         5.95         0.43        31.50 
TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5413 TCGA-06-5414 TCGA-06-5416 
       11.74         3.55         8.35         8.81         8.98         6.71 
TCGA-06-5858 TCGA-06-6388 TCGA-06-6390 TCGA-06-6391 TCGA-06-6698 TCGA-06-6700 
        6.15         5.23         5.39         1.48         4.77         4.77 
TCGA-06-6701 TCGA-06-A5U1 TCGA-06-A7TK TCGA-06-A7TL TCGA-08-0244 TCGA-08-0245 
        4.96         1.87         5.39         5.42        22.68        37.84 
TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0349 TCGA-08-0350 
      115.86         1.74         8.42        25.71         9.80        29.23 
TCGA-08-0351 TCGA-08-0352 TCGA-08-0354 TCGA-08-0356 TCGA-08-0357 TCGA-08-0359 
       65.33         1.28        17.95        31.10        37.58         3.39 
TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0392 TCGA-08-0509 TCGA-08-0512 
       14.93        18.02        15.35         0.72        12.56        42.15 
TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0529 TCGA-08-0531 
       19.33        10.75         4.80         7.27        18.41         7.56 
TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0657 TCGA-12-0662 
       14.73        12.99        34.92        10.45         0.10        38.17 
TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0769 TCGA-12-0772 
       26.66        12.13         3.65        20.38        15.06        53.85 
TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0780 TCGA-12-0819 TCGA-12-0820 
       43.23         7.63         9.73        14.86        24.79        18.48 
TCGA-12-0822 TCGA-12-0828 TCGA-12-0829 TCGA-12-1090 TCGA-12-1091 TCGA-12-1094 
       23.51         8.94        20.58         7.59        33.21        12.23 
TCGA-12-1096 TCGA-12-1098 TCGA-12-1099 TCGA-12-1598 TCGA-12-1600 TCGA-12-3644 
        9.11         3.98         4.14        15.65        14.73        59.77 
TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-5295 TCGA-12-5299 
       44.02        26.93        15.22        10.95        14.93         3.22 
TCGA-12-5301 TCGA-14-0781 TCGA-14-0789 TCGA-14-0790 TCGA-14-0812 TCGA-14-0817 
        2.04         0.95        11.24        13.78         3.25         5.39 
TCGA-14-0865 TCGA-14-0866 TCGA-14-0867 TCGA-14-0871 TCGA-14-1034 TCGA-14-1043 
       16.50        26.33         2.04        28.93        15.95         0.79 
TCGA-14-1401 TCGA-14-1450 TCGA-14-1451 TCGA-14-1452 TCGA-14-1454 TCGA-14-1455 
        3.75        58.78        23.11         7.10        30.18         0.92 
TCGA-14-1456 TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 TCGA-14-1823 
       40.96        12.43         0.99         1.97        17.79        17.85 
TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-3477 
        7.63         5.88         7.17        17.49         7.96         3.78 
TCGA-14-4157 TCGA-15-0742 TCGA-15-1446 TCGA-15-1449 TCGA-16-0848 TCGA-16-0849 
        3.42        13.78        19.10        13.28        17.59        26.07 
TCGA-16-0850 TCGA-16-1055 TCGA-16-1060 TCGA-16-1062 TCGA-16-1460 TCGA-19-0957 
       16.37        10.29         9.14        21.24         6.41        21.90 
TCGA-19-0962 TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 TCGA-19-1389 
        0.66         3.39        10.75         9.07         5.95         4.64 
TCGA-19-1390 TCGA-19-1392 TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 TCGA-19-2621 
       25.38         3.65        12.66         3.25         0.13         1.08 
TCGA-19-2623 TCGA-19-2624 TCGA-19-2631 TCGA-19-4065 TCGA-19-5951 TCGA-19-5953 
        7.53         0.16         7.00         7.04         8.02         4.73 
TCGA-19-5954 TCGA-19-5956 TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J5 TCGA-26-1438 
       12.10        22.49        14.96        17.79        28.54        10.03 
TCGA-26-1440 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 
        9.73         7.13         9.37         9.40        14.86         5.49 
TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 TCGA-26-A7UX TCGA-27-1830 
        8.88        18.97         1.58         7.92        19.33         5.06 
TCGA-27-1831 TCGA-27-1832 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 
       16.60         9.86        40.54        21.30        30.05        14.04 
TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2523 TCGA-27-2524 TCGA-27-2527 
       11.51        24.76        10.39        16.08         7.59        14.40 
TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 TCGA-28-1751 TCGA-28-1752 
       15.78         0.20         2.53         9.21         7.63         8.48 
TCGA-28-1753 TCGA-28-1755 TCGA-28-2509 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 
        1.22         1.55         4.77         5.26        14.93        11.28 
TCGA-28-5211 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 
       11.77        23.44        11.01        13.64         5.16        22.68 
TCGA-28-6450 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 
        5.42         0.10        15.85        19.50         1.18         4.67 
TCGA-32-1986 TCGA-32-1987 TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 
       12.69        14.86        12.23        20.78        15.02        15.95 
TCGA-32-2616 TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 TCGA-32-4210 TCGA-32-5222 
        7.36         8.84        22.78        25.18         3.72        19.23 
TCGA-41-2571 TCGA-41-2575 TCGA-41-3915 TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9S 
        0.85         9.53        11.84        15.12        12.46         4.14 
TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-76-4925 
       14.76         3.45         4.34        14.33         8.22         4.80 
TCGA-76-4926 TCGA-76-4929 TCGA-76-4934 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 
        4.54         3.65         2.53        16.70         3.29         2.70 
TCGA-76-6280 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6661 TCGA-76-6662 
       11.38         8.35        20.98         4.83         0.23         9.27 
TCGA-76-6663 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-RR-A6KA TCGA-RR-A6KC 
        7.73         1.61        17.72        26.30         6.28        20.55 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             0.13              0.10 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           127.59            115.86 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            12.23             11.77 
[1] "0.1 - 127.6 (12.2)" "0.1 - 115.9 (11.8)"
[1] "hr=" "1.1"
D58V2, continuous
D58V3, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    80 118
  9P LOSS WILD-TYPE 144 228
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     80  118
  9P LOSS WILD-TYPE  144  228
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE              80               144
  MALE               118               228
[1] 2 2
[1] FALSE
D58V4, continuous
                   vv
clus                GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  9P LOSS MUTATED                              10                   6
  9P LOSS WILD-TYPE                            17                  12
                   vv
clus                UNTREATED PRIMARY (DE NOVO) GBM
  9P LOSS MUTATED                               182
  9P LOSS WILD-TYPE                             343
D58V5, multiclass
                                 clus
vv                                9P LOSS MUTATED 9P LOSS WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                10                17
  TREATED PRIMARY GBM                           6                12
  UNTREATED PRIMARY (DE NOVO) GBM             182               343
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V6, binary
                   cls
clus                  0   1
  9P LOSS MUTATED   136  62
  9P LOSS WILD-TYPE 246 126
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED    136   62
  9P LOSS WILD-TYPE  246  126
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  NO              136               246
  YES              62               126
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9P LOSS MUTATED       6                        19   167
  9P LOSS WILD-TYPE     7                        30   318
D58V7, multiclass
                           clus
vv                          9P LOSS MUTATED 9P LOSS WILD-TYPE
  ASIAN                                   6                 7
  BLACK OR AFRICAN AMERICAN              19                30
  WHITE                                 167               318
[1] 3 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
  9P LOSS MUTATED     1 170
  9P LOSS WILD-TYPE  11 302
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      1  170
  9P LOSS WILD-TYPE   11  302
                        clus
vv                       9P LOSS MUTATED 9P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                11
  NOT HISPANIC OR LATINO             170               302
[1] 2 2
[1] FALSE

Clustering(59) Variable = 9Q LOSS MUTATION ANALYSIS
D59V1, survival
                   sevent
clus2                 0   1
  9Q LOSS MUTATED    13  79
  9Q LOSS WILD-TYPE  91 386
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               92               477 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               79               386 
$`9Q LOSS MUTATED`
TCGA-02-0016 TCGA-02-0021 TCGA-02-0057 TCGA-02-0064 TCGA-02-0086 TCGA-02-0104 
       87.06        77.65        19.86        19.73         8.81        65.00 
TCGA-02-0107 TCGA-02-0114 TCGA-02-0269 TCGA-02-0285 TCGA-02-0330 TCGA-02-2466 
       17.65        99.98        10.75        13.87        15.91        16.80 
TCGA-02-2470 TCGA-06-0128 TCGA-06-0132 TCGA-06-0141 TCGA-06-0154 TCGA-06-0158 
       12.92        22.72        25.35        10.29        13.94        10.82 
TCGA-06-0162 TCGA-06-0173 TCGA-06-0177 TCGA-06-0188 TCGA-06-0208 TCGA-06-0209 
        3.42         4.47         4.18        44.58         8.42         7.63 
TCGA-06-0210 TCGA-06-0237 TCGA-06-0409 TCGA-06-0412 TCGA-06-0743 TCGA-06-0745 
        7.40        13.64        72.36         9.57        26.40         7.86 
TCGA-06-0876 TCGA-06-1086 TCGA-06-1802 TCGA-06-1806 TCGA-06-2557 TCGA-06-2561 
       46.19         6.84        15.32        15.32         1.08        17.65 
TCGA-06-5412 TCGA-06-5418 TCGA-06-5859 TCGA-06-6694 TCGA-06-A6S1 TCGA-08-0246 
        4.54         2.73         4.57         7.36         2.56         4.18 
TCGA-08-0355 TCGA-08-0358 TCGA-08-0375 TCGA-08-0510 TCGA-08-0516 TCGA-08-0517 
       24.56        22.29        12.23         4.27        19.59        58.68 
TCGA-12-0615 TCGA-12-0707 TCGA-12-0821 TCGA-12-0826 TCGA-12-1089 TCGA-12-1091 
       15.35        28.41        10.62        27.78         5.82        33.21 
TCGA-12-1093 TCGA-12-1602 TCGA-12-3652 TCGA-12-3653 TCGA-14-0736 TCGA-14-0740 
       15.98         6.77        34.92        14.53        15.12        11.97 
TCGA-14-1395 TCGA-14-1396 TCGA-14-1453 TCGA-15-1444 TCGA-15-1447 TCGA-16-0846 
        1.38         1.12         1.15        50.53        53.19         3.91 
TCGA-16-1045 TCGA-16-1047 TCGA-19-0963 TCGA-19-1388 TCGA-19-1786 TCGA-19-2619 
       29.03         4.57        14.27        12.95         7.17         9.67 
TCGA-19-2620 TCGA-19-5950 TCGA-19-5958 TCGA-19-A6J4 TCGA-26-1439 TCGA-27-2521 
        4.87        17.19        14.07         3.98        13.87        10.39 
TCGA-28-1750 TCGA-28-1757 TCGA-28-2506 TCGA-28-2513 TCGA-28-5220 TCGA-32-1970 
        8.35         0.13         6.74         7.30        12.76        15.39 
TCGA-32-4208 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-41-2572 TCGA-74-6584 
       21.14        12.59        19.86        10.85        13.35         7.50 
TCGA-76-6282 TCGA-OX-A56R 
       17.06         5.92 

$`9Q LOSS WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 
       11.77         4.73        18.35        23.18        10.59        35.41 
TCGA-02-0011 TCGA-02-0014 TCGA-02-0015 TCGA-02-0023 TCGA-02-0024 TCGA-02-0025 
       20.71        82.59        20.61        20.12        53.10        42.74 
TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 
       24.59        12.16        90.58         2.83        14.14         3.62 
TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 TCGA-02-0048 
       10.72        10.52        18.31         6.87        14.73         3.22 
TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 TCGA-02-0055 TCGA-02-0058 TCGA-02-0059 
       15.09        12.59         6.54         2.50         8.35         9.57 
TCGA-02-0060 TCGA-02-0068 TCGA-02-0069 TCGA-02-0070 TCGA-02-0071 TCGA-02-0074 
        6.02        26.43        28.70        25.05         5.49        10.19 
TCGA-02-0075 TCGA-02-0079 TCGA-02-0080 TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 
       20.84        27.25        89.72        22.72        12.62        51.32 
TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 TCGA-02-0106 TCGA-02-0111 
       57.76        16.96         3.48        27.02        11.67        23.18 
TCGA-02-0113 TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 TCGA-02-0266 
       92.65        15.65        48.95        16.54        16.93        17.72 
TCGA-02-0271 TCGA-02-0281 TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 
       14.47         3.98        14.20        15.95        12.23         9.90 
TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 
        7.73        10.62         7.33        25.71         4.37        25.12 
TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 
       10.59        12.39        14.50        10.55        47.11        11.34 
TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 
        9.27        16.21         3.35        15.32        15.45        20.32 
TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 
        2.70         6.15        20.38        47.61         6.94         3.98 
TCGA-06-0129 TCGA-06-0130 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 
       33.67        12.95        14.30        26.70        24.23        11.90 
TCGA-06-0140 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 
        0.20         2.20        11.74         2.33        20.09        17.79 
TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0155 
       10.09         8.61        19.46        46.59        12.33        10.45 
TCGA-06-0157 TCGA-06-0159 TCGA-06-0160 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 
        3.19         9.44        11.80        56.91        10.65         5.85 
TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 
       19.66         3.29        13.12         3.22         4.04        91.00 
TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 
       88.14        20.25         3.65        69.90        73.84        27.22 
TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 
       15.42        10.42        38.96         4.67         7.40         5.56 
TCGA-06-0201 TCGA-06-0206 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 
        0.39         7.66        11.84         0.53        15.02        24.16 
TCGA-06-0219 TCGA-06-0221 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 
        0.72        19.82        13.32        20.42        48.69        10.82 
TCGA-06-0397 TCGA-06-0402 TCGA-06-0410 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 
        9.01         0.26         4.70         3.16        35.11        12.62 
TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 
        5.75         5.75         9.80         2.10        23.57        14.20 
TCGA-06-0744 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0877 
       46.88         2.70         2.70         0.92        43.46         5.65 
TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 
        7.17        40.41        16.57        20.78        26.76        23.93 
TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1804 TCGA-06-1805 TCGA-06-2558 
        4.04        26.79        11.84        13.61        33.90        12.49 
TCGA-06-2559 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 
        4.93        12.56        30.64         5.95        16.64         5.98 
TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 
        4.37         0.43        31.50        11.74         3.55         8.35 
TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 TCGA-06-5856 TCGA-06-5858 
        8.81         8.98         8.55         6.71         3.75         6.15 
TCGA-06-6388 TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6695 
        5.23         7.79         5.39         1.48       120.56         8.32 
TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 
       12.85         4.77         1.55         4.77         4.96         4.70 
TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A7TK TCGA-06-A7TL TCGA-08-0244 TCGA-08-0245 
        1.87         3.12         5.39         5.42        22.68        37.84 
TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 
      115.86         1.74         8.42        25.71        12.16         9.80 
TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0356 
       29.23        65.33         1.28         8.42        17.95        31.10 
TCGA-08-0357 TCGA-08-0359 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 
       37.58         3.39        14.93        18.02        15.35        13.97 
TCGA-08-0392 TCGA-08-0509 TCGA-08-0512 TCGA-08-0514 TCGA-08-0518 TCGA-08-0520 
        0.72        12.56        42.15        11.08        19.33        10.75 
TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0616 
        4.80         7.27        15.98        18.41         7.56        14.73 
TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 
       12.99        34.92        10.45         7.59        94.78         0.10 
TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 
       38.17        25.97        26.66        12.13         3.65        20.38 
TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 
       15.06        53.85        43.23         7.63         9.73        14.93 
TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0822 TCGA-12-0827 
       14.86        91.76        24.79        18.48        23.51        38.76 
TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1090 TCGA-12-1092 TCGA-12-1094 
        8.94        20.58       127.59         7.59        21.73        12.23 
TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 TCGA-12-1598 
       15.85         9.11        14.53         3.98         4.14        15.65 
TCGA-12-1599 TCGA-12-1600 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 
       25.68        14.73        59.77        44.02        26.93        15.22 
TCGA-12-3650 TCGA-12-3651 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0781 
       10.95        12.69        14.93         3.22         2.04         0.95 
TCGA-14-0783 TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 TCGA-14-0812 
        6.21        23.05         2.24        11.24        13.78         3.25 
TCGA-14-0813 TCGA-14-0817 TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 TCGA-14-0867 
        1.35         5.39         2.89        16.50        26.33         2.04 
TCGA-14-0871 TCGA-14-1034 TCGA-14-1037 TCGA-14-1043 TCGA-14-1401 TCGA-14-1402 
       28.93        15.95        19.30         0.79         3.75        32.05 
TCGA-14-1450 TCGA-14-1451 TCGA-14-1452 TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 
       58.78        23.11         7.10        30.18         0.92        40.96 
TCGA-14-1458 TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 TCGA-14-1823 
        6.67        12.43         0.99         1.97        17.79        17.85 
TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-3477 
        7.63         5.88         7.17        17.49         7.96         3.78 
TCGA-14-4157 TCGA-15-0742 TCGA-15-1446 TCGA-15-1449 TCGA-16-0848 TCGA-16-0849 
        3.42        13.78        19.10        13.28        17.59        26.07 
TCGA-16-0850 TCGA-16-0861 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 
       16.37         4.31        10.29        14.01         9.14        21.24 
TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 TCGA-19-0962 
       13.97         6.41        11.77        21.90         8.61         0.66 
TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 TCGA-19-1389 TCGA-19-1390 
        3.39        10.75         9.07         5.95         4.64        25.38 
TCGA-19-1392 TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 TCGA-19-2621 TCGA-19-2623 
        3.65        12.66         3.25         0.13         1.08         7.53 
TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 
        0.16         4.08        24.23         7.00         7.04         6.64 
TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 
        8.02        18.90         4.73        12.10         1.78        22.49 
TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1440 
       16.80        14.96        17.79        28.54        10.03         9.73 
TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 
       31.33         7.13         9.37         9.40        14.86         5.49 
TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-26-A7UX 
        8.88        18.97         1.58         7.92         2.33        19.33 
TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 
        5.06        16.60         9.86        24.23        40.54        21.30 
TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2523 
       30.05        14.04        11.51        24.76        10.39        16.08 
TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 
        7.59         2.86        14.40        15.78         0.20         2.53 
TCGA-28-1749 TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 
        9.21         7.63         8.48         1.22         1.55         2.83 
TCGA-28-2502 TCGA-28-2509 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 
        0.66         4.77         5.26        14.93        11.28        17.88 
TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 
       14.53        11.77        31.27        23.44        11.01        13.64 
TCGA-28-5218 TCGA-28-5219 TCGA-28-6450 TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 
        5.16        22.68         5.42        21.07         0.49         0.10 
TCGA-32-1978 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 
       15.85        19.50         1.18         4.67        12.69        14.86 
TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 TCGA-32-2616 
       16.93        12.23        20.78        15.02        15.95         7.36 
TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 TCGA-32-4210 TCGA-32-5222 TCGA-41-2571 
        8.84        22.78        25.18         3.72        19.23         0.85 
TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 
        8.94         9.53         0.99         4.44        11.84         0.20 
TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 
       15.12        12.46         4.14        14.76         3.45        20.91 
TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 
        4.34        14.33         8.22         4.80         4.54         3.09 
TCGA-76-4929 TCGA-76-4931 TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 
        3.65         9.17         2.53        10.78        16.70         3.29 
TCGA-76-6193 TCGA-76-6280 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 
        2.70        11.38         8.35        20.98         4.83         5.03 
TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 
        0.23         9.27         7.73         7.79         1.61        17.72 
TCGA-87-5896 TCGA-RR-A6KA TCGA-RR-A6KC 
       26.30         6.28        20.55 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             0.13              0.10 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            99.98            127.59 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           12.935            11.770 
[1] "0.1 - 100.0 (12.9)" "0.1 - 127.6 (11.8)"
[1] "hr=" "1"  
D59V2, continuous
D59V3, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    40  53
  9Q LOSS WILD-TYPE 184 293
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     40   53
  9Q LOSS WILD-TYPE  184  293
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE              40               184
  MALE                53               293
[1] 2 2
[1] FALSE
D59V4, continuous
                   vv
clus                GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  9Q LOSS MUTATED                               6                   5
  9Q LOSS WILD-TYPE                            21                  13
                   vv
clus                UNTREATED PRIMARY (DE NOVO) GBM
  9Q LOSS MUTATED                                82
  9Q LOSS WILD-TYPE                             443
D59V5, multiclass
                                 clus
vv                                9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                 6                21
  TREATED PRIMARY GBM                           5                13
  UNTREATED PRIMARY (DE NOVO) GBM              82               443
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V6, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    64  29
  9Q LOSS WILD-TYPE 318 159
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     64   29
  9Q LOSS WILD-TYPE  318  159
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  NO               64               318
  YES              29               159
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9Q LOSS MUTATED       1                        12    77
  9Q LOSS WILD-TYPE    12                        37   408
D59V7, multiclass
                           clus
vv                          9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  ASIAN                                   1                12
  BLACK OR AFRICAN AMERICAN              12                37
  WHITE                                  77               408
[1] 3 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
  9Q LOSS MUTATED     0  83
  9Q LOSS WILD-TYPE  12 389
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      0   83
  9Q LOSS WILD-TYPE   12  389
                        clus
vv                       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                12
  NOT HISPANIC OR LATINO              83               389
[1] 2 2
[1] FALSE

Clustering(60) Variable = 10P LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                  0   1
  10P LOSS MUTATED    81 394
  10P LOSS WILD-TYPE  23  71
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               475                 94 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               394                 71 
$`10P LOSS MUTATED`
TCGA-02-0003 TCGA-02-0006 TCGA-02-0009 TCGA-02-0014 TCGA-02-0016 TCGA-02-0021 
        4.73        18.35        10.59        82.59        87.06        77.65 
TCGA-02-0023 TCGA-02-0027 TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 
       20.12        12.16         2.83        14.14         3.62        10.72 
TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0048 TCGA-02-0051 TCGA-02-0052 
       10.52        18.31         6.87         3.22        15.09        12.59 
TCGA-02-0054 TCGA-02-0055 TCGA-02-0057 TCGA-02-0059 TCGA-02-0064 TCGA-02-0068 
        6.54         2.50        19.86         9.57        19.73        26.43 
TCGA-02-0070 TCGA-02-0071 TCGA-02-0074 TCGA-02-0075 TCGA-02-0079 TCGA-02-0084 
       25.05         5.49        10.19        20.84        27.25        12.62 
TCGA-02-0085 TCGA-02-0086 TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 TCGA-02-0106 
       51.32         8.81        16.96         3.48        27.02        11.67 
TCGA-02-0107 TCGA-02-0113 TCGA-02-0115 TCGA-02-0116 TCGA-02-0260 TCGA-02-0269 
       17.65        92.65        15.65        48.95        16.93        10.75 
TCGA-02-0281 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 
        3.98        13.87        14.20        15.95        12.23         9.90 
TCGA-02-0324 TCGA-02-0325 TCGA-02-0330 TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 
        7.73        10.62        15.91        25.71         4.37        25.12 
TCGA-02-0422 TCGA-02-0430 TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 
       14.50        10.55        11.34         9.27        16.21         3.35 
TCGA-02-2466 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 
       16.80        15.32        15.45        20.32         2.70         6.15 
TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0130 
       20.38        47.61         6.94         3.98        22.72        12.95 
TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 
       25.35        14.30        26.70        24.23        11.90         0.20 
TCGA-06-0141 TCGA-06-0143 TCGA-06-0145 TCGA-06-0147 TCGA-06-0149 TCGA-06-0150 
       10.29        11.74         2.33        17.79         8.61        19.46 
TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 
       46.59        12.33        13.94        10.45         3.19        10.82 
TCGA-06-0159 TCGA-06-0162 TCGA-06-0164 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 
        9.44         3.42        56.91         5.85        19.66         3.29 
TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0177 TCGA-06-0179 
       13.12         4.47         3.22         4.04         4.18        20.25 
TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 
        3.65        69.90        73.84        27.22        44.58        15.42 
TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 
       10.42        38.96         4.67         7.40         5.56         0.39 
TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0214 
        7.66         8.42         7.63         7.40        11.84        15.02 
TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 TCGA-06-0241 
       24.16         0.72        19.82        13.64        13.32        48.69 
TCGA-06-0394 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 TCGA-06-0414 
       10.82         0.26        72.36         4.70         9.57        35.11 
TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 
       12.62         5.75         5.75         9.80         2.10        23.57 
TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 
       14.20        26.40        46.88         7.86         2.70         2.70 
TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 TCGA-06-0879 
        0.92        43.46        46.19         5.65         7.17        40.41 
TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1087 TCGA-06-1800 
       16.57        20.78        26.76        23.93         4.04        26.79 
TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-2557 TCGA-06-2558 
       11.84        15.32        13.61        33.90         1.08        12.49 
TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 
       17.65        12.56        30.64         5.95        16.64         5.98 
TCGA-06-2567 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 
        4.37        11.74         3.55         8.35         4.54         8.81 
TCGA-06-5414 TCGA-06-5415 TCGA-06-5418 TCGA-06-5856 TCGA-06-5859 TCGA-06-6388 
        8.98         8.55         2.73         3.75         4.57         5.23 
TCGA-06-6390 TCGA-06-6693 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 
        5.39       120.56         8.32        12.85         4.77         1.55 
TCGA-06-6700 TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK 
        4.77         4.70         1.87         3.12         2.56         5.39 
TCGA-08-0244 TCGA-08-0245 TCGA-08-0246 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 
       22.68        37.84         4.18         1.74         8.42        25.71 
TCGA-08-0348 TCGA-08-0349 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 
       12.16         9.80         1.28         8.42        17.95        24.56 
TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 
       31.10        37.58        22.29         3.39        12.23        14.93 
TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 
       18.02        15.35        13.97         0.72        12.56         4.27 
TCGA-08-0512 TCGA-08-0514 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0529 
       42.15        11.08        19.33        10.75         4.80        18.41 
TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 
       15.35        14.73        12.99        34.92        10.45         7.59 
TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 
       94.78         0.10        38.17        25.97        26.66        12.13 
TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0775 
        3.65        20.38        28.41        15.06        53.85         7.63 
TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 
        9.73        14.93        14.86        24.79        18.48        10.62 
TCGA-12-0822 TCGA-12-0826 TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 
       23.51        27.78        38.76         8.94        20.58       127.59 
TCGA-12-1091 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 
       33.21        15.98        12.23        15.85         9.11        14.53 
TCGA-12-1098 TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 
        3.98        15.65        25.68        14.73         6.77        59.77 
TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 
       44.02        26.93        15.22        10.95        12.69        34.92 
TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 
       14.53        14.93         3.22         2.04        15.12        11.97 
TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 
        0.95         6.21        23.05         2.24        11.24        13.78 
TCGA-14-0812 TCGA-14-0813 TCGA-14-0817 TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 
        3.25         1.35         5.39         2.89        16.50        26.33 
TCGA-14-0867 TCGA-14-0871 TCGA-14-1034 TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 
        2.04        28.93        15.95        19.30         0.79         1.38 
TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 TCGA-14-1452 TCGA-14-1453 
        3.75        32.05        58.78        23.11         7.10         1.15 
TCGA-14-1454 TCGA-14-1455 TCGA-14-1794 TCGA-14-1795 TCGA-14-1823 TCGA-14-1825 
       30.18         0.92         0.99         1.97        17.85         7.63 
TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-15-0742 TCGA-15-1444 
        5.88         7.17        17.49         7.96        13.78        50.53 
TCGA-15-1446 TCGA-15-1449 TCGA-16-0848 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 
       19.10        13.28        17.59        29.03         4.57        10.29 
TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-19-0955 TCGA-19-0957 
       14.01         9.14        21.24        13.97        11.77        21.90 
TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 
        0.66        14.27         3.39        10.75         9.07         5.95 
TCGA-19-1388 TCGA-19-1389 TCGA-19-1392 TCGA-19-1786 TCGA-19-1789 TCGA-19-1791 
       12.95         4.64         3.65         7.17         3.25         0.13 
TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 
        9.67         4.87         1.08         7.53         0.16         4.08 
TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 
       24.23         7.00         7.04         6.64        17.19         8.02 
TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5959 
       18.90         4.73        12.10         1.78        22.49        16.80 
TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 
       14.96        17.79         3.98        28.54        10.03        13.87 
TCGA-26-1440 TCGA-26-1799 TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 
        9.73         9.37         9.40        14.86         5.49         8.88 
TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-26-A7UX TCGA-27-1830 
       18.97         1.58         7.92         2.33        19.33         5.06 
TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 
       16.60         9.86        24.23        40.54        21.30        30.05 
TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 
       14.04        11.51        24.76        10.39        10.39        16.08 
TCGA-27-2524 TCGA-27-2527 TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 
        7.59        14.40        15.78         0.20         2.53         9.21 
TCGA-28-1750 TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 TCGA-28-1757 TCGA-28-2502 
        8.35         7.63         8.48         1.22         0.13         0.66 
TCGA-28-2506 TCGA-28-2509 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 
        6.74         4.77         7.30         5.26        14.93        11.28 
TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 
       17.88        14.53        11.77        31.27        23.44        11.01 
TCGA-28-5216 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1976 
       13.64        22.68        12.76         5.42        15.39         0.49 
TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 
        0.10        15.85        19.50         1.18         4.67        12.69 
TCGA-32-1987 TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 TCGA-32-2634 
       14.86        12.23        20.78        15.02        15.95        22.78 
TCGA-32-2638 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 
       25.18         3.72        12.59        19.86        10.85        19.23 
TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 
        0.85        13.35         8.94         9.53         0.99         4.44 
TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9S TCGA-4W-AA9T 
       11.84         0.20        15.12        12.46         4.14        14.76 
TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 
        3.45        20.91         4.34        14.33         8.22         7.50 
TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-4934 
        4.80         4.54         3.09         3.65         9.17         2.53 
TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 
       10.78        16.70         3.29         2.70        11.38        17.06 
TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 
        8.35        20.98         4.83         5.03         0.23         9.27 
TCGA-76-6663 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R TCGA-RR-A6KA 
        7.73         1.61        17.72        26.30         5.92         6.28 
TCGA-RR-A6KC 
       20.55 

$`10P LOSS WILD-TYPE`
TCGA-02-0001 TCGA-02-0007 TCGA-02-0010 TCGA-02-0011 TCGA-02-0015 TCGA-02-0024 
       11.77        23.18        35.41        20.71        20.61        53.10 
TCGA-02-0025 TCGA-02-0026 TCGA-02-0028 TCGA-02-0047 TCGA-02-0058 TCGA-02-0060 
       42.74        24.59        90.58        14.73         8.35         6.02 
TCGA-02-0069 TCGA-02-0080 TCGA-02-0083 TCGA-02-0087 TCGA-02-0104 TCGA-02-0111 
       28.70        89.72        22.72        57.76        65.00        23.18 
TCGA-02-0114 TCGA-02-0258 TCGA-02-0266 TCGA-02-0271 TCGA-02-0326 TCGA-02-0338 
       99.98        16.54        17.72        14.47         7.33        10.59 
TCGA-02-0339 TCGA-02-0432 TCGA-02-2470 TCGA-06-0129 TCGA-06-0142 TCGA-06-0146 
       12.39        47.11        12.92        33.67         2.20        20.09 
TCGA-06-0148 TCGA-06-0160 TCGA-06-0165 TCGA-06-0176 TCGA-06-0178 TCGA-06-0213 
       10.09        11.80        10.65        91.00        88.14         0.53 
TCGA-06-0240 TCGA-06-0397 TCGA-06-0413 TCGA-06-1086 TCGA-06-1806 TCGA-06-2559 
       20.42         9.01         3.16         6.84        15.32         4.93 
TCGA-06-2569 TCGA-06-2570 TCGA-06-5416 TCGA-06-5858 TCGA-06-6389 TCGA-06-6391 
        0.43        31.50         6.71         6.15         7.79         1.48 
TCGA-06-6694 TCGA-06-6701 TCGA-06-A7TL TCGA-08-0344 TCGA-08-0350 TCGA-08-0351 
        7.36         4.96         5.42       115.86        29.23        65.33 
TCGA-08-0516 TCGA-08-0517 TCGA-08-0524 TCGA-08-0525 TCGA-08-0531 TCGA-12-0773 
       19.59        58.68         7.27        15.98         7.56        43.23 
TCGA-12-0818 TCGA-12-1089 TCGA-12-1090 TCGA-12-1092 TCGA-12-1099 TCGA-14-1396 
       91.76         5.82         7.59        21.73         4.14         1.12 
TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 TCGA-14-1821 TCGA-14-3477 TCGA-14-4157 
       40.96         6.67        12.43        17.79         3.78         3.42 
TCGA-15-1447 TCGA-16-0846 TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 TCGA-16-1460 
       53.19         3.91        26.07        16.37         4.31         6.41 
TCGA-19-0960 TCGA-19-1390 TCGA-19-1787 TCGA-19-5958 TCGA-26-1442 TCGA-26-1443 
        8.61        25.38        12.66        14.07        31.33         7.13 
TCGA-27-2526 TCGA-28-1755 TCGA-28-1756 TCGA-28-5218 TCGA-32-1973 TCGA-32-1991 
        2.86         1.55         2.83         5.16        21.07        16.93 
TCGA-32-2616 TCGA-32-2632 TCGA-32-4208 TCGA-76-6664 
        7.36         8.84        21.14         7.79 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              0.10               0.43 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            127.59             115.86 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            11.770             13.495 
[1] "0.1 - 127.6 (11.8)" "0.4 - 115.9 (13.5)"
[1] "hr=" "1.6"
D60V2, continuous
D60V3, binary
                    cls
clus                   0   1
  10P LOSS MUTATED   181 295
  10P LOSS WILD-TYPE  43  51
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED    181  295
  10P LOSS WILD-TYPE   43   51
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE              181                 43
  MALE                295                 51
[1] 2 2
[1] FALSE
D60V4, continuous
                    vv
clus                 GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  10P LOSS MUTATED                              21                  10
  10P LOSS WILD-TYPE                             6                   8
                    vv
clus                 UNTREATED PRIMARY (DE NOVO) GBM
  10P LOSS MUTATED                               445
  10P LOSS WILD-TYPE                              80
D60V5, multiclass
                                 clus
vv                                10P LOSS MUTATED 10P LOSS WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                 21                  6
  TREATED PRIMARY GBM                           10                  8
  UNTREATED PRIMARY (DE NOVO) GBM              445                 80
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V6, binary
                    cls
clus                   0   1
  10P LOSS MUTATED   317 159
  10P LOSS WILD-TYPE  65  29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED    317  159
  10P LOSS WILD-TYPE   65   29
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  NO               317                 65
  YES              159                 29
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10P LOSS MUTATED       8                        42   406
  10P LOSS WILD-TYPE     5                         7    79
D60V7, multiclass
                           clus
vv                          10P LOSS MUTATED 10P LOSS WILD-TYPE
  ASIAN                                    8                  5
  BLACK OR AFRICAN AMERICAN               42                  7
  WHITE                                  406                 79
[1] 3 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
  10P LOSS MUTATED     8 393
  10P LOSS WILD-TYPE   4  79
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      8  393
  10P LOSS WILD-TYPE    4   79
                        clus
vv                       10P LOSS MUTATED 10P LOSS WILD-TYPE
  HISPANIC OR LATINO                    8                  4
  NOT HISPANIC OR LATINO              393                 79
[1] 2 2
[1] FALSE

Clustering(61) Variable = 10Q LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                  0   1
  10Q LOSS MUTATED    84 402
  10Q LOSS WILD-TYPE  20  63
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               486                 83 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               402                 63 
$`10Q LOSS MUTATED`
TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 TCGA-02-0014 
        4.73        18.35        23.18        10.59        35.41        82.59 
TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0026 TCGA-02-0027 TCGA-02-0033 
       87.06        77.65        20.12        24.59        12.16         2.83 
TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 
       14.14         3.62        10.72        10.52        18.31         6.87 
TCGA-02-0048 TCGA-02-0052 TCGA-02-0054 TCGA-02-0055 TCGA-02-0057 TCGA-02-0059 
        3.22        12.59         6.54         2.50        19.86         9.57 
TCGA-02-0064 TCGA-02-0068 TCGA-02-0070 TCGA-02-0071 TCGA-02-0074 TCGA-02-0075 
       19.73        26.43        25.05         5.49        10.19        20.84 
TCGA-02-0079 TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 TCGA-02-0086 TCGA-02-0089 
       27.25        22.72        12.62        51.32         8.81        16.96 
TCGA-02-0099 TCGA-02-0102 TCGA-02-0106 TCGA-02-0107 TCGA-02-0113 TCGA-02-0115 
        3.48        27.02        11.67        17.65        92.65        15.65 
TCGA-02-0116 TCGA-02-0260 TCGA-02-0269 TCGA-02-0281 TCGA-02-0285 TCGA-02-0289 
       48.95        16.93        10.75         3.98        13.87        14.20 
TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 TCGA-02-0330 
       15.95        12.23         9.90         7.73        10.62        15.91 
TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 TCGA-02-0422 TCGA-02-0430 TCGA-02-0440 
       25.71         4.37        25.12        14.50        10.55        11.34 
TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 TCGA-02-2466 TCGA-02-2483 TCGA-02-2485 
        9.27        16.21         3.35        16.80        15.32        15.45 
TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 
       20.32         2.70         6.15        20.38        47.61         6.94 
TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 
        3.98        22.72        33.67        12.95        25.35        14.30 
TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0143 
       26.70        24.23        11.90         0.20        10.29        11.74 
TCGA-06-0145 TCGA-06-0147 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 
        2.33        17.79         8.61        19.46        46.59        12.33 
TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0162 
       13.94        10.45         3.19        10.82         9.44         3.42 
TCGA-06-0164 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 
       56.91         5.85        19.66         3.29        13.12         4.47 
TCGA-06-0174 TCGA-06-0175 TCGA-06-0177 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 
        3.22         4.04         4.18        20.25         3.65        69.90 
TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 
       73.84        27.22        44.58        15.42        10.42        38.96 
TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 
        4.67         7.40         5.56         0.39         7.66         8.42 
TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 
        7.63         7.40        11.84        15.02        24.16         0.72 
TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 TCGA-06-0241 TCGA-06-0394 TCGA-06-0402 
       19.82        13.64        13.32        48.69        10.82         0.26 
TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 
       72.36         4.70         9.57        35.11        12.62         5.75 
TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 
        5.75         9.80         2.10        23.57        14.20        26.40 
TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 
       46.88         7.86         2.70         2.70         0.92        43.46 
TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 
       46.19         5.65         7.17        40.41        16.57        20.78 
TCGA-06-0939 TCGA-06-1084 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 
       26.76        23.93         4.04        26.79        11.84        15.32 
TCGA-06-1804 TCGA-06-1805 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 
       13.61        33.90         1.08        12.49         4.93        17.65 
TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 
       12.56        30.64         5.95        16.64         5.98         4.37 
TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 
       11.74         3.55         8.35         4.54         8.81         8.98 
TCGA-06-5415 TCGA-06-5418 TCGA-06-5856 TCGA-06-5859 TCGA-06-6388 TCGA-06-6390 
        8.55         2.73         3.75         4.57         5.23         5.39 
TCGA-06-6693 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 
      120.56         8.32        12.85         4.77         1.55         4.77 
TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK TCGA-06-A7TL 
        4.70         1.87         3.12         2.56         5.39         5.42 
TCGA-08-0244 TCGA-08-0245 TCGA-08-0246 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 
       22.68        37.84         4.18         1.74         8.42        25.71 
TCGA-08-0348 TCGA-08-0349 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 
       12.16         9.80         1.28         8.42        17.95        24.56 
TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 
       31.10        37.58        22.29         3.39        12.23        14.93 
TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 
       18.02        15.35        13.97         0.72        12.56         4.27 
TCGA-08-0512 TCGA-08-0514 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0525 
       42.15        11.08        19.33        10.75         4.80        15.98 
TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 
       18.41         7.56        15.35        14.73        12.99        34.92 
TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 
       10.45         7.59        94.78         0.10        38.17        25.97 
TCGA-12-0688 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 
       26.66         3.65        20.38        28.41        15.06        53.85 
TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0819 TCGA-12-0820 
        7.63         9.73        14.93        14.86        24.79        18.48 
TCGA-12-0821 TCGA-12-0822 TCGA-12-0826 TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 
       10.62        23.51        27.78        38.76         8.94        20.58 
TCGA-12-1088 TCGA-12-1089 TCGA-12-1091 TCGA-12-1092 TCGA-12-1094 TCGA-12-1095 
      127.59         5.82        33.21        21.73        12.23        15.85 
TCGA-12-1096 TCGA-12-1097 TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 
        9.11        14.53        15.65        25.68        14.73         6.77 
TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 
       59.77        44.02        26.93        15.22        10.95        12.69 
TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 
       34.92        14.53        14.93         3.22         2.04        15.12 
TCGA-14-0740 TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 
       11.97         0.95         6.21        23.05         2.24        11.24 
TCGA-14-0790 TCGA-14-0812 TCGA-14-0813 TCGA-14-0817 TCGA-14-0862 TCGA-14-0865 
       13.78         3.25         1.35         5.39         2.89        16.50 
TCGA-14-0866 TCGA-14-0867 TCGA-14-0871 TCGA-14-1034 TCGA-14-1037 TCGA-14-1043 
       26.33         2.04        28.93        15.95        19.30         0.79 
TCGA-14-1395 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 TCGA-14-1452 
        1.38         3.75        32.05        58.78        23.11         7.10 
TCGA-14-1453 TCGA-14-1454 TCGA-14-1455 TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 
        1.15        30.18         0.92        12.43         0.99         1.97 
TCGA-14-1823 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 
       17.85         7.63         5.88         7.17        17.49         7.96 
TCGA-14-3477 TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-15-1449 TCGA-16-0848 
        3.78        13.78        50.53        19.10        13.28        17.59 
TCGA-16-0850 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 
       16.37        29.03         4.57        10.29        14.01         9.14 
TCGA-16-1062 TCGA-16-1063 TCGA-19-0957 TCGA-19-0960 TCGA-19-0962 TCGA-19-0963 
       21.24        13.97        21.90         8.61         0.66        14.27 
TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 TCGA-19-1388 TCGA-19-1389 
        3.39        10.75         9.07         5.95        12.95         4.64 
TCGA-19-1392 TCGA-19-1786 TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 
        3.65         7.17         3.25         0.13         9.67         4.87 
TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 
        1.08         7.53         0.16         4.08        24.23         7.00 
TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 
        7.04         6.64        17.19         8.02        18.90         4.73 
TCGA-19-5954 TCGA-19-5955 TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J4 
       12.10         1.78        16.80        14.96        17.79         3.98 
TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 
       10.03        13.87         9.73         7.13         9.37         9.40 
TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 
       14.86         5.49         8.88        18.97         1.58         7.92 
TCGA-26-6174 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 
        2.33        19.33         5.06        16.60         9.86        24.23 
TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 
       40.54        21.30        30.05        14.04        11.51        24.76 
TCGA-27-2519 TCGA-27-2521 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 
       10.39        10.39         7.59         2.86        14.40        15.78 
TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 TCGA-28-1752 
        0.20         2.53         9.21         8.35         7.63         8.48 
TCGA-28-1753 TCGA-28-1755 TCGA-28-1757 TCGA-28-2502 TCGA-28-2506 TCGA-28-2509 
        1.22         1.55         0.13         0.66         6.74         4.77 
TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 
        7.30         5.26        14.93        11.28        17.88        14.53 
TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5219 
       11.77        31.27        23.44        11.01        13.64        22.68 
TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1976 TCGA-32-1977 TCGA-32-1978 
       12.76         5.42        15.39         0.49         0.10        15.85 
TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 TCGA-32-1991 
       19.50         1.18         4.67        12.69        14.86        16.93 
TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 TCGA-32-2634 TCGA-32-2638 
       12.23        20.78        15.02        15.95        22.78        25.18 
TCGA-32-4208 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 
       21.14         3.72        12.59        19.86        10.85        19.23 
TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 
        0.85        13.35         8.94         9.53         0.99         4.44 
TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9S TCGA-4W-AA9T 
       11.84         0.20        15.12        12.46         4.14        14.76 
TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 
        3.45        20.91         4.34        14.33         8.22         7.50 
TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-4934 
        4.80         4.54         3.09         3.65         9.17         2.53 
TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 
       10.78        16.70         3.29         2.70        11.38        17.06 
TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 
        8.35        20.98         4.83         5.03         0.23         9.27 
TCGA-76-6663 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R TCGA-RR-A6KC 
        7.73         1.61        17.72        26.30         5.92        20.55 

$`10Q LOSS WILD-TYPE`
TCGA-02-0001 TCGA-02-0011 TCGA-02-0015 TCGA-02-0024 TCGA-02-0025 TCGA-02-0028 
       11.77        20.71        20.61        53.10        42.74        90.58 
TCGA-02-0047 TCGA-02-0051 TCGA-02-0058 TCGA-02-0060 TCGA-02-0069 TCGA-02-0080 
       14.73        15.09         8.35         6.02        28.70        89.72 
TCGA-02-0087 TCGA-02-0104 TCGA-02-0111 TCGA-02-0114 TCGA-02-0258 TCGA-02-0266 
       57.76        65.00        23.18        99.98        16.54        17.72 
TCGA-02-0271 TCGA-02-0326 TCGA-02-0338 TCGA-02-0339 TCGA-02-0432 TCGA-02-2470 
       14.47         7.33        10.59        12.39        47.11        12.92 
TCGA-06-0142 TCGA-06-0146 TCGA-06-0148 TCGA-06-0160 TCGA-06-0165 TCGA-06-0176 
        2.20        20.09        10.09        11.80        10.65        91.00 
TCGA-06-0178 TCGA-06-0213 TCGA-06-0240 TCGA-06-0397 TCGA-06-0413 TCGA-06-1086 
       88.14         0.53        20.42         9.01         3.16         6.84 
TCGA-06-1806 TCGA-06-2569 TCGA-06-2570 TCGA-06-5416 TCGA-06-5858 TCGA-06-6389 
       15.32         0.43        31.50         6.71         6.15         7.79 
TCGA-06-6391 TCGA-06-6694 TCGA-06-6701 TCGA-08-0344 TCGA-08-0350 TCGA-08-0351 
        1.48         7.36         4.96       115.86        29.23        65.33 
TCGA-08-0516 TCGA-08-0517 TCGA-08-0524 TCGA-12-0691 TCGA-12-0773 TCGA-12-0818 
       19.59        58.68         7.27        12.13        43.23        91.76 
TCGA-12-1090 TCGA-12-1093 TCGA-12-1098 TCGA-12-1099 TCGA-14-1396 TCGA-14-1456 
        7.59        15.98         3.98         4.14         1.12        40.96 
TCGA-14-1458 TCGA-14-1821 TCGA-14-4157 TCGA-15-1447 TCGA-16-0846 TCGA-16-0849 
        6.67        17.79         3.42        53.19         3.91        26.07 
TCGA-16-0861 TCGA-16-1460 TCGA-19-0955 TCGA-19-1390 TCGA-19-1787 TCGA-19-5956 
        4.31         6.41        11.77        25.38        12.66        22.49 
TCGA-19-5958 TCGA-19-A6J5 TCGA-26-1442 TCGA-27-2523 TCGA-28-1756 TCGA-28-5218 
       14.07        28.54        31.33        16.08         2.83         5.16 
TCGA-32-1973 TCGA-32-2616 TCGA-32-2632 TCGA-76-6664 TCGA-RR-A6KA 
       21.07         7.36         8.84         7.79         6.28 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              0.10               0.43 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            127.59             115.86 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             11.74              14.07 
[1] "0.1 - 127.6 (11.7)" "0.4 - 115.9 (14.1)"
[1] "hr=" "1.6"
D61V2, continuous
D61V3, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED   188 299
  10Q LOSS WILD-TYPE  36  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED    188  299
  10Q LOSS WILD-TYPE   36   47
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE              188                 36
  MALE                299                 47
[1] 2 2
[1] FALSE
D61V4, continuous
                    vv
clus                 GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  10Q LOSS MUTATED                              20                  13
  10Q LOSS WILD-TYPE                             7                   5
                    vv
clus                 UNTREATED PRIMARY (DE NOVO) GBM
  10Q LOSS MUTATED                               454
  10Q LOSS WILD-TYPE                              71
D61V5, multiclass
                                 clus
vv                                10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                 20                  7
  TREATED PRIMARY GBM                           13                  5
  UNTREATED PRIMARY (DE NOVO) GBM              454                 71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V6, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED   328 159
  10Q LOSS WILD-TYPE  54  29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED    328  159
  10Q LOSS WILD-TYPE   54   29
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  NO               328                 54
  YES              159                 29
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10Q LOSS MUTATED       8                        42   416
  10Q LOSS WILD-TYPE     5                         7    69
D61V7, multiclass
                           clus
vv                          10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  ASIAN                                    8                  5
  BLACK OR AFRICAN AMERICAN               42                  7
  WHITE                                  416                 69
[1] 3 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
  10Q LOSS MUTATED     8 403
  10Q LOSS WILD-TYPE   4  69
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      8  403
  10Q LOSS WILD-TYPE    4   69
                        clus
vv                       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    8                  4
  NOT HISPANIC OR LATINO              403                 69
[1] 2 2
[1] FALSE

Clustering(62) Variable = 11P LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                  0   1
  11P LOSS MUTATED    18  81
  11P LOSS WILD-TYPE  86 384
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                99                470 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                81                384 
$`11P LOSS MUTATED`
TCGA-02-0001 TCGA-02-0010 TCGA-02-0024 TCGA-02-0033 TCGA-02-0047 TCGA-02-0048 
       11.77        35.41        53.10         2.83        14.73         3.22 
TCGA-02-0052 TCGA-02-0055 TCGA-02-0059 TCGA-02-0069 TCGA-02-0074 TCGA-02-0075 
       12.59         2.50         9.57        28.70        10.19        20.84 
TCGA-02-0084 TCGA-02-0086 TCGA-02-0087 TCGA-02-0113 TCGA-02-0114 TCGA-02-0281 
       12.62         8.81        57.76        92.65        99.98         3.98 
TCGA-02-0332 TCGA-02-0456 TCGA-02-2466 TCGA-06-0128 TCGA-06-0159 TCGA-06-0166 
       25.71         3.35        16.80        22.72         9.44         5.85 
TCGA-06-0174 TCGA-06-0177 TCGA-06-0184 TCGA-06-0192 TCGA-06-0197 TCGA-06-0216 
        3.22         4.18        69.90        38.96         5.56        24.16 
TCGA-06-0221 TCGA-06-0238 TCGA-06-0409 TCGA-06-0410 TCGA-06-0414 TCGA-06-0649 
       19.82        13.32        72.36         4.70        35.11         2.10 
TCGA-06-0686 TCGA-06-0876 TCGA-06-1086 TCGA-06-1800 TCGA-06-1805 TCGA-06-1806 
       14.20        46.19         6.84        26.79        33.90        15.32 
TCGA-06-2558 TCGA-06-2570 TCGA-06-5856 TCGA-06-6389 TCGA-06-6694 TCGA-06-A7TK 
       12.49        31.50         3.75         7.79         7.36         5.39 
TCGA-06-A7TL TCGA-08-0245 TCGA-08-0510 TCGA-08-0520 TCGA-12-0616 TCGA-12-0619 
        5.42        37.84         4.27        10.75        14.73        34.92 
TCGA-12-0691 TCGA-12-0772 TCGA-12-0819 TCGA-12-0822 TCGA-12-1099 TCGA-12-1602 
       12.13        53.85        24.79        23.51         4.14         6.77 
TCGA-12-3646 TCGA-12-3653 TCGA-14-0740 TCGA-14-0783 TCGA-14-0817 TCGA-14-0865 
       44.02        14.53        11.97         6.21         5.39        16.50 
TCGA-14-0867 TCGA-14-0871 TCGA-14-1454 TCGA-14-1459 TCGA-14-1794 TCGA-14-1821 
        2.04        28.93        30.18        12.43         0.99        17.79 
TCGA-14-1823 TCGA-14-3477 TCGA-15-1447 TCGA-15-1449 TCGA-16-0846 TCGA-16-0850 
       17.85         3.78        53.19        13.28         3.91        16.37 
TCGA-16-1045 TCGA-19-1387 TCGA-19-1390 TCGA-19-1392 TCGA-19-2623 TCGA-19-5959 
       29.03         5.95        25.38         3.65         7.53        16.80 
TCGA-19-5960 TCGA-26-1439 TCGA-26-5133 TCGA-27-1830 TCGA-28-1756 TCGA-28-2509 
       14.96        13.87        14.86         5.06         2.83         4.77 
TCGA-28-5216 TCGA-32-1976 TCGA-32-2615 TCGA-32-2632 TCGA-32-4210 TCGA-32-4719 
       13.64         0.49        15.95         8.84         3.72        10.85 
TCGA-41-3915 TCGA-74-6584 TCGA-76-4934 
       11.84         7.50         2.53 

$`11P LOSS WILD-TYPE`
TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0011 TCGA-02-0014 
        4.73        18.35        23.18        10.59        20.71        82.59 
TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0025 TCGA-02-0026 
       20.61        87.06        77.65        20.12        42.74        24.59 
TCGA-02-0027 TCGA-02-0028 TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 
       12.16        90.58        14.14         3.62        10.72        10.52 
TCGA-02-0043 TCGA-02-0046 TCGA-02-0051 TCGA-02-0054 TCGA-02-0057 TCGA-02-0058 
       18.31         6.87        15.09         6.54        19.86         8.35 
TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 TCGA-02-0070 TCGA-02-0071 TCGA-02-0079 
        6.02        19.73        26.43        25.05         5.49        27.25 
TCGA-02-0080 TCGA-02-0083 TCGA-02-0085 TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 
       89.72        22.72        51.32        16.96         3.48        27.02 
TCGA-02-0104 TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 TCGA-02-0115 TCGA-02-0116 
       65.00        11.67        17.65        23.18        15.65        48.95 
TCGA-02-0258 TCGA-02-0260 TCGA-02-0266 TCGA-02-0269 TCGA-02-0271 TCGA-02-0285 
       16.54        16.93        17.72        10.75        14.47        13.87 
TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 
       14.20        15.95        12.23         9.90         7.73        10.62 
TCGA-02-0326 TCGA-02-0330 TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 
        7.33        15.91         4.37        25.12        10.59        12.39 
TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 
       14.50        10.55        47.11        11.34         9.27        16.21 
TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 
       12.92        15.32        15.45        20.32         2.70         6.15 
TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0129 TCGA-06-0130 
       20.38        47.61         6.94         3.98        33.67        12.95 
TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 
       25.35        14.30        26.70        24.23        11.90         0.20 
TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 
       10.29         2.20        11.74         2.33        20.09        17.79 
TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 
       10.09         8.61        19.46        46.59        12.33        13.94 
TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 
       10.45         3.19        10.82        11.80         3.42        56.91 
TCGA-06-0165 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0175 
       10.65        19.66         3.29        13.12         4.47         4.04 
TCGA-06-0176 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0185 TCGA-06-0187 
       91.00        88.14        20.25         3.65        73.84        27.22 
TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0194 TCGA-06-0195 TCGA-06-0201 
       44.58        15.42        10.42         4.67         7.40         0.39 
TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 
        7.66         8.42         7.63         7.40        11.84         0.53 
TCGA-06-0214 TCGA-06-0219 TCGA-06-0237 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 
       15.02         0.72        13.64        20.42        48.69        10.82 
TCGA-06-0397 TCGA-06-0402 TCGA-06-0412 TCGA-06-0413 TCGA-06-0644 TCGA-06-0645 
        9.01         0.26         9.57         3.16        12.62         5.75 
TCGA-06-0646 TCGA-06-0648 TCGA-06-0650 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 
        5.75         9.80        23.57        26.40        46.88         7.86 
TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0877 TCGA-06-0878 
        2.70         2.70         0.92        43.46         5.65         7.17 
TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1087 
       40.41        16.57        20.78        26.76        23.93         4.04 
TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-2557 TCGA-06-2559 TCGA-06-2561 
       11.84        15.32        13.61         1.08         4.93        17.65 
TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 
       12.56        30.64         5.95        16.64         5.98         4.37 
TCGA-06-2569 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 
        0.43        11.74         3.55         8.35         4.54         8.81 
TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 TCGA-06-5418 TCGA-06-5858 TCGA-06-5859 
        8.98         8.55         6.71         2.73         6.15         4.57 
TCGA-06-6388 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6695 TCGA-06-6697 
        5.23         5.39         1.48       120.56         8.32        12.85 
TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A5U1 
        4.77         1.55         4.77         4.96         4.70         1.87 
TCGA-06-A6S0 TCGA-06-A6S1 TCGA-08-0244 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 
        3.12         2.56        22.68         4.18       115.86         1.74 
TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 
        8.42        25.71        12.16         9.80        29.23        65.33 
TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 
        1.28         8.42        17.95        24.56        31.10        37.58 
TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 
       22.29         3.39        12.23        14.93        18.02        15.35 
TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 
       13.97         0.72        12.56        42.15        11.08        19.59 
TCGA-08-0517 TCGA-08-0518 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 
       58.68        19.33         4.80         7.27        15.98        18.41 
TCGA-08-0531 TCGA-12-0615 TCGA-12-0618 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 
        7.56        15.35        12.99        10.45         7.59        94.78 
TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0692 TCGA-12-0703 
        0.10        38.17        25.97        26.66         3.65        20.38 
TCGA-12-0707 TCGA-12-0769 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 
       28.41        15.06        43.23         7.63         9.73        14.93 
TCGA-12-0780 TCGA-12-0818 TCGA-12-0820 TCGA-12-0821 TCGA-12-0826 TCGA-12-0827 
       14.86        91.76        18.48        10.62        27.78        38.76 
TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 
        8.94        20.58       127.59         5.82         7.59        33.21 
TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 
       21.73        15.98        12.23        15.85         9.11        14.53 
TCGA-12-1098 TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 TCGA-12-3644 TCGA-12-3648 
        3.98        15.65        25.68        14.73        59.77        26.93 
TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-5295 TCGA-12-5299 
       15.22        10.95        12.69        34.92        14.93         3.22 
TCGA-12-5301 TCGA-14-0736 TCGA-14-0781 TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 
        2.04        15.12         0.95        23.05         2.24        11.24 
TCGA-14-0790 TCGA-14-0812 TCGA-14-0813 TCGA-14-0862 TCGA-14-0866 TCGA-14-1034 
       13.78         3.25         1.35         2.89        26.33        15.95 
TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 
       19.30         0.79         1.38         1.12         3.75        32.05 
TCGA-14-1450 TCGA-14-1451 TCGA-14-1452 TCGA-14-1453 TCGA-14-1455 TCGA-14-1456 
       58.78        23.11         7.10         1.15         0.92        40.96 
TCGA-14-1458 TCGA-14-1795 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 
        6.67         1.97         7.63         5.88         7.17        17.49 
TCGA-14-2555 TCGA-14-4157 TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-16-0848 
        7.96         3.42        13.78        50.53        19.10        17.59 
TCGA-16-0849 TCGA-16-0861 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 
       26.07         4.31         4.57        10.29        14.01         9.14 
TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 
       21.24        13.97         6.41        11.77        21.90         8.61 
TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 TCGA-19-1388 
        0.66        14.27         3.39        10.75         9.07        12.95 
TCGA-19-1389 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 
        4.64         7.17        12.66         3.25         0.13         9.67 
TCGA-19-2620 TCGA-19-2621 TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 
        4.87         1.08         0.16         4.08        24.23         7.00 
TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 
        7.04         6.64        17.19         8.02        18.90         4.73 
TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-A60I TCGA-19-A6J4 
       12.10         1.78        22.49        14.07        17.79         3.98 
TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 
       28.54        10.03         9.73        31.33         7.13         9.37 
TCGA-26-5132 TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 
        9.40         5.49         8.88        18.97         1.58         7.92 
TCGA-26-6174 TCGA-26-A7UX TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 
        2.33        19.33        16.60         9.86        24.23        40.54 
TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 
       21.30        30.05        14.04        11.51        24.76        10.39 
TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 
       10.39        16.08         7.59         2.86        14.40        15.78 
TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 TCGA-28-1752 
        0.20         2.53         9.21         8.35         7.63         8.48 
TCGA-28-1753 TCGA-28-1755 TCGA-28-1757 TCGA-28-2502 TCGA-28-2506 TCGA-28-2513 
        1.22         1.55         0.13         0.66         6.74         7.30 
TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 
        5.26        14.93        11.28        17.88        14.53        11.77 
TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 
       31.27        23.44        11.01         5.16        22.68        12.76 
TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 
        5.42        15.39        21.07         0.10        15.85        19.50 
TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 TCGA-32-1991 TCGA-32-2491 
        1.18         4.67        12.69        14.86        16.93        12.23 
TCGA-32-2494 TCGA-32-2495 TCGA-32-2616 TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 
       20.78        15.02         7.36        22.78        25.18        21.14 
TCGA-32-4211 TCGA-32-4213 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 
       12.59        19.86        19.23         0.85        13.35         8.94 
TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 
        9.53         0.99         4.44         0.20        15.12        12.46 
TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 
        4.14        14.76         3.45        20.91         4.34        14.33 
TCGA-74-6581 TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 
        8.22         4.80         4.54         3.09         3.65         9.17 
TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 
       10.78        16.70         3.29         2.70        11.38        17.06 
TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 
        8.35        20.98         4.83         5.03         0.23         9.27 
TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R 
        7.73         7.79         1.61        17.72        26.30         5.92 
TCGA-RR-A6KA TCGA-RR-A6KC 
        6.28        20.55 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              0.49               0.10 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             99.98             127.59 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
            12.590             11.755 
[1] "0.5 - 100.0 (12.6)" "0.1 - 127.6 (11.8)"
[1] "hr=" "1.2"
D62V2, continuous
D62V3, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    47  52
  11P LOSS WILD-TYPE 177 294
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     47   52
  11P LOSS WILD-TYPE  177  294
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE               47                177
  MALE                 52                294
[1] 2 2
[1] FALSE
D62V4, continuous
                    vv
clus                 GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  11P LOSS MUTATED                               4                   5
  11P LOSS WILD-TYPE                            23                  13
                    vv
clus                 UNTREATED PRIMARY (DE NOVO) GBM
  11P LOSS MUTATED                                90
  11P LOSS WILD-TYPE                             435
D62V5, multiclass
                                 clus
vv                                11P LOSS MUTATED 11P LOSS WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                  4                 23
  TREATED PRIMARY GBM                            5                 13
  UNTREATED PRIMARY (DE NOVO) GBM               90                435
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V6, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    64  35
  11P LOSS WILD-TYPE 318 153
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     64   35
  11P LOSS WILD-TYPE  318  153
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  NO                64                318
  YES               35                153
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11P LOSS MUTATED       1                        10    85
  11P LOSS WILD-TYPE    12                        39   400
D62V7, multiclass
                           clus
vv                          11P LOSS MUTATED 11P LOSS WILD-TYPE
  ASIAN                                    1                 12
  BLACK OR AFRICAN AMERICAN               10                 39
  WHITE                                   85                400
[1] 3 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
  11P LOSS MUTATED     1  80
  11P LOSS WILD-TYPE  11 392
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      1   80
  11P LOSS WILD-TYPE   11  392
                        clus
vv                       11P LOSS MUTATED 11P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 11
  NOT HISPANIC OR LATINO               80                392
[1] 2 2
[1] FALSE

Clustering(63) Variable = 11Q LOSS MUTATION ANALYSIS
D63V1, survival
                    sevent
clus2                  0   1
  11Q LOSS MUTATED    12  81
  11Q LOSS WILD-TYPE  92 384
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                93                476 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                81                384 
$`11Q LOSS MUTATED`
TCGA-02-0001 TCGA-02-0010 TCGA-02-0024 TCGA-02-0033 TCGA-02-0048 TCGA-02-0052 
       11.77        35.41        53.10         2.83         3.22        12.59 
TCGA-02-0055 TCGA-02-0059 TCGA-02-0069 TCGA-02-0074 TCGA-02-0075 TCGA-02-0086 
        2.50         9.57        28.70        10.19        20.84         8.81 
TCGA-02-0087 TCGA-02-0111 TCGA-02-0113 TCGA-02-0281 TCGA-02-0332 TCGA-02-0339 
       57.76        23.18        92.65         3.98        25.71        12.39 
TCGA-02-0456 TCGA-06-0130 TCGA-06-0159 TCGA-06-0166 TCGA-06-0174 TCGA-06-0177 
        3.35        12.95         9.44         5.85         3.22         4.18 
TCGA-06-0184 TCGA-06-0188 TCGA-06-0190 TCGA-06-0192 TCGA-06-0195 TCGA-06-0197 
       69.90        44.58        10.42        38.96         7.40         5.56 
TCGA-06-0216 TCGA-06-0221 TCGA-06-0238 TCGA-06-0409 TCGA-06-0410 TCGA-06-0414 
       24.16        19.82        13.32        72.36         4.70        35.11 
TCGA-06-0649 TCGA-06-0686 TCGA-06-0876 TCGA-06-1800 TCGA-06-1806 TCGA-06-5856 
        2.10        14.20        46.19        26.79        15.32         3.75 
TCGA-06-6389 TCGA-06-A7TK TCGA-08-0245 TCGA-08-0510 TCGA-08-0520 TCGA-12-0616 
        7.79         5.39        37.84         4.27        10.75        14.73 
TCGA-12-0619 TCGA-12-0691 TCGA-12-0772 TCGA-12-0819 TCGA-12-0822 TCGA-12-1099 
       34.92        12.13        53.85        24.79        23.51         4.14 
TCGA-12-1598 TCGA-12-1602 TCGA-12-3646 TCGA-12-3651 TCGA-12-3653 TCGA-14-0783 
       15.65         6.77        44.02        12.69        14.53         6.21 
TCGA-14-0817 TCGA-14-0865 TCGA-14-0867 TCGA-14-0871 TCGA-14-1454 TCGA-14-1459 
        5.39        16.50         2.04        28.93        30.18        12.43 
TCGA-14-1794 TCGA-14-1823 TCGA-14-3477 TCGA-15-1449 TCGA-16-0846 TCGA-16-0850 
        0.99        17.85         3.78        13.28         3.91        16.37 
TCGA-16-1045 TCGA-19-1387 TCGA-19-1390 TCGA-19-1392 TCGA-19-2623 TCGA-19-5959 
       29.03         5.95        25.38         3.65         7.53        16.80 
TCGA-19-5960 TCGA-26-1439 TCGA-27-1830 TCGA-28-2509 TCGA-28-5216 TCGA-32-1976 
       14.96        13.87         5.06         4.77        13.64         0.49 
TCGA-32-1986 TCGA-32-2615 TCGA-32-2632 TCGA-32-4210 TCGA-32-4719 TCGA-41-3915 
       12.69        15.95         8.84         3.72        10.85        11.84 
TCGA-74-6584 TCGA-76-4934 TCGA-81-5910 
        7.50         2.53         1.61 

$`11Q LOSS WILD-TYPE`
TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0011 TCGA-02-0014 
        4.73        18.35        23.18        10.59        20.71        82.59 
TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0025 TCGA-02-0026 
       20.61        87.06        77.65        20.12        42.74        24.59 
TCGA-02-0027 TCGA-02-0028 TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 
       12.16        90.58        14.14         3.62        10.72        10.52 
TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 TCGA-02-0051 TCGA-02-0054 TCGA-02-0057 
       18.31         6.87        14.73        15.09         6.54        19.86 
TCGA-02-0058 TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 TCGA-02-0070 TCGA-02-0071 
        8.35         6.02        19.73        26.43        25.05         5.49 
TCGA-02-0079 TCGA-02-0080 TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 TCGA-02-0089 
       27.25        89.72        22.72        12.62        51.32        16.96 
TCGA-02-0099 TCGA-02-0102 TCGA-02-0104 TCGA-02-0106 TCGA-02-0107 TCGA-02-0114 
        3.48        27.02        65.00        11.67        17.65        99.98 
TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 TCGA-02-0266 TCGA-02-0269 
       15.65        48.95        16.54        16.93        17.72        10.75 
TCGA-02-0271 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 
       14.47        13.87        14.20        15.95        12.23         9.90 
TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 TCGA-02-0333 TCGA-02-0337 
        7.73        10.62         7.33        15.91         4.37        25.12 
TCGA-02-0338 TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 
       10.59        14.50        10.55        47.11        11.34         9.27 
TCGA-02-0451 TCGA-02-2466 TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 
       16.21        16.80        12.92        15.32        15.45        20.32 
TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 
        2.70         6.15        20.38        47.61         6.94         3.98 
TCGA-06-0128 TCGA-06-0129 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 
       22.72        33.67        25.35        14.30        26.70        24.23 
TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 
       11.90         0.20        10.29         2.20        11.74         2.33 
TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 
       20.09        17.79        10.09         8.61        19.46        46.59 
TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0160 
       12.33        13.94        10.45         3.19        10.82        11.80 
TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 
        3.42        56.91        10.65        19.66         3.29        13.12 
TCGA-06-0173 TCGA-06-0175 TCGA-06-0176 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 
        4.47         4.04        91.00        88.14        20.25         3.65 
TCGA-06-0185 TCGA-06-0187 TCGA-06-0189 TCGA-06-0194 TCGA-06-0201 TCGA-06-0206 
       73.84        27.22        15.42         4.67         0.39         7.66 
TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 
        8.42         7.63         7.40        11.84         0.53        15.02 
TCGA-06-0219 TCGA-06-0237 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 
        0.72        13.64        20.42        48.69        10.82         9.01 
TCGA-06-0402 TCGA-06-0412 TCGA-06-0413 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 
        0.26         9.57         3.16        12.62         5.75         5.75 
TCGA-06-0648 TCGA-06-0650 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 
        9.80        23.57        26.40        46.88         7.86         2.70 
TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0877 TCGA-06-0878 TCGA-06-0879 
        2.70         0.92        43.46         5.65         7.17        40.41 
TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 
       16.57        20.78        26.76        23.93         6.84         4.04 
TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-2557 TCGA-06-2558 
       11.84        15.32        13.61        33.90         1.08        12.49 
TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 
        4.93        17.65        12.56        30.64         5.95        16.64 
TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 
        5.98         4.37         0.43        31.50        11.74         3.55 
TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 
        8.35         4.54         8.81         8.98         8.55         6.71 
TCGA-06-5418 TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 TCGA-06-6390 TCGA-06-6391 
        2.73         6.15         4.57         5.23         5.39         1.48 
TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 
      120.56         7.36         8.32        12.85         4.77         1.55 
TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 
        4.77         4.96         4.70         1.87         3.12         2.56 
TCGA-06-A7TL TCGA-08-0244 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 
        5.42        22.68         4.18       115.86         1.74         8.42 
TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 
       25.71        12.16         9.80        29.23        65.33         1.28 
TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 
        8.42        17.95        24.56        31.10        37.58        22.29 
TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 
        3.39        12.23        14.93        18.02        15.35        13.97 
TCGA-08-0392 TCGA-08-0509 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 
        0.72        12.56        42.15        11.08        19.59        58.68 
TCGA-08-0518 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 
       19.33         4.80         7.27        15.98        18.41         7.56 
TCGA-12-0615 TCGA-12-0618 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 
       15.35        12.99        10.45         7.59        94.78         0.10 
TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 
       38.17        25.97        26.66         3.65        20.38        28.41 
TCGA-12-0769 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 
       15.06        43.23         7.63         9.73        14.93        14.86 
TCGA-12-0818 TCGA-12-0820 TCGA-12-0821 TCGA-12-0826 TCGA-12-0827 TCGA-12-0828 
       91.76        18.48        10.62        27.78        38.76         8.94 
TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 TCGA-12-1092 
       20.58       127.59         5.82         7.59        33.21        21.73 
TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 
       15.98        12.23        15.85         9.11        14.53         3.98 
TCGA-12-1599 TCGA-12-1600 TCGA-12-3644 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 
       25.68        14.73        59.77        26.93        15.22        10.95 
TCGA-12-3652 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 
       34.92        14.93         3.22         2.04        15.12        11.97 
TCGA-14-0781 TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 TCGA-14-0812 
        0.95        23.05         2.24        11.24        13.78         3.25 
TCGA-14-0813 TCGA-14-0862 TCGA-14-0866 TCGA-14-1034 TCGA-14-1037 TCGA-14-1043 
        1.35         2.89        26.33        15.95        19.30         0.79 
TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 
        1.38         1.12         3.75        32.05        58.78        23.11 
TCGA-14-1452 TCGA-14-1453 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1795 
        7.10         1.15         0.92        40.96         6.67         1.97 
TCGA-14-1821 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 
       17.79         7.63         5.88         7.17        17.49         7.96 
TCGA-14-4157 TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 TCGA-16-0848 
        3.42        13.78        50.53        19.10        53.19        17.59 
TCGA-16-0849 TCGA-16-0861 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 
       26.07         4.31         4.57        10.29        14.01         9.14 
TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 
       21.24        13.97         6.41        11.77        21.90         8.61 
TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 TCGA-19-1388 
        0.66        14.27         3.39        10.75         9.07        12.95 
TCGA-19-1389 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 
        4.64         7.17        12.66         3.25         0.13         9.67 
TCGA-19-2620 TCGA-19-2621 TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 
        4.87         1.08         0.16         4.08        24.23         7.00 
TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 
        7.04         6.64        17.19         8.02        18.90         4.73 
TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-A60I TCGA-19-A6J4 
       12.10         1.78        22.49        14.07        17.79         3.98 
TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 
       28.54        10.03         9.73        31.33         7.13         9.37 
TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 
        9.40        14.86         5.49         8.88        18.97         1.58 
TCGA-26-6173 TCGA-26-6174 TCGA-26-A7UX TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 
        7.92         2.33        19.33        16.60         9.86        24.23 
TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 
       40.54        21.30        30.05        14.04        11.51        24.76 
TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 
       10.39        10.39        16.08         7.59         2.86        14.40 
TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 
       15.78         0.20         2.53         9.21         8.35         7.63 
TCGA-28-1752 TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 TCGA-28-2502 
        8.48         1.22         1.55         2.83         0.13         0.66 
TCGA-28-2506 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 
        6.74         7.30         5.26        14.93        11.28        17.88 
TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5218 
       14.53        11.77        31.27        23.44        11.01         5.16 
TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 TCGA-32-1977 
       22.68        12.76         5.42        15.39        21.07         0.10 
TCGA-32-1978 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1987 TCGA-32-1991 
       15.85        19.50         1.18         4.67        14.86        16.93 
TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2616 TCGA-32-2634 TCGA-32-2638 
       12.23        20.78        15.02         7.36        22.78        25.18 
TCGA-32-4208 TCGA-32-4211 TCGA-32-4213 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 
       21.14        12.59        19.86        19.23         0.85        13.35 
TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-4097 TCGA-41-5651 
        8.94         9.53         0.99         4.44         0.20        15.12 
TCGA-41-6646 TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 
       12.46         4.14        14.76         3.45        20.91         4.34 
TCGA-74-6578 TCGA-74-6581 TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 
       14.33         8.22         4.80         4.54         3.09         3.65 
TCGA-76-4931 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 
        9.17        10.78        16.70         3.29         2.70        11.38 
TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 
       17.06         8.35        20.98         4.83         5.03         0.23 
TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R 
        9.27         7.73         7.79        17.72        26.30         5.92 
TCGA-RR-A6KA TCGA-RR-A6KC 
        6.28        20.55 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              0.49               0.10 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             92.65             127.59 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            12.430             11.785 
[1] "0.5 - 92.7 (12.4)"  "0.1 - 127.6 (11.8)"
[1] "hr=" "1"  
D63V2, continuous
D63V3, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    40  53
  11Q LOSS WILD-TYPE 184 293
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     40   53
  11Q LOSS WILD-TYPE  184  293
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE               40                184
  MALE                 53                293
[1] 2 2
[1] FALSE
D63V4, continuous
                    vv
clus                 GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  11Q LOSS MUTATED                               3                   3
  11Q LOSS WILD-TYPE                            24                  15
                    vv
clus                 UNTREATED PRIMARY (DE NOVO) GBM
  11Q LOSS MUTATED                                87
  11Q LOSS WILD-TYPE                             438
D63V5, multiclass
                                 clus
vv                                11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                  3                 24
  TREATED PRIMARY GBM                            3                 15
  UNTREATED PRIMARY (DE NOVO) GBM               87                438
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V6, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    58  35
  11Q LOSS WILD-TYPE 324 153
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     58   35
  11Q LOSS WILD-TYPE  324  153
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  NO                58                324
  YES               35                153
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11Q LOSS MUTATED       2                         7    81
  11Q LOSS WILD-TYPE    11                        42   404
D63V7, multiclass
                           clus
vv                          11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  ASIAN                                    2                 11
  BLACK OR AFRICAN AMERICAN                7                 42
  WHITE                                   81                404
[1] 3 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
  11Q LOSS MUTATED     0  77
  11Q LOSS WILD-TYPE  12 395
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      0   77
  11Q LOSS WILD-TYPE   12  395
                        clus
vv                       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 12
  NOT HISPANIC OR LATINO               77                395
[1] 2 2
[1] FALSE

Clustering(64) Variable = 12P LOSS MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                  0   1
  12P LOSS MUTATED     8  50
  12P LOSS WILD-TYPE  96 415
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                58                511 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                50                415 
$`12P LOSS MUTATED`
TCGA-02-0026 TCGA-02-0034 TCGA-02-0055 TCGA-02-0075 TCGA-02-0102 TCGA-02-0104 
       24.59        14.14         2.50        20.84        27.02        65.00 
TCGA-02-0113 TCGA-06-0147 TCGA-06-0149 TCGA-06-0159 TCGA-06-0177 TCGA-06-0182 
       92.65        17.79         8.61         9.44         4.18         3.65 
TCGA-06-0190 TCGA-06-0195 TCGA-06-0197 TCGA-06-0221 TCGA-06-0237 TCGA-06-0414 
       10.42         7.40         5.56        19.82        13.64        35.11 
TCGA-06-0686 TCGA-06-5856 TCGA-06-6390 TCGA-08-0245 TCGA-08-0349 TCGA-08-0386 
       14.20         3.75         5.39        37.84         9.80        18.02 
TCGA-08-0510 TCGA-08-0514 TCGA-12-0619 TCGA-12-0670 TCGA-12-1600 TCGA-12-1602 
        4.27        11.08        34.92        25.97        14.73         6.77 
TCGA-12-3646 TCGA-14-0783 TCGA-14-0817 TCGA-14-0867 TCGA-14-0871 TCGA-14-1451 
       44.02         6.21         5.39         2.04        28.93        23.11 
TCGA-14-1794 TCGA-14-3477 TCGA-16-0849 TCGA-16-0850 TCGA-16-1055 TCGA-19-0960 
        0.99         3.78        26.07        16.37        10.29         8.61 
TCGA-19-1385 TCGA-19-1388 TCGA-19-1390 TCGA-19-2623 TCGA-19-2624 TCGA-19-4065 
       10.75        12.95        25.38         7.53         0.16         7.04 
TCGA-19-5960 TCGA-26-1438 TCGA-26-5132 TCGA-26-5136 TCGA-27-1836 TCGA-28-5204 
       14.96        10.03         9.40        18.97        30.05        14.93 
TCGA-32-1978 TCGA-32-2494 TCGA-32-4210 TCGA-76-6193 
       15.85        20.78         3.72         2.70 

$`12P LOSS WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 
       11.77         4.73        18.35        23.18        10.59        35.41 
TCGA-02-0011 TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 
       20.71        82.59        20.61        87.06        77.65        20.12 
TCGA-02-0024 TCGA-02-0025 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0037 
       53.10        42.74        12.16        90.58         2.83         3.62 
TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 TCGA-02-0048 
       10.72        10.52        18.31         6.87        14.73         3.22 
TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 TCGA-02-0057 TCGA-02-0058 TCGA-02-0059 
       15.09        12.59         6.54        19.86         8.35         9.57 
TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 TCGA-02-0069 TCGA-02-0070 TCGA-02-0071 
        6.02        19.73        26.43        28.70        25.05         5.49 
TCGA-02-0074 TCGA-02-0079 TCGA-02-0080 TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 
       10.19        27.25        89.72        22.72        12.62        51.32 
TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 TCGA-02-0106 TCGA-02-0107 
        8.81        57.76        16.96         3.48        11.67        17.65 
TCGA-02-0111 TCGA-02-0114 TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 
       23.18        99.98        15.65        48.95        16.54        16.93 
TCGA-02-0266 TCGA-02-0269 TCGA-02-0271 TCGA-02-0281 TCGA-02-0285 TCGA-02-0289 
       17.72        10.75        14.47         3.98        13.87        14.20 
TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 
       15.95        12.23         9.90         7.73        10.62         7.33 
TCGA-02-0330 TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 
       15.91        25.71         4.37        25.12        10.59        12.39 
TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 
       14.50        10.55        47.11        11.34         9.27        16.21 
TCGA-02-0456 TCGA-02-2466 TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 
        3.35        16.80        12.92        15.32        15.45        20.32 
TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 
        2.70         6.15        20.38        47.61         6.94         3.98 
TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 
       22.72        33.67        12.95        25.35        14.30        26.70 
TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 
       24.23        11.90         0.20        10.29         2.20        11.74 
TCGA-06-0145 TCGA-06-0146 TCGA-06-0148 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 
        2.33        20.09        10.09        19.46        46.59        12.33 
TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0160 TCGA-06-0162 
       13.94        10.45         3.19        10.82        11.80         3.42 
TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 
       56.91        10.65         5.85        19.66         3.29        13.12 
TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0178 TCGA-06-0179 
        4.47         3.22         4.04        91.00        88.14        20.25 
TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0192 
       69.90        73.84        27.22        44.58        15.42        38.96 
TCGA-06-0194 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 
        4.67         0.39         7.66         8.42         7.63         7.40 
TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0238 
       11.84         0.53        15.02        24.16         0.72        13.32 
TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 
       20.42        48.69        10.82         9.01         0.26        72.36 
TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 
        4.70         9.57         3.16        12.62         5.75         5.75 
TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 
        9.80         2.10        23.57        26.40        46.88         7.86 
TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 
        2.70         2.70         0.92        43.46        46.19         5.65 
TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 
        7.17        40.41        16.57        20.78        26.76        23.93 
TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 
        6.84         4.04        26.79        11.84        15.32        13.61 
TCGA-06-1805 TCGA-06-1806 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 
       33.90        15.32         1.08        12.49         4.93        17.65 
TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 
       12.56        30.64         5.95        16.64         5.98         4.37 
TCGA-06-2569 TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 
        0.43        31.50        11.74         3.55         8.35         4.54 
TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 TCGA-06-5418 TCGA-06-5858 
        8.81         8.98         8.55         6.71         2.73         6.15 
TCGA-06-5859 TCGA-06-6388 TCGA-06-6389 TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 
        4.57         5.23         7.79         1.48       120.56         7.36 
TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 
        8.32        12.85         4.77         1.55         4.77         4.96 
TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK TCGA-06-A7TL 
        4.70         1.87         3.12         2.56         5.39         5.42 
TCGA-08-0244 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 
       22.68         4.18       115.86         1.74         8.42        25.71 
TCGA-08-0348 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 
       12.16        29.23        65.33         1.28         8.42        17.95 
TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 
       24.56        31.10        37.58        22.29         3.39        12.23 
TCGA-08-0380 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0512 
       14.93        15.35        13.97         0.72        12.56        42.15 
TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 
       19.59        58.68        19.33        10.75         4.80         7.27 
TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 
       15.98        18.41         7.56        15.35        14.73        12.99 
TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0688 
       10.45         7.59        94.78         0.10        38.17        26.66 
TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 
       12.13         3.65        20.38        28.41        15.06        53.85 
TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 
       43.23         7.63         9.73        14.93        14.86        91.76 
TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 TCGA-12-0826 TCGA-12-0827 
       24.79        18.48        10.62        23.51        27.78        38.76 
TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 
        8.94        20.58       127.59         5.82         7.59        33.21 
TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 
       21.73        15.98        12.23        15.85         9.11        14.53 
TCGA-12-1098 TCGA-12-1099 TCGA-12-1598 TCGA-12-1599 TCGA-12-3644 TCGA-12-3648 
        3.98         4.14        15.65        25.68        59.77        26.93 
TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 
       15.22        10.95        12.69        34.92        14.53        14.93 
TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 TCGA-14-0786 
        3.22         2.04        15.12        11.97         0.95        23.05 
TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 TCGA-14-0812 TCGA-14-0813 TCGA-14-0862 
        2.24        11.24        13.78         3.25         1.35         2.89 
TCGA-14-0865 TCGA-14-0866 TCGA-14-1034 TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 
       16.50        26.33        15.95        19.30         0.79         1.38 
TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1452 TCGA-14-1453 
        1.12         3.75        32.05        58.78         7.10         1.15 
TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 TCGA-14-1795 
       30.18         0.92        40.96         6.67        12.43         1.97 
TCGA-14-1821 TCGA-14-1823 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 
       17.79        17.85         7.63         5.88         7.17        17.49 
TCGA-14-2555 TCGA-14-4157 TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 
        7.96         3.42        13.78        50.53        19.10        53.19 
TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 
       13.28         3.91        17.59         4.31        29.03         4.57 
TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 
       14.01         9.14        21.24        13.97         6.41        11.77 
TCGA-19-0957 TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 TCGA-19-1386 TCGA-19-1387 
       21.90         0.66        14.27         3.39         9.07         5.95 
TCGA-19-1389 TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 
        4.64         3.65         7.17        12.66         3.25         0.13 
TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 
        9.67         4.87         1.08         4.08        24.23         7.00 
TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 
        6.64        17.19         8.02        18.90         4.73        12.10 
TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-A60I TCGA-19-A6J4 
        1.78        22.49        14.07        16.80        17.79         3.98 
TCGA-19-A6J5 TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 
       28.54        13.87         9.73        31.33         7.13         9.37 
TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 
       14.86         5.49         8.88         1.58         7.92         2.33 
TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 
       19.33         5.06        16.60         9.86        24.23        40.54 
TCGA-27-1835 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 
       21.30        14.04        11.51        24.76        10.39        10.39 
TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1746 
       16.08         7.59         2.86        14.40        15.78         0.20 
TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 
        2.53         9.21         8.35         7.63         8.48         1.22 
TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 TCGA-28-2502 TCGA-28-2506 TCGA-28-2509 
        1.55         2.83         0.13         0.66         6.74         4.77 
TCGA-28-2513 TCGA-28-2514 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 
        7.30         5.26        11.28        17.88        14.53        11.77 
TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 
       31.27        23.44        11.01        13.64         5.16        22.68 
TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 
       12.76         5.42        15.39        21.07         0.49         0.10 
TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 TCGA-32-1991 
       19.50         1.18         4.67        12.69        14.86        16.93 
TCGA-32-2491 TCGA-32-2495 TCGA-32-2615 TCGA-32-2616 TCGA-32-2632 TCGA-32-2634 
       12.23        15.02        15.95         7.36         8.84        22.78 
TCGA-32-2638 TCGA-32-4208 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 
       25.18        21.14        12.59        19.86        10.85        19.23 
TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 
        0.85        13.35         8.94         9.53         0.99         4.44 
TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9S TCGA-4W-AA9T 
       11.84         0.20        15.12        12.46         4.14        14.76 
TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 
        3.45        20.91         4.34        14.33         8.22         7.50 
TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-4934 
        4.80         4.54         3.09         3.65         9.17         2.53 
TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 
       10.78        16.70         3.29        11.38        17.06         8.35 
TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 
       20.98         4.83         5.03         0.23         9.27         7.73 
TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R TCGA-RR-A6KA 
        7.79         1.61        17.72        26.30         5.92         6.28 
TCGA-RR-A6KC 
       20.55 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              0.16               0.10 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             92.65             127.59 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
            12.015             11.840 
[1] "0.2 - 92.7 (12.0)"  "0.1 - 127.6 (11.8)"
[1] "hr=" "1"  
D64V2, continuous
D64V3, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    20  38
  12P LOSS WILD-TYPE 204 308
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     20   38
  12P LOSS WILD-TYPE  204  308
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE               20                204
  MALE                 38                308
[1] 2 2
[1] FALSE
D64V4, continuous
                    vv
clus                 GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  12P LOSS MUTATED                               1                   2
  12P LOSS WILD-TYPE                            26                  16
                    vv
clus                 UNTREATED PRIMARY (DE NOVO) GBM
  12P LOSS MUTATED                                55
  12P LOSS WILD-TYPE                             470
D64V5, multiclass
                                 clus
vv                                12P LOSS MUTATED 12P LOSS WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                  1                 26
  TREATED PRIMARY GBM                            2                 16
  UNTREATED PRIMARY (DE NOVO) GBM               55                470
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V6, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    42  16
  12P LOSS WILD-TYPE 340 172
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     42   16
  12P LOSS WILD-TYPE  340  172
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  NO                42                340
  YES               16                172
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12P LOSS MUTATED       0                         2    53
  12P LOSS WILD-TYPE    13                        47   432
D64V7, multiclass
                           clus
vv                          12P LOSS MUTATED 12P LOSS WILD-TYPE
  ASIAN                                    0                 13
  BLACK OR AFRICAN AMERICAN                2                 47
  WHITE                                   53                432
[1] 3 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
  12P LOSS MUTATED     1  49
  12P LOSS WILD-TYPE  11 423
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      1   49
  12P LOSS WILD-TYPE   11  423
                        clus
vv                       12P LOSS MUTATED 12P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 11
  NOT HISPANIC OR LATINO               49                423
[1] 2 2
[1] FALSE

Clustering(65) Variable = 12Q LOSS MUTATION ANALYSIS
D65V1, survival
                    sevent
clus2                  0   1
  12Q LOSS MUTATED     9  48
  12Q LOSS WILD-TYPE  95 417
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                57                512 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                48                417 
$`12Q LOSS MUTATED`
TCGA-02-0034 TCGA-02-0055 TCGA-02-0075 TCGA-02-0084 TCGA-02-0102 TCGA-02-0113 
       14.14         2.50        20.84        12.62        27.02        92.65 
TCGA-02-2466 TCGA-06-0146 TCGA-06-0147 TCGA-06-0149 TCGA-06-0159 TCGA-06-0177 
       16.80        20.09        17.79         8.61         9.44         4.18 
TCGA-06-0182 TCGA-06-0184 TCGA-06-0190 TCGA-06-0197 TCGA-06-0221 TCGA-06-0237 
        3.65        69.90        10.42         5.56        19.82        13.64 
TCGA-06-0414 TCGA-06-0686 TCGA-06-5856 TCGA-06-6389 TCGA-06-6390 TCGA-08-0245 
       35.11        14.20         3.75         7.79         5.39        37.84 
TCGA-08-0349 TCGA-08-0386 TCGA-08-0510 TCGA-08-0514 TCGA-12-0619 TCGA-12-0670 
        9.80        18.02         4.27        11.08        34.92        25.97 
TCGA-12-1600 TCGA-12-1602 TCGA-12-3646 TCGA-14-0740 TCGA-14-0783 TCGA-14-0813 
       14.73         6.77        44.02        11.97         6.21         1.35 
TCGA-14-0817 TCGA-14-0867 TCGA-14-0871 TCGA-14-1451 TCGA-14-1794 TCGA-14-3477 
        5.39         2.04        28.93        23.11         0.99         3.78 
TCGA-15-1447 TCGA-16-0849 TCGA-16-0850 TCGA-19-1388 TCGA-19-1390 TCGA-19-2623 
       53.19        26.07        16.37        12.95        25.38         7.53 
TCGA-19-2624 TCGA-19-4065 TCGA-19-5960 TCGA-26-1438 TCGA-26-5132 TCGA-26-5136 
        0.16         7.04        14.96        10.03         9.40        18.97 
TCGA-32-1978 TCGA-32-4210 TCGA-76-6193 
       15.85         3.72         2.70 

$`12Q LOSS WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 
       11.77         4.73        18.35        23.18        10.59        35.41 
TCGA-02-0011 TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 
       20.71        82.59        20.61        87.06        77.65        20.12 
TCGA-02-0024 TCGA-02-0025 TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 
       53.10        42.74        24.59        12.16        90.58         2.83 
TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 
        3.62        10.72        10.52        18.31         6.87        14.73 
TCGA-02-0048 TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 TCGA-02-0057 TCGA-02-0058 
        3.22        15.09        12.59         6.54        19.86         8.35 
TCGA-02-0059 TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 TCGA-02-0069 TCGA-02-0070 
        9.57         6.02        19.73        26.43        28.70        25.05 
TCGA-02-0071 TCGA-02-0074 TCGA-02-0079 TCGA-02-0080 TCGA-02-0083 TCGA-02-0085 
        5.49        10.19        27.25        89.72        22.72        51.32 
TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 TCGA-02-0104 TCGA-02-0106 
        8.81        57.76        16.96         3.48        65.00        11.67 
TCGA-02-0107 TCGA-02-0111 TCGA-02-0114 TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 
       17.65        23.18        99.98        15.65        48.95        16.54 
TCGA-02-0260 TCGA-02-0266 TCGA-02-0269 TCGA-02-0271 TCGA-02-0281 TCGA-02-0285 
       16.93        17.72        10.75        14.47         3.98        13.87 
TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 
       14.20        15.95        12.23         9.90         7.73        10.62 
TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 
        7.33        15.91        25.71         4.37        25.12        10.59 
TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 
       12.39        14.50        10.55        47.11        11.34         9.27 
TCGA-02-0451 TCGA-02-0456 TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 
       16.21         3.35        12.92        15.32        15.45        20.32 
TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 
        2.70         6.15        20.38        47.61         6.94         3.98 
TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 
       22.72        33.67        12.95        25.35        14.30        26.70 
TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 
       24.23        11.90         0.20        10.29         2.20        11.74 
TCGA-06-0145 TCGA-06-0148 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 
        2.33        10.09        19.46        46.59        12.33        13.94 
TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 
       10.45         3.19        10.82        11.80         3.42        56.91 
TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 
       10.65         5.85        19.66         3.29        13.12         4.47 
TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0178 TCGA-06-0179 TCGA-06-0185 
        3.22         4.04        91.00        88.14        20.25        73.84 
TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 
       27.22        44.58        15.42        38.96         4.67         7.40 
TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 
        0.39         7.66         8.42         7.63         7.40        11.84 
TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0238 TCGA-06-0240 
        0.53        15.02        24.16         0.72        13.32        20.42 
TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 
       48.69        10.82         9.01         0.26        72.36         4.70 
TCGA-06-0412 TCGA-06-0413 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 
        9.57         3.16        12.62         5.75         5.75         9.80 
TCGA-06-0649 TCGA-06-0650 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 
        2.10        23.57        26.40        46.88         7.86         2.70 
TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 
        2.70         0.92        43.46        46.19         5.65         7.17 
TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 
       40.41        16.57        20.78        26.76        23.93         6.84 
TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 
        4.04        26.79        11.84        15.32        13.61        33.90 
TCGA-06-1806 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 
       15.32         1.08        12.49         4.93        17.65        12.56 
TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 
       30.64         5.95        16.64         5.98         4.37         0.43 
TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 
       31.50        11.74         3.55         8.35         4.54         8.81 
TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 TCGA-06-5418 TCGA-06-5858 TCGA-06-5859 
        8.98         8.55         6.71         2.73         6.15         4.57 
TCGA-06-6388 TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 
        5.23         1.48       120.56         7.36         8.32        12.85 
TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A5U1 
        4.77         1.55         4.77         4.96         4.70         1.87 
TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK TCGA-06-A7TL TCGA-08-0244 TCGA-08-0246 
        3.12         2.56         5.39         5.42        22.68         4.18 
TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0350 
      115.86         1.74         8.42        25.71        12.16        29.23 
TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 
       65.33         1.28         8.42        17.95        24.56        31.10 
TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0389 
       37.58        22.29         3.39        12.23        14.93        15.35 
TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0512 TCGA-08-0516 TCGA-08-0517 
       13.97         0.72        12.56        42.15        19.59        58.68 
TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 
       19.33        10.75         4.80         7.27        15.98        18.41 
TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0620 TCGA-12-0654 
        7.56        15.35        14.73        12.99        10.45         7.59 
TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 
       94.78         0.10        38.17        26.66        12.13         3.65 
TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 
       20.38        28.41        15.06        53.85        43.23         7.63 
TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 
        9.73        14.93        14.86        91.76        24.79        18.48 
TCGA-12-0821 TCGA-12-0822 TCGA-12-0826 TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 
       10.62        23.51        27.78        38.76         8.94        20.58 
TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 
      127.59         5.82         7.59        33.21        21.73        15.98 
TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 
       12.23        15.85         9.11        14.53         3.98         4.14 
TCGA-12-1598 TCGA-12-1599 TCGA-12-3644 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 
       15.65        25.68        59.77        26.93        15.22        10.95 
TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 
       12.69        34.92        14.53        14.93         3.22         2.04 
TCGA-14-0736 TCGA-14-0781 TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 
       15.12         0.95        23.05         2.24        11.24        13.78 
TCGA-14-0812 TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 TCGA-14-1034 TCGA-14-1037 
        3.25         2.89        16.50        26.33        15.95        19.30 
TCGA-14-1043 TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 
        0.79         1.38         1.12         3.75        32.05        58.78 
TCGA-14-1452 TCGA-14-1453 TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 
        7.10         1.15        30.18         0.92        40.96         6.67 
TCGA-14-1459 TCGA-14-1795 TCGA-14-1821 TCGA-14-1823 TCGA-14-1825 TCGA-14-1827 
       12.43         1.97        17.79        17.85         7.63         5.88 
TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-4157 TCGA-15-0742 TCGA-15-1444 
        7.17        17.49         7.96         3.42        13.78        50.53 
TCGA-15-1446 TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 TCGA-16-0861 TCGA-16-1045 
       19.10        13.28         3.91        17.59         4.31        29.03 
TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 
        4.57        10.29        14.01         9.14        21.24        13.97 
TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 TCGA-19-0962 TCGA-19-0963 
        6.41        11.77        21.90         8.61         0.66        14.27 
TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 TCGA-19-1389 TCGA-19-1392 
        3.39        10.75         9.07         5.95         4.64         3.65 
TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 
        7.17        12.66         3.25         0.13         9.67         4.87 
TCGA-19-2621 TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-5947 TCGA-19-5950 
        1.08         4.08        24.23         7.00         6.64        17.19 
TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 
        8.02        18.90         4.73        12.10         1.78        22.49 
TCGA-19-5958 TCGA-19-5959 TCGA-19-A60I TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1439 
       14.07        16.80        17.79         3.98        28.54        13.87 
TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 TCGA-26-5133 TCGA-26-5134 
        9.73        31.33         7.13         9.37        14.86         5.49 
TCGA-26-5135 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-26-A7UX TCGA-27-1830 
        8.88         1.58         7.92         2.33        19.33         5.06 
TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 
       16.60         9.86        24.23        40.54        21.30        30.05 
TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 
       14.04        11.51        24.76        10.39        10.39        16.08 
TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 
        7.59         2.86        14.40        15.78         0.20         2.53 
TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 TCGA-28-1755 
        9.21         8.35         7.63         8.48         1.22         1.55 
TCGA-28-1756 TCGA-28-1757 TCGA-28-2502 TCGA-28-2506 TCGA-28-2509 TCGA-28-2513 
        2.83         0.13         0.66         6.74         4.77         7.30 
TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 
        5.26        14.93        11.28        17.88        14.53        11.77 
TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 
       31.27        23.44        11.01        13.64         5.16        22.68 
TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 
       12.76         5.42        15.39        21.07         0.49         0.10 
TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 TCGA-32-1991 
       19.50         1.18         4.67        12.69        14.86        16.93 
TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 TCGA-32-2616 TCGA-32-2632 
       12.23        20.78        15.02        15.95         7.36         8.84 
TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 
       22.78        25.18        21.14        12.59        19.86        10.85 
TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 
       19.23         0.85        13.35         8.94         9.53         0.99 
TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9S 
        4.44        11.84         0.20        15.12        12.46         4.14 
TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 
       14.76         3.45        20.91         4.34        14.33         8.22 
TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 
        7.50         4.80         4.54         3.09         3.65         9.17 
TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6280 TCGA-76-6282 
        2.53        10.78        16.70         3.29        11.38        17.06 
TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 
        8.35        20.98         4.83         5.03         0.23         9.27 
TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R 
        7.73         7.79         1.61        17.72        26.30         5.92 
TCGA-RR-A6KA TCGA-RR-A6KC 
        6.28        20.55 

  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
              0.16               0.10 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             92.65             127.59 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             12.62              11.84 
[1] "0.2 - 92.7 (12.6)"  "0.1 - 127.6 (11.8)"
[1] "hr=" "1"  
D65V2, continuous
D65V3, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    20  37
  12Q LOSS WILD-TYPE 204 309
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     20   37
  12Q LOSS WILD-TYPE  204  309
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FEMALE               20                204
  MALE                 37                309
[1] 2 2
[1] FALSE
D65V4, continuous
                    vv
clus                 GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  12Q LOSS MUTATED                               1                   3
  12Q LOSS WILD-TYPE                            26                  15
                    vv
clus                 UNTREATED PRIMARY (DE NOVO) GBM
  12Q LOSS MUTATED                                53
  12Q LOSS WILD-TYPE                             472
D65V5, multiclass
                                 clus
vv                                12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                  1                 26
  TREATED PRIMARY GBM                            3                 15
  UNTREATED PRIMARY (DE NOVO) GBM               53                472
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V6, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    39  18
  12Q LOSS WILD-TYPE 343 170
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     39   18
  12Q LOSS WILD-TYPE  343  170
     clus
vv    12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  NO                39                343
  YES               18                170
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12Q LOSS MUTATED       0                         2    52
  12Q LOSS WILD-TYPE    13                        47   433
D65V7, multiclass
                           clus
vv                          12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  ASIAN                                    0                 13
  BLACK OR AFRICAN AMERICAN                2                 47
  WHITE                                   52                433
[1] 3 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
  12Q LOSS MUTATED     2  45
  12Q LOSS WILD-TYPE  10 427
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      2   45
  12Q LOSS WILD-TYPE   10  427
                        clus
vv                       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                 10
  NOT HISPANIC OR LATINO               45                427
[1] 2 2
[1] FALSE

Clustering(66) Variable = 13Q LOSS MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                  0   1
  13Q LOSS MUTATED    35 149
  13Q LOSS WILD-TYPE  69 316
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               184                385 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               149                316 
$`13Q LOSS MUTATED`
TCGA-02-0006 TCGA-02-0007 TCGA-02-0010 TCGA-02-0011 TCGA-02-0033 TCGA-02-0034 
       18.35        23.18        35.41        20.71         2.83        14.14 
TCGA-02-0039 TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 TCGA-02-0055 TCGA-02-0059 
       10.52        15.09        12.59         6.54         2.50         9.57 
TCGA-02-0064 TCGA-02-0068 TCGA-02-0069 TCGA-02-0075 TCGA-02-0079 TCGA-02-0099 
       19.73        26.43        28.70        20.84        27.25         3.48 
TCGA-02-0106 TCGA-02-0113 TCGA-02-0115 TCGA-02-0325 TCGA-02-0330 TCGA-02-0339 
       11.67        92.65        15.65        10.62        15.91        12.39 
TCGA-02-0440 TCGA-02-0446 TCGA-02-0456 TCGA-02-2483 TCGA-06-0122 TCGA-06-0128 
       11.34         9.27         3.35        15.32         6.15        22.72 
TCGA-06-0130 TCGA-06-0138 TCGA-06-0140 TCGA-06-0147 TCGA-06-0149 TCGA-06-0152 
       12.95        24.23         0.20        17.79         8.61        12.33 
TCGA-06-0158 TCGA-06-0159 TCGA-06-0162 TCGA-06-0164 TCGA-06-0166 TCGA-06-0168 
       10.82         9.44         3.42        56.91         5.85        19.66 
TCGA-06-0177 TCGA-06-0182 TCGA-06-0184 TCGA-06-0188 TCGA-06-0192 TCGA-06-0195 
        4.18         3.65        69.90        44.58        38.96         7.40 
TCGA-06-0197 TCGA-06-0206 TCGA-06-0209 TCGA-06-0214 TCGA-06-0219 TCGA-06-0402 
        5.56         7.66         7.63        15.02         0.72         0.26 
TCGA-06-0410 TCGA-06-0414 TCGA-06-0648 TCGA-06-0649 TCGA-06-0745 TCGA-06-0875 
        4.70        35.11         9.80         2.10         7.86        43.46 
TCGA-06-0881 TCGA-06-1087 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 
       16.57         4.04        15.32        13.61        33.90        15.32 
TCGA-06-2557 TCGA-06-2558 TCGA-06-2567 TCGA-06-5408 TCGA-06-5412 TCGA-06-5414 
        1.08        12.49         4.37        11.74         4.54         8.98 
TCGA-06-5416 TCGA-06-5856 TCGA-06-5859 TCGA-06-6389 TCGA-06-6694 TCGA-06-A7TK 
        6.71         3.75         4.57         7.79         7.36         5.39 
TCGA-08-0245 TCGA-08-0246 TCGA-08-0347 TCGA-08-0349 TCGA-08-0354 TCGA-08-0359 
       37.84         4.18        25.71         9.80        17.95         3.39 
TCGA-08-0389 TCGA-08-0392 TCGA-08-0510 TCGA-08-0512 TCGA-08-0516 TCGA-08-0517 
       15.35         0.72         4.27        42.15        19.59        58.68 
TCGA-08-0520 TCGA-12-0615 TCGA-12-0662 TCGA-12-0691 TCGA-12-0769 TCGA-12-0772 
       10.75        15.35        38.17        12.13        15.06        53.85 
TCGA-12-0776 TCGA-12-0819 TCGA-12-0826 TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 
        9.73        24.79        27.78        38.76         8.94        20.58 
TCGA-12-1088 TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1096 
      127.59        33.21        21.73        15.98        12.23         9.11 
TCGA-12-1097 TCGA-12-1099 TCGA-12-1598 TCGA-12-3644 TCGA-12-3646 TCGA-12-3653 
       14.53         4.14        15.65        59.77        44.02        14.53 
TCGA-12-5295 TCGA-14-0736 TCGA-14-0740 TCGA-14-0783 TCGA-14-0787 TCGA-14-0812 
       14.93        15.12        11.97         6.21         2.24         3.25 
TCGA-14-0862 TCGA-14-0865 TCGA-14-1034 TCGA-14-1396 TCGA-14-1451 TCGA-14-1453 
        2.89        16.50        15.95         1.12        23.11         1.15 
TCGA-14-1454 TCGA-14-1456 TCGA-14-1458 TCGA-14-1823 TCGA-14-1825 TCGA-14-3477 
       30.18        40.96         6.67        17.85         7.63         3.78 
TCGA-15-0742 TCGA-15-1444 TCGA-15-1447 TCGA-15-1449 TCGA-16-0846 TCGA-16-0849 
       13.78        50.53        53.19        13.28         3.91        26.07 
TCGA-16-0850 TCGA-16-1045 TCGA-19-1385 TCGA-19-1387 TCGA-19-1392 TCGA-19-2621 
       16.37        29.03        10.75         5.95         3.65         1.08 
TCGA-19-2625 TCGA-19-2629 TCGA-19-4065 TCGA-19-5947 TCGA-19-A60I TCGA-26-1439 
        4.08        24.23         7.04         6.64        17.79        13.87 
TCGA-26-5133 TCGA-26-6173 TCGA-27-1830 TCGA-27-1834 TCGA-27-2519 TCGA-27-2521 
       14.86         7.92         5.06        40.54        10.39        10.39 
TCGA-28-1746 TCGA-28-1750 TCGA-28-1752 TCGA-28-2502 TCGA-28-2509 TCGA-28-5215 
        0.20         8.35         8.48         0.66         4.77        11.01 
TCGA-28-5216 TCGA-28-5219 TCGA-32-1976 TCGA-32-1987 TCGA-32-2616 TCGA-32-2634 
       13.64        22.68         0.49        14.86         7.36        22.78 
TCGA-32-4210 TCGA-32-4719 TCGA-41-2573 TCGA-41-3392 TCGA-41-3915 TCGA-41-4097 
        3.72        10.85         8.94         0.99        11.84         0.20 
TCGA-4W-AA9S TCGA-74-6584 TCGA-76-4929 TCGA-76-4934 TCGA-76-4935 TCGA-76-6193 
        4.14         7.50         3.65         2.53        10.78         2.70 
TCGA-76-6285 TCGA-76-6286 TCGA-76-6661 TCGA-81-5911 
        8.35        20.98         0.23        17.72 

$`13Q LOSS WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0009 TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 
       11.77         4.73        10.59        82.59        20.61        87.06 
TCGA-02-0021 TCGA-02-0023 TCGA-02-0024 TCGA-02-0025 TCGA-02-0026 TCGA-02-0027 
       77.65        20.12        53.10        42.74        24.59        12.16 
TCGA-02-0028 TCGA-02-0037 TCGA-02-0038 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 
       90.58         3.62        10.72        18.31         6.87        14.73 
TCGA-02-0048 TCGA-02-0057 TCGA-02-0058 TCGA-02-0060 TCGA-02-0070 TCGA-02-0071 
        3.22        19.86         8.35         6.02        25.05         5.49 
TCGA-02-0074 TCGA-02-0080 TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 TCGA-02-0086 
       10.19        89.72        22.72        12.62        51.32         8.81 
TCGA-02-0087 TCGA-02-0089 TCGA-02-0102 TCGA-02-0104 TCGA-02-0107 TCGA-02-0111 
       57.76        16.96        27.02        65.00        17.65        23.18 
TCGA-02-0114 TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 TCGA-02-0266 TCGA-02-0269 
       99.98        48.95        16.54        16.93        17.72        10.75 
TCGA-02-0271 TCGA-02-0281 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 
       14.47         3.98        13.87        14.20        15.95        12.23 
TCGA-02-0321 TCGA-02-0324 TCGA-02-0326 TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 
        9.90         7.73         7.33        25.71         4.37        25.12 
TCGA-02-0338 TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 TCGA-02-0451 TCGA-02-2466 
       10.59        14.50        10.55        47.11        16.21        16.80 
TCGA-02-2470 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0124 TCGA-06-0125 
       12.92        15.45        20.32         2.70        20.38        47.61 
TCGA-06-0126 TCGA-06-0127 TCGA-06-0129 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 
        6.94         3.98        33.67        25.35        14.30        26.70 
TCGA-06-0139 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 
       11.90        10.29         2.20        11.74         2.33        20.09 
TCGA-06-0148 TCGA-06-0150 TCGA-06-0151 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 
       10.09        19.46        46.59        13.94        10.45         3.19 
TCGA-06-0160 TCGA-06-0165 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 
       11.80        10.65         3.29        13.12         4.47         3.22 
TCGA-06-0175 TCGA-06-0176 TCGA-06-0178 TCGA-06-0179 TCGA-06-0185 TCGA-06-0187 
        4.04        91.00        88.14        20.25        73.84        27.22 
TCGA-06-0189 TCGA-06-0190 TCGA-06-0194 TCGA-06-0201 TCGA-06-0208 TCGA-06-0210 
       15.42        10.42         4.67         0.39         8.42         7.40 
TCGA-06-0211 TCGA-06-0213 TCGA-06-0216 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 
       11.84         0.53        24.16        19.82        13.64        13.32 
TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0409 TCGA-06-0412 
       20.42        48.69        10.82         9.01        72.36         9.57 
TCGA-06-0413 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0650 TCGA-06-0686 
        3.16        12.62         5.75         5.75        23.57        14.20 
TCGA-06-0743 TCGA-06-0744 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0876 
       26.40        46.88         2.70         2.70         0.92        46.19 
TCGA-06-0877 TCGA-06-0878 TCGA-06-0879 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 
        5.65         7.17        40.41        20.78        26.76        23.93 
TCGA-06-1086 TCGA-06-1800 TCGA-06-1801 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 
        6.84        26.79        11.84         4.93        17.65        12.56 
TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2569 TCGA-06-2570 
       30.64         5.95        16.64         5.98         0.43        31.50 
TCGA-06-5410 TCGA-06-5411 TCGA-06-5413 TCGA-06-5415 TCGA-06-5418 TCGA-06-5858 
        3.55         8.35         8.81         8.55         2.73         6.15 
TCGA-06-6388 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6695 TCGA-06-6697 
        5.23         5.39         1.48       120.56         8.32        12.85 
TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A5U1 
        4.77         1.55         4.77         4.96         4.70         1.87 
TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TL TCGA-08-0244 TCGA-08-0344 TCGA-08-0345 
        3.12         2.56         5.42        22.68       115.86         1.74 
TCGA-08-0346 TCGA-08-0348 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 
        8.42        12.16        29.23        65.33         1.28         8.42 
TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0375 TCGA-08-0380 
       24.56        31.10        37.58        22.29        12.23        14.93 
TCGA-08-0386 TCGA-08-0390 TCGA-08-0509 TCGA-08-0514 TCGA-08-0518 TCGA-08-0521 
       18.02        13.97        12.56        11.08        19.33         4.80 
TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0616 TCGA-12-0618 
        7.27        15.98        18.41         7.56        14.73        12.99 
TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0670 
       34.92        10.45         7.59        94.78         0.10        25.97 
TCGA-12-0688 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0773 TCGA-12-0775 
       26.66         3.65        20.38        28.41        43.23         7.63 
TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 
       14.93        14.86        91.76        18.48        10.62        23.51 
TCGA-12-1089 TCGA-12-1090 TCGA-12-1095 TCGA-12-1098 TCGA-12-1599 TCGA-12-1600 
        5.82         7.59        15.85         3.98        25.68        14.73 
TCGA-12-1602 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 
        6.77        26.93        15.22        10.95        12.69        34.92 
TCGA-12-5299 TCGA-12-5301 TCGA-14-0781 TCGA-14-0786 TCGA-14-0789 TCGA-14-0790 
        3.22         2.04         0.95        23.05        11.24        13.78 
TCGA-14-0813 TCGA-14-0817 TCGA-14-0866 TCGA-14-0867 TCGA-14-0871 TCGA-14-1037 
        1.35         5.39        26.33         2.04        28.93        19.30 
TCGA-14-1043 TCGA-14-1395 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1452 
        0.79         1.38         3.75        32.05        58.78         7.10 
TCGA-14-1455 TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 TCGA-14-1827 
        0.92        12.43         0.99         1.97        17.79         5.88 
TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-4157 TCGA-15-1446 TCGA-16-0848 
        7.17        17.49         7.96         3.42        19.10        17.59 
TCGA-16-0861 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 
        4.31         4.57        10.29        14.01         9.14        21.24 
TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 TCGA-19-0962 
       13.97         6.41        11.77        21.90         8.61         0.66 
TCGA-19-0963 TCGA-19-0964 TCGA-19-1386 TCGA-19-1388 TCGA-19-1389 TCGA-19-1390 
       14.27         3.39         9.07        12.95         4.64        25.38 
TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 
        7.17        12.66         3.25         0.13         9.67         4.87 
TCGA-19-2623 TCGA-19-2624 TCGA-19-2631 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 
        7.53         0.16         7.00        17.19         8.02        18.90 
TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 
        4.73        12.10         1.78        22.49        14.07        16.80 
TCGA-19-5960 TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1440 TCGA-26-1442 
       14.96         3.98        28.54        10.03         9.73        31.33 
TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 
        7.13         9.37         9.40         5.49         8.88        18.97 
TCGA-26-5139 TCGA-26-6174 TCGA-26-A7UX TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 
        1.58         2.33        19.33        16.60         9.86        24.23 
TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2523 
       21.30        30.05        14.04        11.51        24.76        16.08 
TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1747 TCGA-28-1749 
        7.59         2.86        14.40        15.78         2.53         9.21 
TCGA-28-1751 TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 TCGA-28-2506 
        7.63         1.22         1.55         2.83         0.13         6.74 
TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 
        7.30         5.26        14.93        11.28        17.88        14.53 
TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5218 TCGA-28-5220 TCGA-28-6450 
       11.77        31.27        23.44         5.16        12.76         5.42 
TCGA-32-1970 TCGA-32-1973 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 TCGA-32-1980 
       15.39        21.07         0.10        15.85        19.50         1.18 
TCGA-32-1982 TCGA-32-1986 TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 
        4.67        12.69        16.93        12.23        20.78        15.02 
TCGA-32-2615 TCGA-32-2632 TCGA-32-2638 TCGA-32-4208 TCGA-32-4211 TCGA-32-4213 
       15.95         8.84        25.18        21.14        12.59        19.86 
TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2575 TCGA-41-3393 TCGA-41-5651 
       19.23         0.85        13.35         9.53         4.44        15.12 
TCGA-41-6646 TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 
       12.46        14.76         3.45        20.91         4.34        14.33 
TCGA-74-6581 TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4931 TCGA-76-6191 
        8.22         4.80         4.54         3.09         9.17        16.70 
TCGA-76-6192 TCGA-76-6280 TCGA-76-6282 TCGA-76-6656 TCGA-76-6657 TCGA-76-6662 
        3.29        11.38        17.06         4.83         5.03         9.27 
TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-87-5896 TCGA-OX-A56R TCGA-RR-A6KA 
        7.73         7.79         1.61        26.30         5.92         6.28 
TCGA-RR-A6KC 
       20.55 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               0.2                0.1 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            127.59             120.56 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            11.505             12.160 
[1] "0.2 - 127.6 (11.5)" "0.1 - 120.6 (12.2)"
[1] "hr=" "1"  
D66V2, continuous
D66V3, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    72 112
  13Q LOSS WILD-TYPE 152 234
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     72  112
  13Q LOSS WILD-TYPE  152  234
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE               72                152
  MALE                112                234
[1] 2 2
[1] FALSE
D66V4, continuous
                    vv
clus                 GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  13Q LOSS MUTATED                               7                   4
  13Q LOSS WILD-TYPE                            20                  14
                    vv
clus                 UNTREATED PRIMARY (DE NOVO) GBM
  13Q LOSS MUTATED                               173
  13Q LOSS WILD-TYPE                             352
D66V5, multiclass
                                 clus
vv                                13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                  7                 20
  TREATED PRIMARY GBM                            4                 14
  UNTREATED PRIMARY (DE NOVO) GBM              173                352
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V6, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED   121  63
  13Q LOSS WILD-TYPE 261 125
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED    121   63
  13Q LOSS WILD-TYPE  261  125
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  NO               121                261
  YES               63                125
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  13Q LOSS MUTATED       5                        12   161
  13Q LOSS WILD-TYPE     8                        37   324
D66V7, multiclass
                           clus
vv                          13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  ASIAN                                    5                  8
  BLACK OR AFRICAN AMERICAN               12                 37
  WHITE                                  161                324
[1] 3 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
  13Q LOSS MUTATED     3 153
  13Q LOSS WILD-TYPE   9 319
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      3  153
  13Q LOSS WILD-TYPE    9  319
                        clus
vv                       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  9
  NOT HISPANIC OR LATINO              153                319
[1] 2 2
[1] FALSE

Clustering(67) Variable = 14Q LOSS MUTATION ANALYSIS
D67V1, survival
                    sevent
clus2                  0   1
  14Q LOSS MUTATED    30 115
  14Q LOSS WILD-TYPE  74 350
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               145                424 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               115                350 
$`14Q LOSS MUTATED`
TCGA-02-0007 TCGA-02-0010 TCGA-02-0011 TCGA-02-0016 TCGA-02-0024 TCGA-02-0025 
       23.18        35.41        20.71        87.06        53.10        42.74 
TCGA-02-0034 TCGA-02-0039 TCGA-02-0047 TCGA-02-0048 TCGA-02-0051 TCGA-02-0055 
       14.14        10.52        14.73         3.22        15.09         2.50 
TCGA-02-0060 TCGA-02-0074 TCGA-02-0086 TCGA-02-0099 TCGA-02-0107 TCGA-02-0113 
        6.02        10.19         8.81         3.48        17.65        92.65 
TCGA-02-0281 TCGA-02-0324 TCGA-02-0325 TCGA-02-0330 TCGA-02-0332 TCGA-02-0446 
        3.98         7.73        10.62        15.91        25.71         9.27 
TCGA-02-0456 TCGA-02-2466 TCGA-02-2483 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 
        3.35        16.80        15.32        22.72        33.67        12.95 
TCGA-06-0138 TCGA-06-0141 TCGA-06-0143 TCGA-06-0146 TCGA-06-0162 TCGA-06-0166 
       24.23        10.29        11.74        20.09         3.42         5.85 
TCGA-06-0171 TCGA-06-0188 TCGA-06-0194 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 
       13.12        44.58         4.67        24.16         0.72        19.82 
TCGA-06-0241 TCGA-06-0409 TCGA-06-0410 TCGA-06-0644 TCGA-06-0646 TCGA-06-0649 
       48.69        72.36         4.70        12.62         5.75         2.10 
TCGA-06-0745 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0878 
        7.86         2.70         0.92        43.46        46.19         7.17 
TCGA-06-1084 TCGA-06-2561 TCGA-06-5411 TCGA-06-5416 TCGA-06-5856 TCGA-06-5859 
       23.93        17.65         8.35         6.71         3.75         4.57 
TCGA-06-6389 TCGA-06-6390 TCGA-06-6697 TCGA-06-6699 TCGA-06-A5U1 TCGA-06-A6S1 
        7.79         5.39        12.85         1.55         1.87         2.56 
TCGA-06-A7TL TCGA-08-0245 TCGA-08-0380 TCGA-08-0390 TCGA-08-0392 TCGA-08-0512 
        5.42        37.84        14.93        13.97         0.72        42.15 
TCGA-08-0520 TCGA-12-0615 TCGA-12-0616 TCGA-12-0654 TCGA-12-0662 TCGA-12-0692 
       10.75        15.35        14.73         7.59        38.17         3.65 
TCGA-12-0821 TCGA-12-0827 TCGA-12-1088 TCGA-12-1089 TCGA-12-1091 TCGA-12-1092 
       10.62        38.76       127.59         5.82        33.21        21.73 
TCGA-12-1096 TCGA-12-1598 TCGA-12-1602 TCGA-12-3653 TCGA-12-5295 TCGA-14-0736 
        9.11        15.65         6.77        14.53        14.93        15.12 
TCGA-14-0783 TCGA-14-0813 TCGA-14-0817 TCGA-14-0862 TCGA-14-0865 TCGA-14-1396 
        6.21         1.35         5.39         2.89        16.50         1.12 
TCGA-14-1455 TCGA-14-1823 TCGA-14-1829 TCGA-14-3477 TCGA-15-1447 TCGA-16-0861 
        0.92        17.85         7.17         3.78        53.19         4.31 
TCGA-16-1045 TCGA-19-1389 TCGA-19-1390 TCGA-19-1791 TCGA-19-2623 TCGA-19-2629 
       29.03         4.64        25.38         0.13         7.53        24.23 
TCGA-19-5947 TCGA-19-5956 TCGA-19-5960 TCGA-19-A6J4 TCGA-26-1439 TCGA-26-1440 
        6.64        22.49        14.96         3.98        13.87         9.73 
TCGA-26-5133 TCGA-26-5134 TCGA-27-1832 TCGA-27-1834 TCGA-27-2519 TCGA-27-2527 
       14.86         5.49         9.86        40.54        10.39        14.40 
TCGA-28-1750 TCGA-28-1756 TCGA-28-2506 TCGA-28-2509 TCGA-28-2514 TCGA-28-5207 
        8.35         2.83         6.74         4.77         5.26        11.28 
TCGA-28-5213 TCGA-28-5215 TCGA-28-5216 TCGA-28-5220 TCGA-32-1976 TCGA-32-1980 
       31.27        11.01        13.64        12.76         0.49         1.18 
TCGA-32-2615 TCGA-32-2634 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-4097 
       15.95        22.78         8.94         9.53         0.99         0.20 
TCGA-76-4928 TCGA-76-4929 TCGA-76-4934 TCGA-76-6193 TCGA-76-6282 TCGA-76-6285 
        3.09         3.65         2.53         2.70        17.06         8.35 
TCGA-OX-A56R 
        5.92 

$`14Q LOSS WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0009 TCGA-02-0014 TCGA-02-0015 
       11.77         4.73        18.35        10.59        82.59        20.61 
TCGA-02-0021 TCGA-02-0023 TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 
       77.65        20.12        24.59        12.16        90.58         2.83 
TCGA-02-0037 TCGA-02-0038 TCGA-02-0043 TCGA-02-0046 TCGA-02-0052 TCGA-02-0054 
        3.62        10.72        18.31         6.87        12.59         6.54 
TCGA-02-0057 TCGA-02-0058 TCGA-02-0059 TCGA-02-0064 TCGA-02-0068 TCGA-02-0069 
       19.86         8.35         9.57        19.73        26.43        28.70 
TCGA-02-0070 TCGA-02-0071 TCGA-02-0075 TCGA-02-0079 TCGA-02-0080 TCGA-02-0083 
       25.05         5.49        20.84        27.25        89.72        22.72 
TCGA-02-0084 TCGA-02-0085 TCGA-02-0087 TCGA-02-0089 TCGA-02-0102 TCGA-02-0104 
       12.62        51.32        57.76        16.96        27.02        65.00 
TCGA-02-0106 TCGA-02-0111 TCGA-02-0114 TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 
       11.67        23.18        99.98        15.65        48.95        16.54 
TCGA-02-0260 TCGA-02-0266 TCGA-02-0269 TCGA-02-0271 TCGA-02-0285 TCGA-02-0289 
       16.93        17.72        10.75        14.47        13.87        14.20 
TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 TCGA-02-0326 TCGA-02-0333 TCGA-02-0337 
       15.95        12.23         9.90         7.33         4.37        25.12 
TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 
       10.59        12.39        14.50        10.55        47.11        11.34 
TCGA-02-0451 TCGA-02-2470 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 
       16.21        12.92        15.45        20.32         2.70         6.15 
TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0132 TCGA-06-0133 
       20.38        47.61         6.94         3.98        25.35        14.30 
TCGA-06-0137 TCGA-06-0139 TCGA-06-0140 TCGA-06-0142 TCGA-06-0145 TCGA-06-0147 
       26.70        11.90         0.20         2.20         2.33        17.79 
TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 
       10.09         8.61        19.46        46.59        12.33        13.94 
TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0164 
       10.45         3.19        10.82         9.44        11.80        56.91 
TCGA-06-0165 TCGA-06-0168 TCGA-06-0169 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 
       10.65        19.66         3.29         4.47         3.22         4.04 
TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 
       91.00         4.18        88.14        20.25         3.65        69.90 
TCGA-06-0185 TCGA-06-0187 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0195 
       73.84        27.22        15.42        10.42        38.96         7.40 
TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 
        5.56         0.39         7.66         8.42         7.63         7.40 
TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 
       11.84         0.53        15.02        13.64        13.32        20.42 
TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 
       10.82         9.01         0.26         9.57         3.16        35.11 
TCGA-06-0645 TCGA-06-0648 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 
        5.75         9.80        23.57        14.20        26.40        46.88 
TCGA-06-0747 TCGA-06-0877 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 
        2.70         5.65        40.41        16.57        20.78        26.76 
TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 
        6.84         4.04        26.79        11.84        15.32        13.61 
TCGA-06-1805 TCGA-06-1806 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2562 
       33.90        15.32         1.08        12.49         4.93        12.56 
TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 
       30.64         5.95        16.64         5.98         4.37         0.43 
TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 
       31.50        11.74         3.55         4.54         8.81         8.98 
TCGA-06-5415 TCGA-06-5418 TCGA-06-5858 TCGA-06-6388 TCGA-06-6391 TCGA-06-6693 
        8.55         2.73         6.15         5.23         1.48       120.56 
TCGA-06-6694 TCGA-06-6695 TCGA-06-6698 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 
        7.36         8.32         4.77         4.77         4.96         4.70 
TCGA-06-A6S0 TCGA-06-A7TK TCGA-08-0244 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 
        3.12         5.39        22.68         4.18       115.86         1.74 
TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 
        8.42        25.71        12.16         9.80        29.23        65.33 
TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 
        1.28         8.42        17.95        24.56        31.10        37.58 
TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0386 TCGA-08-0389 TCGA-08-0509 
       22.29         3.39        12.23        18.02        15.35        12.56 
TCGA-08-0510 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0521 
        4.27        11.08        19.59        58.68        19.33         4.80 
TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0618 TCGA-12-0619 
        7.27        15.98        18.41         7.56        12.99        34.92 
TCGA-12-0620 TCGA-12-0656 TCGA-12-0657 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 
       10.45        94.78         0.10        25.97        26.66        12.13 
TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 
       20.38        28.41        15.06        53.85        43.23         7.63 
TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 
        9.73        14.93        14.86        91.76        24.79        18.48 
TCGA-12-0822 TCGA-12-0826 TCGA-12-0828 TCGA-12-0829 TCGA-12-1090 TCGA-12-1093 
       23.51        27.78         8.94        20.58         7.59        15.98 
TCGA-12-1094 TCGA-12-1095 TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 TCGA-12-1599 
       12.23        15.85        14.53         3.98         4.14        25.68 
TCGA-12-1600 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 
       14.73        59.77        44.02        26.93        15.22        10.95 
TCGA-12-3651 TCGA-12-3652 TCGA-12-5299 TCGA-12-5301 TCGA-14-0740 TCGA-14-0781 
       12.69        34.92         3.22         2.04        11.97         0.95 
TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 TCGA-14-0812 TCGA-14-0866 
       23.05         2.24        11.24        13.78         3.25        26.33 
TCGA-14-0867 TCGA-14-0871 TCGA-14-1034 TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 
        2.04        28.93        15.95        19.30         0.79         1.38 
TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 TCGA-14-1452 TCGA-14-1453 
        3.75        32.05        58.78        23.11         7.10         1.15 
TCGA-14-1454 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 
       30.18        40.96         6.67        12.43         0.99         1.97 
TCGA-14-1821 TCGA-14-1825 TCGA-14-1827 TCGA-14-2554 TCGA-14-2555 TCGA-14-4157 
       17.79         7.63         5.88        17.49         7.96         3.42 
TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 
       13.78        50.53        19.10        13.28         3.91        17.59 
TCGA-16-0849 TCGA-16-0850 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 
       26.07        16.37         4.57        10.29        14.01         9.14 
TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 
       21.24        13.97         6.41        11.77        21.90         8.61 
TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 
        0.66        14.27         3.39        10.75         9.07         5.95 
TCGA-19-1388 TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 TCGA-19-2619 
       12.95         3.65         7.17        12.66         3.25         9.67 
TCGA-19-2620 TCGA-19-2621 TCGA-19-2624 TCGA-19-2625 TCGA-19-2631 TCGA-19-4065 
        4.87         1.08         0.16         4.08         7.00         7.04 
TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 
       17.19         8.02        18.90         4.73        12.10         1.78 
TCGA-19-5958 TCGA-19-5959 TCGA-19-A60I TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1442 
       14.07        16.80        17.79        28.54        10.03        31.33 
TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 
        7.13         9.37         9.40         8.88        18.97         1.58 
TCGA-26-6173 TCGA-26-6174 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 TCGA-27-1833 
        7.92         2.33        19.33         5.06        16.60        24.23 
TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2521 
       21.30        30.05        14.04        11.51        24.76        10.39 
TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 
       16.08         7.59         2.86        15.78         0.20         2.53 
TCGA-28-1749 TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 TCGA-28-1755 TCGA-28-1757 
        9.21         7.63         8.48         1.22         1.55         0.13 
TCGA-28-2502 TCGA-28-2513 TCGA-28-5204 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 
        0.66         7.30        14.93        17.88        14.53        11.77 
TCGA-28-5214 TCGA-28-5218 TCGA-28-5219 TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 
       23.44         5.16        22.68         5.42        15.39        21.07 
TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 
        0.10        15.85        19.50         4.67        12.69        14.86 
TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2616 TCGA-32-2632 
       16.93        12.23        20.78        15.02         7.36         8.84 
TCGA-32-2638 TCGA-32-4208 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 
       25.18        21.14         3.72        12.59        19.86        10.85 
TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-3393 TCGA-41-3915 TCGA-41-5651 
       19.23         0.85        13.35         4.44        11.84        15.12 
TCGA-41-6646 TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 
       12.46         4.14        14.76         3.45        20.91         4.34 
TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 TCGA-76-4931 
       14.33         8.22         7.50         4.80         4.54         9.17 
TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6280 TCGA-76-6286 TCGA-76-6656 
       10.78        16.70         3.29        11.38        20.98         4.83 
TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 
        5.03         0.23         9.27         7.73         7.79         1.61 
TCGA-81-5911 TCGA-87-5896 TCGA-RR-A6KA TCGA-RR-A6KC 
       17.72        26.30         6.28        20.55 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              0.13               0.10 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            127.59             120.56 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             10.39              12.23 
[1] "0.1 - 127.6 (10.4)" "0.1 - 120.6 (12.2)"
[1] "hr=" "1"  
D67V2, continuous
D67V3, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    62  83
  14Q LOSS WILD-TYPE 162 263
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     62   83
  14Q LOSS WILD-TYPE  162  263
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE               62                162
  MALE                 83                263
[1] 2 2
[1] FALSE
D67V4, continuous
                    vv
clus                 GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  14Q LOSS MUTATED                               5                   6
  14Q LOSS WILD-TYPE                            22                  12
                    vv
clus                 UNTREATED PRIMARY (DE NOVO) GBM
  14Q LOSS MUTATED                               134
  14Q LOSS WILD-TYPE                             391
D67V5, multiclass
                                 clus
vv                                14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                  5                 22
  TREATED PRIMARY GBM                            6                 12
  UNTREATED PRIMARY (DE NOVO) GBM              134                391
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V6, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    99  46
  14Q LOSS WILD-TYPE 283 142
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     99   46
  14Q LOSS WILD-TYPE  283  142
     clus
vv    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  NO                99                283
  YES               46                142
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  14Q LOSS MUTATED       4                        17   120
  14Q LOSS WILD-TYPE     9                        32   365
D67V7, multiclass
                           clus
vv                          14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  ASIAN                                    4                  9
  BLACK OR AFRICAN AMERICAN               17                 32
  WHITE                                  120                365
[1] 3 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
  14Q LOSS MUTATED     1 121
  14Q LOSS WILD-TYPE  11 351
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      1  121
  14Q LOSS WILD-TYPE   11  351
                        clus
vv                       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 11
  NOT HISPANIC OR LATINO              121                351
[1] 2 2
[1] FALSE

Clustering(68) Variable = 15Q LOSS MUTATION ANALYSIS
D68V1, survival
                    sevent
clus2                  0   1
  15Q LOSS MUTATED    20  84
  15Q LOSS WILD-TYPE  84 381
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               104                465 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                84                381 
$`15Q LOSS MUTATED`
TCGA-02-0003 TCGA-02-0034 TCGA-02-0047 TCGA-02-0048 TCGA-02-0051 TCGA-02-0054 
        4.73        14.14        14.73         3.22        15.09         6.54 
TCGA-02-0074 TCGA-02-0079 TCGA-02-0084 TCGA-02-0087 TCGA-02-0113 TCGA-02-0115 
       10.19        27.25        12.62        57.76        92.65        15.65 
TCGA-02-0258 TCGA-02-0266 TCGA-02-0269 TCGA-02-0281 TCGA-02-0324 TCGA-06-0124 
       16.54        17.72        10.75         3.98         7.73        20.38 
TCGA-06-0128 TCGA-06-0129 TCGA-06-0174 TCGA-06-0188 TCGA-06-0192 TCGA-06-0209 
       22.72        33.67         3.22        44.58        38.96         7.63 
TCGA-06-0213 TCGA-06-0216 TCGA-06-0237 TCGA-06-0402 TCGA-06-0410 TCGA-06-0645 
        0.53        24.16        13.64         0.26         4.70         5.75 
TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0875 TCGA-06-1801 TCGA-06-2558 
        5.75         9.80         2.10        43.46        11.84        12.49 
TCGA-06-5416 TCGA-06-5856 TCGA-06-6694 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A7TK 
        6.71         3.75         7.36         1.87         3.12         5.39 
TCGA-06-A7TL TCGA-08-0246 TCGA-08-0344 TCGA-08-0348 TCGA-08-0359 TCGA-08-0386 
        5.42         4.18       115.86        12.16         3.39        18.02 
TCGA-08-0510 TCGA-12-0618 TCGA-12-0619 TCGA-12-1088 TCGA-12-1096 TCGA-12-1099 
        4.27        12.99        34.92       127.59         9.11         4.14 
TCGA-12-1600 TCGA-12-1602 TCGA-12-3646 TCGA-14-0783 TCGA-14-0817 TCGA-14-0867 
       14.73         6.77        44.02         6.21         5.39         2.04 
TCGA-14-1794 TCGA-15-1447 TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 
        0.99        53.19        13.28         3.91        17.59        26.07 
TCGA-16-0850 TCGA-16-1045 TCGA-19-1385 TCGA-19-1387 TCGA-19-1390 TCGA-19-1392 
       16.37        29.03        10.75         5.95        25.38         3.65 
TCGA-19-2629 TCGA-19-5955 TCGA-19-5956 TCGA-26-1438 TCGA-26-1439 TCGA-26-6174 
       24.23         1.78        22.49        10.03        13.87         2.33 
TCGA-27-1830 TCGA-27-1834 TCGA-27-2519 TCGA-27-2524 TCGA-28-1746 TCGA-28-1750 
        5.06        40.54        10.39         7.59         0.20         8.35 
TCGA-28-1756 TCGA-28-5215 TCGA-28-5219 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 
        2.83        11.01        22.68        15.39        21.07         0.49 
TCGA-32-2616 TCGA-32-2634 TCGA-32-4210 TCGA-32-4211 TCGA-32-4719 TCGA-41-2573 
        7.36        22.78         3.72        12.59        10.85         8.94 
TCGA-41-3915 TCGA-41-5651 TCGA-4W-AA9S TCGA-76-4929 TCGA-76-4935 TCGA-76-6191 
       11.84        15.12         4.14         3.65        10.78        16.70 
TCGA-76-6285 TCGA-76-6286 
        8.35        20.98 

$`15Q LOSS WILD-TYPE`
TCGA-02-0001 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 TCGA-02-0011 
       11.77        18.35        23.18        10.59        35.41        20.71 
TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0024 
       82.59        20.61        87.06        77.65        20.12        53.10 
TCGA-02-0025 TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0037 
       42.74        24.59        12.16        90.58         2.83         3.62 
TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0052 TCGA-02-0055 
       10.72        10.52        18.31         6.87        12.59         2.50 
TCGA-02-0057 TCGA-02-0058 TCGA-02-0059 TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 
       19.86         8.35         9.57         6.02        19.73        26.43 
TCGA-02-0069 TCGA-02-0070 TCGA-02-0071 TCGA-02-0075 TCGA-02-0080 TCGA-02-0083 
       28.70        25.05         5.49        20.84        89.72        22.72 
TCGA-02-0085 TCGA-02-0086 TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 TCGA-02-0104 
       51.32         8.81        16.96         3.48        27.02        65.00 
TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 TCGA-02-0114 TCGA-02-0116 TCGA-02-0260 
       11.67        17.65        23.18        99.98        48.95        16.93 
TCGA-02-0271 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 
       14.47        13.87        14.20        15.95        12.23         9.90 
TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 
       10.62         7.33        15.91        25.71         4.37        25.12 
TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 
       10.59        12.39        14.50        10.55        47.11        11.34 
TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 TCGA-02-2466 TCGA-02-2470 TCGA-02-2483 
        9.27        16.21         3.35        16.80        12.92        15.32 
TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0125 TCGA-06-0126 
       15.45        20.32         2.70         6.15        47.61         6.94 
TCGA-06-0127 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 
        3.98        12.95        25.35        14.30        26.70        24.23 
TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 
       11.90         0.20        10.29         2.20        11.74         2.33 
TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 
       20.09        17.79        10.09         8.61        19.46        46.59 
TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 
       12.33        13.94        10.45         3.19        10.82         9.44 
TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 
       11.80         3.42        56.91        10.65         5.85        19.66 
TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 
        3.29        13.12         4.47         4.04        91.00         4.18 
TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 
       88.14        20.25         3.65        69.90        73.84        27.22 
TCGA-06-0189 TCGA-06-0190 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 
       15.42        10.42         4.67         7.40         5.56         0.39 
TCGA-06-0206 TCGA-06-0208 TCGA-06-0210 TCGA-06-0211 TCGA-06-0214 TCGA-06-0219 
        7.66         8.42         7.40        11.84        15.02         0.72 
TCGA-06-0221 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 
       19.82        13.32        20.42        48.69        10.82         9.01 
TCGA-06-0409 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0650 
       72.36         9.57         3.16        35.11        12.62        23.57 
TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 
       14.20        26.40        46.88         7.86         2.70         2.70 
TCGA-06-0750 TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 
        0.92        46.19         5.65         7.17        40.41        16.57 
TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 
       20.78        26.76        23.93         6.84         4.04        26.79 
TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 TCGA-06-2557 TCGA-06-2559 
       15.32        13.61        33.90        15.32         1.08         4.93 
TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 
       17.65        12.56        30.64         5.95        16.64         5.98 
TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 
        4.37         0.43        31.50        11.74         3.55         8.35 
TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5418 TCGA-06-5858 
        4.54         8.81         8.98         8.55         2.73         6.15 
TCGA-06-5859 TCGA-06-6388 TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 
        4.57         5.23         7.79         5.39         1.48       120.56 
TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 
        8.32        12.85         4.77         1.55         4.77         4.96 
TCGA-06-A5U0 TCGA-06-A6S1 TCGA-08-0244 TCGA-08-0245 TCGA-08-0345 TCGA-08-0346 
        4.70         2.56        22.68        37.84         1.74         8.42 
TCGA-08-0347 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 
       25.71         9.80        29.23        65.33         1.28         8.42 
TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0375 
       17.95        24.56        31.10        37.58        22.29        12.23 
TCGA-08-0380 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0512 
       14.93        15.35        13.97         0.72        12.56        42.15 
TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 
       11.08        19.59        58.68        19.33        10.75         4.80 
TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 
        7.27        15.98        18.41         7.56        15.35        14.73 
TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 
       10.45         7.59        94.78         0.10        38.17        25.97 
TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 
       26.66        12.13         3.65        20.38        28.41        15.06 
TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 
       53.85        43.23         7.63         9.73        14.93        14.86 
TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 TCGA-12-0826 
       91.76        24.79        18.48        10.62        23.51        27.78 
TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 
       38.76         8.94        20.58         5.82         7.59        33.21 
TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1097 TCGA-12-1098 
       21.73        15.98        12.23        15.85        14.53         3.98 
TCGA-12-1598 TCGA-12-1599 TCGA-12-3644 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 
       15.65        25.68        59.77        26.93        15.22        10.95 
TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 
       12.69        34.92        14.53        14.93         3.22         2.04 
TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 
       15.12        11.97         0.95        23.05         2.24        11.24 
TCGA-14-0790 TCGA-14-0812 TCGA-14-0813 TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 
       13.78         3.25         1.35         2.89        16.50        26.33 
TCGA-14-0871 TCGA-14-1034 TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 TCGA-14-1396 
       28.93        15.95        19.30         0.79         1.38         1.12 
TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 TCGA-14-1452 TCGA-14-1453 
        3.75        32.05        58.78        23.11         7.10         1.15 
TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 TCGA-14-1795 
       30.18         0.92        40.96         6.67        12.43         1.97 
TCGA-14-1821 TCGA-14-1823 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 
       17.79        17.85         7.63         5.88         7.17        17.49 
TCGA-14-2555 TCGA-14-3477 TCGA-14-4157 TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 
        7.96         3.78         3.42        13.78        50.53        19.10 
TCGA-16-0861 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 
        4.31         4.57        10.29        14.01         9.14        21.24 
TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 TCGA-19-0962 
       13.97         6.41        11.77        21.90         8.61         0.66 
TCGA-19-0963 TCGA-19-0964 TCGA-19-1386 TCGA-19-1388 TCGA-19-1389 TCGA-19-1786 
       14.27         3.39         9.07        12.95         4.64         7.17 
TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 
       12.66         3.25         0.13         9.67         4.87         1.08 
TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 
        7.53         0.16         4.08         7.00         7.04         6.64 
TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5958 
       17.19         8.02        18.90         4.73        12.10        14.07 
TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1440 
       16.80        14.96        17.79         3.98        28.54         9.73 
TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 
       31.33         7.13         9.37         9.40        14.86         5.49 
TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 TCGA-26-A7UX TCGA-27-1831 
        8.88        18.97         1.58         7.92        19.33        16.60 
TCGA-27-1832 TCGA-27-1833 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 
        9.86        24.23        21.30        30.05        14.04        11.51 
TCGA-27-2518 TCGA-27-2521 TCGA-27-2523 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 
       24.76        10.39        16.08         2.86        14.40        15.78 
TCGA-28-1747 TCGA-28-1749 TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 TCGA-28-1755 
        2.53         9.21         7.63         8.48         1.22         1.55 
TCGA-28-1757 TCGA-28-2502 TCGA-28-2506 TCGA-28-2509 TCGA-28-2513 TCGA-28-2514 
        0.13         0.66         6.74         4.77         7.30         5.26 
TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 
       14.93        11.28        17.88        14.53        11.77        31.27 
TCGA-28-5214 TCGA-28-5216 TCGA-28-5218 TCGA-28-5220 TCGA-28-6450 TCGA-32-1977 
       23.44        13.64         5.16        12.76         5.42         0.10 
TCGA-32-1978 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 
       15.85        19.50         1.18         4.67        12.69        14.86 
TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 TCGA-32-2632 
       16.93        12.23        20.78        15.02        15.95         8.84 
TCGA-32-2638 TCGA-32-4208 TCGA-32-4213 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 
       25.18        21.14        19.86        19.23         0.85        13.35 
TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-4097 TCGA-41-6646 TCGA-4W-AA9T 
        9.53         0.99         4.44         0.20        12.46        14.76 
TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 
        3.45        20.91         4.34        14.33         8.22         7.50 
TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4931 TCGA-76-4934 TCGA-76-6192 
        4.80         4.54         3.09         9.17         2.53         3.29 
TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 
        2.70        11.38        17.06         4.83         5.03         0.23 
TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
        9.27         7.73         7.79         1.61        17.72        26.30 
TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC 
        5.92         6.28        20.55 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               0.2                0.1 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            127.59             120.56 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             10.75              12.23 
[1] "0.2 - 127.6 (10.8)" "0.1 - 120.6 (12.2)"
[1] "hr=" "1"  
D68V2, continuous
D68V3, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED    44  61
  15Q LOSS WILD-TYPE 180 285
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     44   61
  15Q LOSS WILD-TYPE  180  285
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE               44                180
  MALE                 61                285
[1] 2 2
[1] FALSE
D68V4, continuous
                    vv
clus                 GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  15Q LOSS MUTATED                               6                   2
  15Q LOSS WILD-TYPE                            21                  16
                    vv
clus                 UNTREATED PRIMARY (DE NOVO) GBM
  15Q LOSS MUTATED                                97
  15Q LOSS WILD-TYPE                             428
D68V5, multiclass
                                 clus
vv                                15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                  6                 21
  TREATED PRIMARY GBM                            2                 16
  UNTREATED PRIMARY (DE NOVO) GBM               97                428
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V6, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED    61  44
  15Q LOSS WILD-TYPE 321 144
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     61   44
  15Q LOSS WILD-TYPE  321  144
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  NO                61                321
  YES               44                144
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  15Q LOSS MUTATED       2                         8    91
  15Q LOSS WILD-TYPE    11                        41   394
D68V7, multiclass
                           clus
vv                          15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  ASIAN                                    2                 11
  BLACK OR AFRICAN AMERICAN                8                 41
  WHITE                                   91                394
[1] 3 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
  15Q LOSS MUTATED     4  88
  15Q LOSS WILD-TYPE   8 384
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      4   88
  15Q LOSS WILD-TYPE    8  384
                        clus
vv                       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  8
  NOT HISPANIC OR LATINO               88                384
[1] 2 2
[1] FALSE

Clustering(69) Variable = 16P LOSS MUTATION ANALYSIS
D69V1, survival
                    sevent
clus2                  0   1
  16P LOSS MUTATED     8  55
  16P LOSS WILD-TYPE  96 410
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                63                506 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                55                410 
$`16P LOSS MUTATED`
TCGA-02-0009 TCGA-02-0025 TCGA-02-0052 TCGA-02-0055 TCGA-02-0074 TCGA-02-0258 
       10.59        42.74        12.59         2.50        10.19        16.54 
TCGA-02-0266 TCGA-02-0281 TCGA-02-0456 TCGA-02-2486 TCGA-06-0132 TCGA-06-0164 
       17.72         3.98         3.35        20.32        25.35        56.91 
TCGA-06-0168 TCGA-06-0171 TCGA-06-0177 TCGA-06-0214 TCGA-06-0216 TCGA-06-0221 
       19.66        13.12         4.18        15.02        24.16        19.82 
TCGA-06-0394 TCGA-06-0414 TCGA-06-0645 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 
       10.82        35.11         5.75        14.20        26.40        46.88 
TCGA-06-0879 TCGA-06-1087 TCGA-06-2557 TCGA-06-2569 TCGA-06-5859 TCGA-06-6389 
       40.41         4.04         1.08         0.43         4.57         7.79 
TCGA-06-6698 TCGA-06-6700 TCGA-06-A6S0 TCGA-08-0353 TCGA-08-0392 TCGA-08-0509 
        4.77         4.77         3.12         8.42         0.72        12.56 
TCGA-08-0514 TCGA-12-0619 TCGA-12-0776 TCGA-12-0826 TCGA-12-1099 TCGA-12-1600 
       11.08        34.92         9.73        27.78         4.14        14.73 
TCGA-12-3653 TCGA-14-0812 TCGA-14-0813 TCGA-14-0871 TCGA-14-1823 TCGA-19-1392 
       14.53         3.25         1.35        28.93        17.85         3.65 
TCGA-19-5953 TCGA-19-5955 TCGA-19-5956 TCGA-27-1835 TCGA-27-2521 TCGA-27-2524 
        4.73         1.78        22.49        21.30        10.39         7.59 
TCGA-28-1750 TCGA-28-5204 TCGA-28-5216 TCGA-32-1978 TCGA-32-1980 TCGA-32-4210 
        8.35        14.93        13.64        15.85         1.18         3.72 
TCGA-41-3915 TCGA-76-4925 TCGA-76-4928 
       11.84         4.80         3.09 

$`16P LOSS WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0010 TCGA-02-0011 
       11.77         4.73        18.35        23.18        35.41        20.71 
TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0024 
       82.59        20.61        87.06        77.65        20.12        53.10 
TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 
       24.59        12.16        90.58         2.83        14.14         3.62 
TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 TCGA-02-0048 
       10.72        10.52        18.31         6.87        14.73         3.22 
TCGA-02-0051 TCGA-02-0054 TCGA-02-0057 TCGA-02-0058 TCGA-02-0059 TCGA-02-0060 
       15.09         6.54        19.86         8.35         9.57         6.02 
TCGA-02-0064 TCGA-02-0068 TCGA-02-0069 TCGA-02-0070 TCGA-02-0071 TCGA-02-0075 
       19.73        26.43        28.70        25.05         5.49        20.84 
TCGA-02-0079 TCGA-02-0080 TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 TCGA-02-0086 
       27.25        89.72        22.72        12.62        51.32         8.81 
TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 TCGA-02-0104 TCGA-02-0106 
       57.76        16.96         3.48        27.02        65.00        11.67 
TCGA-02-0107 TCGA-02-0111 TCGA-02-0113 TCGA-02-0114 TCGA-02-0115 TCGA-02-0116 
       17.65        23.18        92.65        99.98        15.65        48.95 
TCGA-02-0260 TCGA-02-0269 TCGA-02-0271 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 
       16.93        10.75        14.47        13.87        14.20        15.95 
TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 
       12.23         9.90         7.73        10.62         7.33        15.91 
TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 
       25.71         4.37        25.12        10.59        12.39        14.50 
TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 TCGA-02-2466 
       10.55        47.11        11.34         9.27        16.21        16.80 
TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 
       12.92        15.32        15.45         2.70         6.15        20.38 
TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 
       47.61         6.94         3.98        22.72        33.67        12.95 
TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 
       14.30        26.70        24.23        11.90         0.20        10.29 
TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 
        2.20        11.74         2.33        20.09        17.79        10.09 
TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 
        8.61        19.46        46.59        12.33        13.94        10.45 
TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 TCGA-06-0165 
        3.19        10.82         9.44        11.80         3.42        10.65 
TCGA-06-0166 TCGA-06-0169 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 
        5.85         3.29         4.47         3.22         4.04        91.00 
TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 
       88.14        20.25         3.65        69.90        73.84        27.22 
TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 
       44.58        15.42        10.42        38.96         4.67         7.40 
TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 
        5.56         0.39         7.66         8.42         7.63         7.40 
TCGA-06-0211 TCGA-06-0213 TCGA-06-0219 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 
       11.84         0.53         0.72        13.64        13.32        20.42 
TCGA-06-0241 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 
       48.69         9.01         0.26        72.36         4.70         9.57 
TCGA-06-0413 TCGA-06-0644 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 
        3.16        12.62         5.75         9.80         2.10        23.57 
TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 
        7.86         2.70         2.70         0.92        43.46        46.19 
TCGA-06-0877 TCGA-06-0878 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 
        5.65         7.17        16.57        20.78        26.76        23.93 
TCGA-06-1086 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 
        6.84        26.79        11.84        15.32        13.61        33.90 
TCGA-06-1806 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 
       15.32        12.49         4.93        17.65        12.56        30.64 
TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2570 TCGA-06-5408 
        5.95        16.64         5.98         4.37        31.50        11.74 
TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 
        3.55         8.35         4.54         8.81         8.98         8.55 
TCGA-06-5416 TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 TCGA-06-6388 TCGA-06-6390 
        6.71         2.73         3.75         6.15         5.23         5.39 
TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 TCGA-06-6699 
        1.48       120.56         7.36         8.32        12.85         1.55 
TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S1 TCGA-06-A7TK TCGA-06-A7TL 
        4.96         4.70         1.87         2.56         5.39         5.42 
TCGA-08-0244 TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 
       22.68        37.84         4.18       115.86         1.74         8.42 
TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 
       25.71        12.16         9.80        29.23        65.33         1.28 
TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 
       17.95        24.56        31.10        37.58        22.29         3.39 
TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0510 
       12.23        14.93        18.02        15.35        13.97         4.27 
TCGA-08-0512 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 
       42.15        19.59        58.68        19.33        10.75         4.80 
TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 
        7.27        15.98        18.41         7.56        15.35        14.73 
TCGA-12-0618 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 
       12.99        10.45         7.59        94.78         0.10        38.17 
TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 
       25.97        26.66        12.13         3.65        20.38        28.41 
TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0778 TCGA-12-0780 
       15.06        53.85        43.23         7.63        14.93        14.86 
TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 TCGA-12-0827 
       91.76        24.79        18.48        10.62        23.51        38.76 
TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 
        8.94        20.58       127.59         5.82         7.59        33.21 
TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 
       21.73        15.98        12.23        15.85         9.11        14.53 
TCGA-12-1098 TCGA-12-1598 TCGA-12-1599 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 
        3.98        15.65        25.68         6.77        59.77        44.02 
TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-5295 
       26.93        15.22        10.95        12.69        34.92        14.93 
TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 TCGA-14-0783 
        3.22         2.04        15.12        11.97         0.95         6.21 
TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 TCGA-14-0817 TCGA-14-0862 
       23.05         2.24        11.24        13.78         5.39         2.89 
TCGA-14-0865 TCGA-14-0866 TCGA-14-0867 TCGA-14-1034 TCGA-14-1037 TCGA-14-1043 
       16.50        26.33         2.04        15.95        19.30         0.79 
TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 
        1.38         1.12         3.75        32.05        58.78        23.11 
TCGA-14-1452 TCGA-14-1453 TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 
        7.10         1.15        30.18         0.92        40.96         6.67 
TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 TCGA-14-1825 TCGA-14-1827 
       12.43         0.99         1.97        17.79         7.63         5.88 
TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-3477 TCGA-14-4157 TCGA-15-0742 
        7.17        17.49         7.96         3.78         3.42        13.78 
TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 
       50.53        19.10        53.19        13.28         3.91        17.59 
TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 
       26.07        16.37         4.31        29.03         4.57        10.29 
TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 
       14.01         9.14        21.24        13.97         6.41        11.77 
TCGA-19-0957 TCGA-19-0960 TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 
       21.90         8.61         0.66        14.27         3.39        10.75 
TCGA-19-1386 TCGA-19-1387 TCGA-19-1388 TCGA-19-1389 TCGA-19-1390 TCGA-19-1786 
        9.07         5.95        12.95         4.64        25.38         7.17 
TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 
       12.66         3.25         0.13         9.67         4.87         1.08 
TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 
        7.53         0.16         4.08        24.23         7.00         7.04 
TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5954 TCGA-19-5958 
        6.64        17.19         8.02        18.90        12.10        14.07 
TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 
       16.80        14.96        17.79         3.98        28.54        10.03 
TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 
       13.87         9.73        31.33         7.13         9.37         9.40 
TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 
       14.86         5.49         8.88        18.97         1.58         7.92 
TCGA-26-6174 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 
        2.33        19.33         5.06        16.60         9.86        24.23 
TCGA-27-1834 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 
       40.54        30.05        14.04        11.51        24.76        10.39 
TCGA-27-2523 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 
       16.08         2.86        14.40        15.78         0.20         2.53 
TCGA-28-1749 TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 
        9.21         7.63         8.48         1.22         1.55         2.83 
TCGA-28-1757 TCGA-28-2502 TCGA-28-2506 TCGA-28-2509 TCGA-28-2513 TCGA-28-2514 
        0.13         0.66         6.74         4.77         7.30         5.26 
TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 
       11.28        17.88        14.53        11.77        31.27        23.44 
TCGA-28-5215 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 
       11.01         5.16        22.68        12.76         5.42        15.39 
TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 TCGA-32-1979 TCGA-32-1982 TCGA-32-1986 
       21.07         0.49         0.10        19.50         4.67        12.69 
TCGA-32-1987 TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 
       14.86        16.93        12.23        20.78        15.02        15.95 
TCGA-32-2616 TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4211 
        7.36         8.84        22.78        25.18        21.14        12.59 
TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 
       19.86        10.85        19.23         0.85        13.35         8.94 
TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 
        9.53         0.99         4.44         0.20        15.12        12.46 
TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 
        4.14        14.76         3.45        20.91         4.34        14.33 
TCGA-74-6581 TCGA-74-6584 TCGA-76-4926 TCGA-76-4929 TCGA-76-4931 TCGA-76-4934 
        8.22         7.50         4.54         3.65         9.17         2.53 
TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 
       10.78        16.70         3.29         2.70        11.38        17.06 
TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 
        8.35        20.98         4.83         5.03         0.23         9.27 
TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R 
        7.73         7.79         1.61        17.72        26.30         5.92 
TCGA-RR-A6KA TCGA-RR-A6KC 
        6.28        20.55 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              0.43               0.10 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             56.91             127.59 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
            10.820             12.035 
[1] "0.4 - 56.9 (10.8)"  "0.1 - 127.6 (12.0)"
[1] "hr=" "1.3"
D69V2, continuous
D69V3, binary
                    cls
clus                   0   1
  16P LOSS MUTATED    23  40
  16P LOSS WILD-TYPE 201 306
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     23   40
  16P LOSS WILD-TYPE  201  306
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE               23                201
  MALE                 40                306
[1] 2 2
[1] FALSE
D69V4, continuous
                    vv
clus                 GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  16P LOSS MUTATED                               1                   0
  16P LOSS WILD-TYPE                            26                  18
                    vv
clus                 UNTREATED PRIMARY (DE NOVO) GBM
  16P LOSS MUTATED                                62
  16P LOSS WILD-TYPE                             463
D69V5, multiclass
                                 clus
vv                                16P LOSS MUTATED 16P LOSS WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                  1                 26
  TREATED PRIMARY GBM                            0                 18
  UNTREATED PRIMARY (DE NOVO) GBM               62                463
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V6, binary
                    cls
clus                   0   1
  16P LOSS MUTATED    36  27
  16P LOSS WILD-TYPE 346 161
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     36   27
  16P LOSS WILD-TYPE  346  161
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  NO                36                346
  YES               27                161
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16P LOSS MUTATED       1                         5    56
  16P LOSS WILD-TYPE    12                        44   429
D69V7, multiclass
                           clus
vv                          16P LOSS MUTATED 16P LOSS WILD-TYPE
  ASIAN                                    1                 12
  BLACK OR AFRICAN AMERICAN                5                 44
  WHITE                                   56                429
[1] 3 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
  16P LOSS MUTATED     1  55
  16P LOSS WILD-TYPE  11 417
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      1   55
  16P LOSS WILD-TYPE   11  417
                        clus
vv                       16P LOSS MUTATED 16P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 11
  NOT HISPANIC OR LATINO               55                417
[1] 2 2
[1] FALSE

Clustering(70) Variable = 16Q LOSS MUTATION ANALYSIS
D70V1, survival
                    sevent
clus2                  0   1
  16Q LOSS MUTATED     9  73
  16Q LOSS WILD-TYPE  95 392
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                82                487 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                73                392 
$`16Q LOSS MUTATED`
TCGA-02-0009 TCGA-02-0052 TCGA-02-0055 TCGA-02-0074 TCGA-02-0114 TCGA-02-0258 
       10.59        12.59         2.50        10.19        99.98        16.54 
TCGA-02-0266 TCGA-02-0281 TCGA-02-0321 TCGA-02-0337 TCGA-02-0456 TCGA-02-2486 
       17.72         3.98         9.90        25.12         3.35        20.32 
TCGA-06-0132 TCGA-06-0164 TCGA-06-0168 TCGA-06-0171 TCGA-06-0177 TCGA-06-0214 
       25.35        56.91        19.66        13.12         4.18        15.02 
TCGA-06-0216 TCGA-06-0221 TCGA-06-0394 TCGA-06-0414 TCGA-06-0645 TCGA-06-0686 
       24.16        19.82        10.82        35.11         5.75        14.20 
TCGA-06-0743 TCGA-06-0744 TCGA-06-0749 TCGA-06-0879 TCGA-06-0882 TCGA-06-1087 
       26.40        46.88         2.70        40.41        20.78         4.04 
TCGA-06-2557 TCGA-06-2569 TCGA-06-5418 TCGA-06-5859 TCGA-06-6389 TCGA-06-6693 
        1.08         0.43         2.73         4.57         7.79       120.56 
TCGA-06-6698 TCGA-06-6700 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-08-0353 TCGA-08-0392 
        4.77         4.77         3.12         2.56         8.42         0.72 
TCGA-08-0509 TCGA-08-0520 TCGA-08-0525 TCGA-12-0618 TCGA-12-0619 TCGA-12-0654 
       12.56        10.75        15.98        12.99        34.92         7.59 
TCGA-12-0692 TCGA-12-0826 TCGA-12-1099 TCGA-12-1600 TCGA-12-3653 TCGA-12-5295 
        3.65        27.78         4.14        14.73        14.53        14.93 
TCGA-12-5301 TCGA-14-0736 TCGA-14-0812 TCGA-14-0813 TCGA-14-0862 TCGA-14-0871 
        2.04        15.12         3.25         1.35         2.89        28.93 
TCGA-14-1823 TCGA-16-1045 TCGA-19-1389 TCGA-19-5953 TCGA-19-5955 TCGA-19-5956 
       17.85        29.03         4.64         4.73         1.78        22.49 
TCGA-27-1832 TCGA-27-2521 TCGA-27-2524 TCGA-28-1750 TCGA-28-1755 TCGA-28-5204 
        9.86        10.39         7.59         8.35         1.55        14.93 
TCGA-28-5216 TCGA-32-1973 TCGA-32-1978 TCGA-32-1980 TCGA-32-1987 TCGA-32-2494 
       13.64        21.07        15.85         1.18        14.86        20.78 
TCGA-32-4210 TCGA-41-3915 TCGA-74-6578 TCGA-76-4928 
        3.72        11.84        14.33         3.09 

$`16Q LOSS WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0010 TCGA-02-0011 
       11.77         4.73        18.35        23.18        35.41        20.71 
TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0024 
       82.59        20.61        87.06        77.65        20.12        53.10 
TCGA-02-0025 TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 
       42.74        24.59        12.16        90.58         2.83        14.14 
TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 
        3.62        10.72        10.52        18.31         6.87        14.73 
TCGA-02-0048 TCGA-02-0051 TCGA-02-0054 TCGA-02-0057 TCGA-02-0058 TCGA-02-0059 
        3.22        15.09         6.54        19.86         8.35         9.57 
TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 TCGA-02-0069 TCGA-02-0070 TCGA-02-0071 
        6.02        19.73        26.43        28.70        25.05         5.49 
TCGA-02-0075 TCGA-02-0079 TCGA-02-0080 TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 
       20.84        27.25        89.72        22.72        12.62        51.32 
TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 TCGA-02-0104 
        8.81        57.76        16.96         3.48        27.02        65.00 
TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 TCGA-02-0113 TCGA-02-0115 TCGA-02-0116 
       11.67        17.65        23.18        92.65        15.65        48.95 
TCGA-02-0260 TCGA-02-0269 TCGA-02-0271 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 
       16.93        10.75        14.47        13.87        14.20        15.95 
TCGA-02-0317 TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 
       12.23         7.73        10.62         7.33        15.91        25.71 
TCGA-02-0333 TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 
        4.37        10.59        12.39        14.50        10.55        47.11 
TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 TCGA-02-2466 TCGA-02-2470 TCGA-02-2483 
       11.34         9.27        16.21        16.80        12.92        15.32 
TCGA-02-2485 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 
       15.45         2.70         6.15        20.38        47.61         6.94 
TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 TCGA-06-0133 TCGA-06-0137 
        3.98        22.72        33.67        12.95        14.30        26.70 
TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 
       24.23        11.90         0.20        10.29         2.20        11.74 
TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 
        2.33        20.09        17.79        10.09         8.61        19.46 
TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 
       46.59        12.33        13.94        10.45         3.19        10.82 
TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 TCGA-06-0165 TCGA-06-0166 TCGA-06-0169 
        9.44        11.80         3.42        10.65         5.85         3.29 
TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0178 TCGA-06-0179 
        4.47         3.22         4.04        91.00        88.14        20.25 
TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 
        3.65        69.90        73.84        27.22        44.58        15.42 
TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 
       10.42        38.96         4.67         7.40         5.56         0.39 
TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 
        7.66         8.42         7.63         7.40        11.84         0.53 
TCGA-06-0219 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0397 
        0.72        13.64        13.32        20.42        48.69         9.01 
TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0644 
        0.26        72.36         4.70         9.57         3.16        12.62 
TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0745 TCGA-06-0747 
        5.75         9.80         2.10        23.57         7.86         2.70 
TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 TCGA-06-0881 
        0.92        43.46        46.19         5.65         7.17        16.57 
TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 
       26.76        23.93         6.84        26.79        11.84        15.32 
TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 
       13.61        33.90        15.32        12.49         4.93        17.65 
TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 
       12.56        30.64         5.95        16.64         5.98         4.37 
TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 
       31.50        11.74         3.55         8.35         4.54         8.81 
TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 TCGA-06-5856 TCGA-06-5858 TCGA-06-6388 
        8.98         8.55         6.71         3.75         6.15         5.23 
TCGA-06-6390 TCGA-06-6391 TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 TCGA-06-6699 
        5.39         1.48         7.36         8.32        12.85         1.55 
TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A7TK TCGA-06-A7TL TCGA-08-0244 
        4.96         4.70         1.87         5.39         5.42        22.68 
TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 
       37.84         4.18       115.86         1.74         8.42        25.71 
TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0354 
       12.16         9.80        29.23        65.33         1.28        17.95 
TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 
       24.56        31.10        37.58        22.29         3.39        12.23 
TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0510 TCGA-08-0512 
       14.93        18.02        15.35        13.97         4.27        42.15 
TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0521 TCGA-08-0524 
       11.08        19.59        58.68        19.33         4.80         7.27 
TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0620 TCGA-12-0656 
       18.41         7.56        15.35        14.73        10.45        94.78 
TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0703 
        0.10        38.17        25.97        26.66        12.13        20.38 
TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 
       28.41        15.06        53.85        43.23         7.63         9.73 
TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 
       14.93        14.86        91.76        24.79        18.48        10.62 
TCGA-12-0822 TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 
       23.51        38.76         8.94        20.58       127.59         5.82 
TCGA-12-1090 TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 
        7.59        33.21        21.73        15.98        12.23        15.85 
TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1598 TCGA-12-1599 TCGA-12-1602 
        9.11        14.53         3.98        15.65        25.68         6.77 
TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 
       59.77        44.02        26.93        15.22        10.95        12.69 
TCGA-12-3652 TCGA-12-5299 TCGA-14-0740 TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 
       34.92         3.22        11.97         0.95         6.21        23.05 
TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 TCGA-14-0817 TCGA-14-0865 TCGA-14-0866 
        2.24        11.24        13.78         5.39        16.50        26.33 
TCGA-14-0867 TCGA-14-1034 TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 TCGA-14-1396 
        2.04        15.95        19.30         0.79         1.38         1.12 
TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 TCGA-14-1452 TCGA-14-1453 
        3.75        32.05        58.78        23.11         7.10         1.15 
TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 TCGA-14-1794 
       30.18         0.92        40.96         6.67        12.43         0.99 
TCGA-14-1795 TCGA-14-1821 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 
        1.97        17.79         7.63         5.88         7.17        17.49 
TCGA-14-2555 TCGA-14-3477 TCGA-14-4157 TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 
        7.96         3.78         3.42        13.78        50.53        19.10 
TCGA-15-1447 TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 
       53.19        13.28         3.91        17.59        26.07        16.37 
TCGA-16-0861 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 
        4.31         4.57        10.29        14.01         9.14        21.24 
TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 TCGA-19-0962 
       13.97         6.41        11.77        21.90         8.61         0.66 
TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 TCGA-19-1388 
       14.27         3.39        10.75         9.07         5.95        12.95 
TCGA-19-1390 TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 
       25.38         3.65         7.17        12.66         3.25         0.13 
TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 
        9.67         4.87         1.08         7.53         0.16         4.08 
TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 
       24.23         7.00         7.04         6.64        17.19         8.02 
TCGA-19-5952 TCGA-19-5954 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I 
       18.90        12.10        14.07        16.80        14.96        17.79 
TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 
        3.98        28.54        10.03        13.87         9.73        31.33 
TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 
        7.13         9.37         9.40        14.86         5.49         8.88 
TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-26-A7UX TCGA-27-1830 
       18.97         1.58         7.92         2.33        19.33         5.06 
TCGA-27-1831 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 
       16.60        24.23        40.54        21.30        30.05        14.04 
TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2523 TCGA-27-2526 TCGA-27-2527 
       11.51        24.76        10.39        16.08         2.86        14.40 
TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 TCGA-28-1751 TCGA-28-1752 
       15.78         0.20         2.53         9.21         7.63         8.48 
TCGA-28-1753 TCGA-28-1756 TCGA-28-1757 TCGA-28-2502 TCGA-28-2506 TCGA-28-2509 
        1.22         2.83         0.13         0.66         6.74         4.77 
TCGA-28-2513 TCGA-28-2514 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 
        7.30         5.26        11.28        17.88        14.53        11.77 
TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 
       31.27        23.44        11.01         5.16        22.68        12.76 
TCGA-28-6450 TCGA-32-1970 TCGA-32-1976 TCGA-32-1977 TCGA-32-1979 TCGA-32-1982 
        5.42        15.39         0.49         0.10        19.50         4.67 
TCGA-32-1986 TCGA-32-1991 TCGA-32-2491 TCGA-32-2495 TCGA-32-2615 TCGA-32-2616 
       12.69        16.93        12.23        15.02        15.95         7.36 
TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4211 TCGA-32-4213 
        8.84        22.78        25.18        21.14        12.59        19.86 
TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 
       10.85        19.23         0.85        13.35         8.94         9.53 
TCGA-41-3392 TCGA-41-3393 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9S 
        0.99         4.44         0.20        15.12        12.46         4.14 
TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6581 TCGA-74-6584 
       14.76         3.45        20.91         4.34         8.22         7.50 
TCGA-76-4925 TCGA-76-4926 TCGA-76-4929 TCGA-76-4931 TCGA-76-4934 TCGA-76-4935 
        4.80         4.54         3.65         9.17         2.53        10.78 
TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 
       16.70         3.29         2.70        11.38        17.06         8.35 
TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 
       20.98         4.83         5.03         0.23         9.27         7.73 
TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R TCGA-RR-A6KA 
        7.79         1.61        17.72        26.30         5.92         6.28 
TCGA-RR-A6KC 
       20.55 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              0.43               0.10 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
            120.56             127.59 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             11.33              11.90 
[1] "0.4 - 120.6 (11.3)" "0.1 - 127.6 (11.9)"
[1] "hr=" "1.2"
D70V2, continuous
D70V3, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED    32  50
  16Q LOSS WILD-TYPE 192 296
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     32   50
  16Q LOSS WILD-TYPE  192  296
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE               32                192
  MALE                 50                296
[1] 2 2
[1] FALSE
D70V4, continuous
                    vv
clus                 GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  16Q LOSS MUTATED                               2                   1
  16Q LOSS WILD-TYPE                            25                  17
                    vv
clus                 UNTREATED PRIMARY (DE NOVO) GBM
  16Q LOSS MUTATED                                79
  16Q LOSS WILD-TYPE                             446
D70V5, multiclass
                                 clus
vv                                16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                  2                 25
  TREATED PRIMARY GBM                            1                 17
  UNTREATED PRIMARY (DE NOVO) GBM               79                446
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V6, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED    47  35
  16Q LOSS WILD-TYPE 335 153
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     47   35
  16Q LOSS WILD-TYPE  335  153
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  NO                47                335
  YES               35                153
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16Q LOSS MUTATED       1                         9    69
  16Q LOSS WILD-TYPE    12                        40   416
D70V7, multiclass
                           clus
vv                          16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  ASIAN                                    1                 12
  BLACK OR AFRICAN AMERICAN                9                 40
  WHITE                                   69                416
[1] 3 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
  16Q LOSS MUTATED     2  70
  16Q LOSS WILD-TYPE  10 402
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      2   70
  16Q LOSS WILD-TYPE   10  402
                        clus
vv                       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                 10
  NOT HISPANIC OR LATINO               70                402
[1] 2 2
[1] FALSE

Clustering(71) Variable = 17P LOSS MUTATION ANALYSIS
D71V1, survival
                    sevent
clus2                  0   1
  17P LOSS MUTATED    13  50
  17P LOSS WILD-TYPE  91 415
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                63                506 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                50                415 
$`17P LOSS MUTATED`
TCGA-02-0001 TCGA-02-0033 TCGA-02-0051 TCGA-02-0055 TCGA-02-0059 TCGA-02-0069 
       11.77         2.83        15.09         2.50         9.57        28.70 
TCGA-02-0079 TCGA-02-0086 TCGA-02-0104 TCGA-02-0106 TCGA-02-0113 TCGA-02-0258 
       27.25         8.81        65.00        11.67        92.65        16.54 
TCGA-02-0269 TCGA-06-0130 TCGA-06-0147 TCGA-06-0149 TCGA-06-0152 TCGA-06-0159 
       10.75        12.95        17.79         8.61        12.33         9.44 
TCGA-06-0177 TCGA-06-0184 TCGA-06-0187 TCGA-06-0189 TCGA-06-0190 TCGA-06-0197 
        4.18        69.90        27.22        15.42        10.42         5.56 
TCGA-06-0410 TCGA-06-0644 TCGA-06-2561 TCGA-06-5408 TCGA-08-0245 TCGA-08-0353 
        4.70        12.62        17.65        11.74        37.84         8.42 
TCGA-08-0386 TCGA-08-0390 TCGA-12-0619 TCGA-12-0772 TCGA-12-0826 TCGA-12-1098 
       18.02        13.97        34.92        53.85        27.78         3.98 
TCGA-12-3653 TCGA-14-0871 TCGA-14-1396 TCGA-14-1453 TCGA-15-1447 TCGA-15-1449 
       14.53        28.93         1.12         1.15        53.19        13.28 
TCGA-16-0846 TCGA-19-0960 TCGA-19-2623 TCGA-19-4065 TCGA-19-A60I TCGA-26-1442 
        3.91         8.61         7.53         7.04        17.79        31.33 
TCGA-26-5133 TCGA-27-1835 TCGA-28-2509 TCGA-28-5215 TCGA-32-1976 TCGA-32-2491 
       14.86        21.30         4.77        11.01         0.49        12.23 
TCGA-41-2573 TCGA-41-3392 TCGA-41-3915 TCGA-41-5651 TCGA-4W-AA9S TCGA-76-4925 
        8.94         0.99        11.84        15.12         4.14         4.80 
TCGA-76-4934 TCGA-76-6285 TCGA-76-6662 
        2.53         8.35         9.27 

$`17P LOSS WILD-TYPE`
TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 TCGA-02-0011 
        4.73        18.35        23.18        10.59        35.41        20.71 
TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0024 
       82.59        20.61        87.06        77.65        20.12        53.10 
TCGA-02-0025 TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0034 TCGA-02-0037 
       42.74        24.59        12.16        90.58        14.14         3.62 
TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 TCGA-02-0048 
       10.72        10.52        18.31         6.87        14.73         3.22 
TCGA-02-0052 TCGA-02-0054 TCGA-02-0057 TCGA-02-0058 TCGA-02-0060 TCGA-02-0064 
       12.59         6.54        19.86         8.35         6.02        19.73 
TCGA-02-0068 TCGA-02-0070 TCGA-02-0071 TCGA-02-0074 TCGA-02-0075 TCGA-02-0080 
       26.43        25.05         5.49        10.19        20.84        89.72 
TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 
       22.72        12.62        51.32        57.76        16.96         3.48 
TCGA-02-0102 TCGA-02-0107 TCGA-02-0111 TCGA-02-0114 TCGA-02-0115 TCGA-02-0116 
       27.02        17.65        23.18        99.98        15.65        48.95 
TCGA-02-0260 TCGA-02-0266 TCGA-02-0271 TCGA-02-0281 TCGA-02-0285 TCGA-02-0289 
       16.93        17.72        14.47         3.98        13.87        14.20 
TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 
       15.95        12.23         9.90         7.73        10.62         7.33 
TCGA-02-0330 TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 
       15.91        25.71         4.37        25.12        10.59        12.39 
TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 
       14.50        10.55        47.11        11.34         9.27        16.21 
TCGA-02-0456 TCGA-02-2466 TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 
        3.35        16.80        12.92        15.32        15.45        20.32 
TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 
        2.70         6.15        20.38        47.61         6.94         3.98 
TCGA-06-0128 TCGA-06-0129 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 
       22.72        33.67        25.35        14.30        26.70        24.23 
TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 
       11.90         0.20        10.29         2.20        11.74         2.33 
TCGA-06-0146 TCGA-06-0148 TCGA-06-0150 TCGA-06-0151 TCGA-06-0154 TCGA-06-0155 
       20.09        10.09        19.46        46.59        13.94        10.45 
TCGA-06-0157 TCGA-06-0158 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 
        3.19        10.82        11.80         3.42        56.91        10.65 
TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 
        5.85        19.66         3.29        13.12         4.47         3.22 
TCGA-06-0175 TCGA-06-0176 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0185 
        4.04        91.00        88.14        20.25         3.65        73.84 
TCGA-06-0188 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0201 TCGA-06-0206 
       44.58        38.96         4.67         7.40         0.39         7.66 
TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 
        8.42         7.63         7.40        11.84         0.53        15.02 
TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 
       24.16         0.72        19.82        13.64        13.32        20.42 
TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0412 
       48.69        10.82         9.01         0.26        72.36         9.57 
TCGA-06-0413 TCGA-06-0414 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 
        3.16        35.11         5.75         5.75         9.80         2.10 
TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 
       23.57        14.20        26.40        46.88         7.86         2.70 
TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 
        2.70         0.92        43.46        46.19         5.65         7.17 
TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 
       40.41        16.57        20.78        26.76        23.93         6.84 
TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 
        4.04        26.79        11.84        15.32        13.61        33.90 
TCGA-06-1806 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2562 TCGA-06-2563 
       15.32         1.08        12.49         4.93        12.56        30.64 
TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 
        5.95        16.64         5.98         4.37         0.43        31.50 
TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 
        3.55         8.35         4.54         8.81         8.98         8.55 
TCGA-06-5416 TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 
        6.71         2.73         3.75         6.15         4.57         5.23 
TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 
        7.79         5.39         1.48       120.56         7.36         8.32 
TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 
       12.85         4.77         1.55         4.77         4.96         4.70 
TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK TCGA-06-A7TL TCGA-08-0244 
        1.87         3.12         2.56         5.39         5.42        22.68 
TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 
        4.18       115.86         1.74         8.42        25.71        12.16 
TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0354 TCGA-08-0355 
        9.80        29.23        65.33         1.28        17.95        24.56 
TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 
       31.10        37.58        22.29         3.39        12.23        14.93 
TCGA-08-0389 TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 
       15.35         0.72        12.56         4.27        42.15        11.08 
TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 
       19.59        58.68        19.33        10.75         4.80         7.27 
TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 
       15.98        18.41         7.56        15.35        14.73        12.99 
TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 
       10.45         7.59        94.78         0.10        38.17        25.97 
TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 
       26.66        12.13         3.65        20.38        28.41        15.06 
TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 
       43.23         7.63         9.73        14.93        14.86        91.76 
TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 TCGA-12-0827 TCGA-12-0828 
       24.79        18.48        10.62        23.51        38.76         8.94 
TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 TCGA-12-1092 
       20.58       127.59         5.82         7.59        33.21        21.73 
TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1099 
       15.98        12.23        15.85         9.11        14.53         4.14 
TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 
       15.65        25.68        14.73         6.77        59.77        44.02 
TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-5295 
       26.93        15.22        10.95        12.69        34.92        14.93 
TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 TCGA-14-0783 
        3.22         2.04        15.12        11.97         0.95         6.21 
TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 TCGA-14-0812 TCGA-14-0813 
       23.05         2.24        11.24        13.78         3.25         1.35 
TCGA-14-0817 TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 TCGA-14-0867 TCGA-14-1034 
        5.39         2.89        16.50        26.33         2.04        15.95 
TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 
       19.30         0.79         1.38         3.75        32.05        58.78 
TCGA-14-1451 TCGA-14-1452 TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 
       23.11         7.10        30.18         0.92        40.96         6.67 
TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 TCGA-14-1823 TCGA-14-1825 
       12.43         0.99         1.97        17.79        17.85         7.63 
TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-3477 TCGA-14-4157 
        5.88         7.17        17.49         7.96         3.78         3.42 
TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 
       13.78        50.53        19.10        17.59        26.07        16.37 
TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 
        4.31        29.03         4.57        10.29        14.01         9.14 
TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 TCGA-19-0962 
       21.24        13.97         6.41        11.77        21.90         0.66 
TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 TCGA-19-1388 
       14.27         3.39        10.75         9.07         5.95        12.95 
TCGA-19-1389 TCGA-19-1390 TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 
        4.64        25.38         3.65         7.17        12.66         3.25 
TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2624 TCGA-19-2625 
        0.13         9.67         4.87         1.08         0.16         4.08 
TCGA-19-2629 TCGA-19-2631 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 
       24.23         7.00         6.64        17.19         8.02        18.90 
TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 
        4.73        12.10         1.78        22.49        14.07        16.80 
TCGA-19-5960 TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 
       14.96         3.98        28.54        10.03        13.87         9.73 
TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 
        7.13         9.37         9.40         5.49         8.88        18.97 
TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 
        1.58         7.92         2.33        19.33         5.06        16.60 
TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 
        9.86        24.23        40.54        30.05        14.04        11.51 
TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 
       24.76        10.39        10.39        16.08         7.59         2.86 
TCGA-27-2527 TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 
       14.40        15.78         0.20         2.53         9.21         8.35 
TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 
        7.63         8.48         1.22         1.55         2.83         0.13 
TCGA-28-2502 TCGA-28-2506 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 
        0.66         6.74         7.30         5.26        14.93        11.28 
TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5216 
       17.88        14.53        11.77        31.27        23.44        13.64 
TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 
        5.16        22.68        12.76         5.42        15.39        21.07 
TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 
        0.10        15.85        19.50         1.18         4.67        12.69 
TCGA-32-1987 TCGA-32-1991 TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 TCGA-32-2616 
       14.86        16.93        20.78        15.02        15.95         7.36 
TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4210 TCGA-32-4211 
        8.84        22.78        25.18        21.14         3.72        12.59 
TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2575 
       19.86        10.85        19.23         0.85        13.35         9.53 
TCGA-41-3393 TCGA-41-4097 TCGA-41-6646 TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 
        4.44         0.20        12.46        14.76         3.45        20.91 
TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 TCGA-76-4926 TCGA-76-4928 
        4.34        14.33         8.22         7.50         4.54         3.09 
TCGA-76-4929 TCGA-76-4931 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 
        3.65         9.17        10.78        16.70         3.29         2.70 
TCGA-76-6280 TCGA-76-6282 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 
       11.38        17.06        20.98         4.83         5.03         0.23 
TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R 
        7.73         7.79         1.61        17.72        26.30         5.92 
TCGA-RR-A6KA TCGA-RR-A6KC 
        6.28        20.55 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              0.49               0.10 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             92.65             127.59 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            11.770             11.935 
[1] "0.5 - 92.7 (11.8)"  "0.1 - 127.6 (11.9)"
[1] "hr=" "1.1"
D71V2, continuous
D71V3, binary
                    cls
clus                   0   1
  17P LOSS MUTATED    28  35
  17P LOSS WILD-TYPE 196 311
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     28   35
  17P LOSS WILD-TYPE  196  311
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE               28                196
  MALE                 35                311
[1] 2 2
[1] FALSE
D71V4, continuous
                    vv
clus                 GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  17P LOSS MUTATED                               3                   1
  17P LOSS WILD-TYPE                            24                  17
                    vv
clus                 UNTREATED PRIMARY (DE NOVO) GBM
  17P LOSS MUTATED                                59
  17P LOSS WILD-TYPE                             466
D71V5, multiclass
                                 clus
vv                                17P LOSS MUTATED 17P LOSS WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                  3                 24
  TREATED PRIMARY GBM                            1                 17
  UNTREATED PRIMARY (DE NOVO) GBM               59                466
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V6, binary
                    cls
clus                   0   1
  17P LOSS MUTATED    37  26
  17P LOSS WILD-TYPE 345 162
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     37   26
  17P LOSS WILD-TYPE  345  162
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  NO                37                345
  YES               26                162
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17P LOSS MUTATED       1                         5    57
  17P LOSS WILD-TYPE    12                        44   428
D71V7, multiclass
                           clus
vv                          17P LOSS MUTATED 17P LOSS WILD-TYPE
  ASIAN                                    1                 12
  BLACK OR AFRICAN AMERICAN                5                 44
  WHITE                                   57                428
[1] 3 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
  17P LOSS MUTATED     1  53
  17P LOSS WILD-TYPE  11 419
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      1   53
  17P LOSS WILD-TYPE   11  419
                        clus
vv                       17P LOSS MUTATED 17P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 11
  NOT HISPANIC OR LATINO               53                419
[1] 2 2
[1] FALSE

Clustering(72) Variable = 17Q LOSS MUTATION ANALYSIS
D72V1, survival
                    sevent
clus2                  0   1
  17Q LOSS MUTATED     5  35
  17Q LOSS WILD-TYPE  99 430
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                40                529 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                35                430 
$`17Q LOSS MUTATED`
TCGA-02-0001 TCGA-02-0033 TCGA-02-0051 TCGA-02-0055 TCGA-02-0059 TCGA-02-0079 
       11.77         2.83        15.09         2.50         9.57        27.25 
TCGA-02-0106 TCGA-02-0113 TCGA-02-0258 TCGA-02-0269 TCGA-06-0130 TCGA-06-0147 
       11.67        92.65        16.54        10.75        12.95        17.79 
TCGA-06-0149 TCGA-06-0152 TCGA-06-0159 TCGA-06-0177 TCGA-06-0184 TCGA-06-0187 
        8.61        12.33         9.44         4.18        69.90        27.22 
TCGA-06-0189 TCGA-06-0190 TCGA-06-0197 TCGA-06-0644 TCGA-06-5408 TCGA-08-0353 
       15.42        10.42         5.56        12.62        11.74         8.42 
TCGA-08-0386 TCGA-12-0772 TCGA-12-0826 TCGA-12-1098 TCGA-12-3653 TCGA-14-0871 
       18.02        53.85        27.78         3.98        14.53        28.93 
TCGA-14-1453 TCGA-15-1447 TCGA-19-2623 TCGA-19-4065 TCGA-28-2509 TCGA-32-2491 
        1.15        53.19         7.53         7.04         4.77        12.23 
TCGA-41-3392 TCGA-41-5651 TCGA-76-4934 TCGA-76-6285 
        0.99        15.12         2.53         8.35 

$`17Q LOSS WILD-TYPE`
TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 TCGA-02-0011 
        4.73        18.35        23.18        10.59        35.41        20.71 
TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0024 
       82.59        20.61        87.06        77.65        20.12        53.10 
TCGA-02-0025 TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0034 TCGA-02-0037 
       42.74        24.59        12.16        90.58        14.14         3.62 
TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 TCGA-02-0048 
       10.72        10.52        18.31         6.87        14.73         3.22 
TCGA-02-0052 TCGA-02-0054 TCGA-02-0057 TCGA-02-0058 TCGA-02-0060 TCGA-02-0064 
       12.59         6.54        19.86         8.35         6.02        19.73 
TCGA-02-0068 TCGA-02-0069 TCGA-02-0070 TCGA-02-0071 TCGA-02-0074 TCGA-02-0075 
       26.43        28.70        25.05         5.49        10.19        20.84 
TCGA-02-0080 TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 
       89.72        22.72        12.62        51.32         8.81        57.76 
TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 TCGA-02-0104 TCGA-02-0107 TCGA-02-0111 
       16.96         3.48        27.02        65.00        17.65        23.18 
TCGA-02-0114 TCGA-02-0115 TCGA-02-0116 TCGA-02-0260 TCGA-02-0266 TCGA-02-0271 
       99.98        15.65        48.95        16.93        17.72        14.47 
TCGA-02-0281 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 
        3.98        13.87        14.20        15.95        12.23         9.90 
TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 TCGA-02-0333 
        7.73        10.62         7.33        15.91        25.71         4.37 
TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 
       25.12        10.59        12.39        14.50        10.55        47.11 
TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 TCGA-02-2466 TCGA-02-2470 
       11.34         9.27        16.21         3.35        16.80        12.92 
TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 
       15.32        15.45        20.32         2.70         6.15        20.38 
TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0132 
       47.61         6.94         3.98        22.72        33.67        25.35 
TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 
       14.30        26.70        24.23        11.90         0.20        10.29 
TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0148 TCGA-06-0150 
        2.20        11.74         2.33        20.09        10.09        19.46 
TCGA-06-0151 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0160 
       46.59        13.94        10.45         3.19        10.82        11.80 
TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 
        3.42        56.91        10.65         5.85        19.66         3.29 
TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0178 
       13.12         4.47         3.22         4.04        91.00        88.14 
TCGA-06-0179 TCGA-06-0182 TCGA-06-0185 TCGA-06-0188 TCGA-06-0192 TCGA-06-0194 
       20.25         3.65        73.84        44.58        38.96         4.67 
TCGA-06-0195 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 
        7.40         0.39         7.66         8.42         7.63         7.40 
TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 
       11.84         0.53        15.02        24.16         0.72        19.82 
TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 
       13.64        13.32        20.42        48.69        10.82         9.01 
TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 
        0.26        72.36         4.70         9.57         3.16        35.11 
TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 
        5.75         5.75         9.80         2.10        23.57        14.20 
TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 
       26.40        46.88         7.86         2.70         2.70         0.92 
TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 
       43.46        46.19         5.65         7.17        40.41        16.57 
TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 
       20.78        26.76        23.93         6.84         4.04        26.79 
TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 TCGA-06-2557 
       11.84        15.32        13.61        33.90        15.32         1.08 
TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 
       12.49         4.93        17.65        12.56        30.64         5.95 
TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-5410 
       16.64         5.98         4.37         0.43        31.50         3.55 
TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 
        8.35         4.54         8.81         8.98         8.55         6.71 
TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 TCGA-06-6389 
        2.73         3.75         6.15         4.57         5.23         7.79 
TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 
        5.39         1.48       120.56         7.36         8.32        12.85 
TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A5U1 
        4.77         1.55         4.77         4.96         4.70         1.87 
TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK TCGA-06-A7TL TCGA-08-0244 TCGA-08-0245 
        3.12         2.56         5.39         5.42        22.68        37.84 
TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 
        4.18       115.86         1.74         8.42        25.71        12.16 
TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0354 TCGA-08-0355 
        9.80        29.23        65.33         1.28        17.95        24.56 
TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 
       31.10        37.58        22.29         3.39        12.23        14.93 
TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 
       15.35        13.97         0.72        12.56         4.27        42.15 
TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 
       11.08        19.59        58.68        19.33        10.75         4.80 
TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 
        7.27        15.98        18.41         7.56        15.35        14.73 
TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 
       12.99        34.92        10.45         7.59        94.78         0.10 
TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 
       38.17        25.97        26.66        12.13         3.65        20.38 
TCGA-12-0707 TCGA-12-0769 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 
       28.41        15.06        43.23         7.63         9.73        14.93 
TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 
       14.86        91.76        24.79        18.48        10.62        23.51 
TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 
       38.76         8.94        20.58       127.59         5.82         7.59 
TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 
       33.21        21.73        15.98        12.23        15.85         9.11 
TCGA-12-1097 TCGA-12-1099 TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 
       14.53         4.14        15.65        25.68        14.73         6.77 
TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 
       59.77        44.02        26.93        15.22        10.95        12.69 
TCGA-12-3652 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 
       34.92        14.93         3.22         2.04        15.12        11.97 
TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 
        0.95         6.21        23.05         2.24        11.24        13.78 
TCGA-14-0812 TCGA-14-0813 TCGA-14-0817 TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 
        3.25         1.35         5.39         2.89        16.50        26.33 
TCGA-14-0867 TCGA-14-1034 TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 TCGA-14-1396 
        2.04        15.95        19.30         0.79         1.38         1.12 
TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 TCGA-14-1452 TCGA-14-1454 
        3.75        32.05        58.78        23.11         7.10        30.18 
TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 
        0.92        40.96         6.67        12.43         0.99         1.97 
TCGA-14-1821 TCGA-14-1823 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 
       17.79        17.85         7.63         5.88         7.17        17.49 
TCGA-14-2555 TCGA-14-3477 TCGA-14-4157 TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 
        7.96         3.78         3.42        13.78        50.53        19.10 
TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 
       13.28         3.91        17.59        26.07        16.37         4.31 
TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 
       29.03         4.57        10.29        14.01         9.14        21.24 
TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 TCGA-19-0962 
       13.97         6.41        11.77        21.90         8.61         0.66 
TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 TCGA-19-1388 
       14.27         3.39        10.75         9.07         5.95        12.95 
TCGA-19-1389 TCGA-19-1390 TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 
        4.64        25.38         3.65         7.17        12.66         3.25 
TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2624 TCGA-19-2625 
        0.13         9.67         4.87         1.08         0.16         4.08 
TCGA-19-2629 TCGA-19-2631 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 
       24.23         7.00         6.64        17.19         8.02        18.90 
TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 
        4.73        12.10         1.78        22.49        14.07        16.80 
TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 
       14.96        17.79         3.98        28.54        10.03        13.87 
TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5133 
        9.73        31.33         7.13         9.37         9.40        14.86 
TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 
        5.49         8.88        18.97         1.58         7.92         2.33 
TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 
       19.33         5.06        16.60         9.86        24.23        40.54 
TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 
       21.30        30.05        14.04        11.51        24.76        10.39 
TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 
       10.39        16.08         7.59         2.86        14.40        15.78 
TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 TCGA-28-1752 
        0.20         2.53         9.21         8.35         7.63         8.48 
TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 TCGA-28-2502 TCGA-28-2506 
        1.22         1.55         2.83         0.13         0.66         6.74 
TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 
        7.30         5.26        14.93        11.28        17.88        14.53 
TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 
       11.77        31.27        23.44        11.01        13.64         5.16 
TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 
       22.68        12.76         5.42        15.39        21.07         0.49 
TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 
        0.10        15.85        19.50         1.18         4.67        12.69 
TCGA-32-1987 TCGA-32-1991 TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 TCGA-32-2616 
       14.86        16.93        20.78        15.02        15.95         7.36 
TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4210 TCGA-32-4211 
        8.84        22.78        25.18        21.14         3.72        12.59 
TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 
       19.86        10.85        19.23         0.85        13.35         8.94 
TCGA-41-2575 TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-41-6646 TCGA-4W-AA9S 
        9.53         4.44        11.84         0.20        12.46         4.14 
TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 
       14.76         3.45        20.91         4.34        14.33         8.22 
TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 
        7.50         4.80         4.54         3.09         3.65         9.17 
TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 
       10.78        16.70         3.29         2.70        11.38        17.06 
TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 
       20.98         4.83         5.03         0.23         9.27         7.73 
TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R TCGA-RR-A6KA 
        7.79         1.61        17.72        26.30         5.92         6.28 
TCGA-RR-A6KC 
       20.55 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              0.99               0.10 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             92.65             127.59 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
            11.755             11.900 
[1] "1.0 - 92.7 (11.8)"  "0.1 - 127.6 (11.9)"
[1] "hr=" "1.1"
D72V2, continuous
D72V3, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    18  22
  17Q LOSS WILD-TYPE 206 324
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     18   22
  17Q LOSS WILD-TYPE  206  324
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE               18                206
  MALE                 22                324
[1] 2 2
[1] FALSE
D72V4, continuous
                    vv
clus                 GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  17Q LOSS MUTATED                               1                   1
  17Q LOSS WILD-TYPE                            26                  17
                    vv
clus                 UNTREATED PRIMARY (DE NOVO) GBM
  17Q LOSS MUTATED                                38
  17Q LOSS WILD-TYPE                             487
D72V5, multiclass
                                 clus
vv                                17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                  1                 26
  TREATED PRIMARY GBM                            1                 17
  UNTREATED PRIMARY (DE NOVO) GBM               38                487
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V6, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    21  19
  17Q LOSS WILD-TYPE 361 169
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     21   19
  17Q LOSS WILD-TYPE  361  169
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  NO                21                361
  YES               19                169
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17Q LOSS MUTATED       0                         2    38
  17Q LOSS WILD-TYPE    13                        47   447
D72V7, multiclass
                           clus
vv                          17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  ASIAN                                    0                 13
  BLACK OR AFRICAN AMERICAN                2                 47
  WHITE                                   38                447
[1] 3 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
  17Q LOSS MUTATED     1  33
  17Q LOSS WILD-TYPE  11 439
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      1   33
  17Q LOSS WILD-TYPE   11  439
                        clus
vv                       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 11
  NOT HISPANIC OR LATINO               33                439
[1] 2 2
[1] FALSE

Clustering(73) Variable = 18P LOSS MUTATION ANALYSIS
D73V1, survival
                    sevent
clus2                  0   1
  18P LOSS MUTATED    17  53
  18P LOSS WILD-TYPE  87 412
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                70                499 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                53                412 
$`18P LOSS MUTATED`
TCGA-02-0006 TCGA-02-0010 TCGA-02-0011 TCGA-02-0034 TCGA-02-0075 TCGA-02-0079 
       18.35        35.41        20.71        14.14        20.84        27.25 
TCGA-02-0106 TCGA-02-0111 TCGA-02-0113 TCGA-02-0324 TCGA-02-2470 TCGA-06-0129 
       11.67        23.18        92.65         7.73        12.92        33.67 
TCGA-06-0151 TCGA-06-0171 TCGA-06-0173 TCGA-06-0206 TCGA-06-0213 TCGA-06-0237 
       46.59        13.12         4.47         7.66         0.53        13.64 
TCGA-06-0648 TCGA-06-0649 TCGA-06-0876 TCGA-06-1086 TCGA-06-1800 TCGA-06-1806 
        9.80         2.10        46.19         6.84        26.79        15.32 
TCGA-06-5408 TCGA-06-5859 TCGA-06-6694 TCGA-06-6695 TCGA-06-A5U0 TCGA-08-0245 
       11.74         4.57         7.36         8.32         4.70        37.84 
TCGA-08-0350 TCGA-08-0510 TCGA-08-0525 TCGA-12-0776 TCGA-12-0826 TCGA-12-1088 
       29.23         4.27        15.98         9.73        27.78       127.59 
TCGA-12-1096 TCGA-14-0812 TCGA-14-0817 TCGA-14-1453 TCGA-14-4157 TCGA-16-0846 
        9.11         3.25         5.39         1.15         3.42         3.91 
TCGA-16-0850 TCGA-19-1390 TCGA-19-4065 TCGA-19-5960 TCGA-26-1438 TCGA-26-1439 
       16.37        25.38         7.04        14.96        10.03        13.87 
TCGA-26-5133 TCGA-27-1830 TCGA-27-1834 TCGA-27-1838 TCGA-28-1750 TCGA-28-2514 
       14.86         5.06        40.54        11.51         8.35         5.26 
TCGA-28-5207 TCGA-28-5213 TCGA-28-5216 TCGA-32-1976 TCGA-32-2491 TCGA-32-2634 
       11.28        31.27        13.64         0.49        12.23        22.78 
TCGA-32-4210 TCGA-41-3392 TCGA-4W-AA9S TCGA-74-6575 TCGA-76-4925 TCGA-76-4929 
        3.72         0.99         4.14        20.91         4.80         3.65 
TCGA-76-6191 TCGA-76-6285 TCGA-76-6286 TCGA-81-5911 
       16.70         8.35        20.98        17.72 

$`18P LOSS WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0007 TCGA-02-0009 TCGA-02-0014 TCGA-02-0015 
       11.77         4.73        23.18        10.59        82.59        20.61 
TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0024 TCGA-02-0025 TCGA-02-0026 
       87.06        77.65        20.12        53.10        42.74        24.59 
TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 
       12.16        90.58         2.83         3.62        10.72        10.52 
TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 TCGA-02-0048 TCGA-02-0051 TCGA-02-0052 
       18.31         6.87        14.73         3.22        15.09        12.59 
TCGA-02-0054 TCGA-02-0055 TCGA-02-0057 TCGA-02-0058 TCGA-02-0059 TCGA-02-0060 
        6.54         2.50        19.86         8.35         9.57         6.02 
TCGA-02-0064 TCGA-02-0068 TCGA-02-0069 TCGA-02-0070 TCGA-02-0071 TCGA-02-0074 
       19.73        26.43        28.70        25.05         5.49        10.19 
TCGA-02-0080 TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 
       89.72        22.72        12.62        51.32         8.81        57.76 
TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 TCGA-02-0104 TCGA-02-0107 TCGA-02-0114 
       16.96         3.48        27.02        65.00        17.65        99.98 
TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 TCGA-02-0266 TCGA-02-0269 
       15.65        48.95        16.54        16.93        17.72        10.75 
TCGA-02-0271 TCGA-02-0281 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 
       14.47         3.98        13.87        14.20        15.95        12.23 
TCGA-02-0321 TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 TCGA-02-0333 
        9.90        10.62         7.33        15.91        25.71         4.37 
TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 
       25.12        10.59        12.39        14.50        10.55        47.11 
TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 TCGA-02-2466 TCGA-02-2483 
       11.34         9.27        16.21         3.35        16.80        15.32 
TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 
       15.45        20.32         2.70         6.15        20.38        47.61 
TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 
        6.94         3.98        22.72        12.95        25.35        14.30 
TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 
       26.70        24.23        11.90         0.20        10.29         2.20 
TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 
       11.74         2.33        20.09        17.79        10.09         8.61 
TCGA-06-0150 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 
       19.46        12.33        13.94        10.45         3.19        10.82 
TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 
        9.44        11.80         3.42        56.91        10.65         5.85 
TCGA-06-0168 TCGA-06-0169 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 
       19.66         3.29         3.22         4.04        91.00         4.18 
TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 
       88.14        20.25         3.65        69.90        73.84        27.22 
TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 
       44.58        15.42        10.42        38.96         4.67         7.40 
TCGA-06-0197 TCGA-06-0201 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 
        5.56         0.39         8.42         7.63         7.40        11.84 
TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0238 TCGA-06-0240 
       15.02        24.16         0.72        19.82        13.32        20.42 
TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 
       48.69        10.82         9.01         0.26        72.36         4.70 
TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 
        9.57         3.16        35.11        12.62         5.75         5.75 
TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 
       23.57        14.20        26.40        46.88         7.86         2.70 
TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0877 TCGA-06-0878 TCGA-06-0879 
        2.70         0.92        43.46         5.65         7.17        40.41 
TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1087 TCGA-06-1801 
       16.57        20.78        26.76        23.93         4.04        11.84 
TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 
       15.32        13.61        33.90         1.08        12.49         4.93 
TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 
       17.65        12.56        30.64         5.95        16.64         5.98 
TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 
        4.37         0.43        31.50         3.55         8.35         4.54 
TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 TCGA-06-5418 TCGA-06-5856 
        8.81         8.98         8.55         6.71         2.73         3.75 
TCGA-06-5858 TCGA-06-6388 TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 
        6.15         5.23         7.79         5.39         1.48       120.56 
TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U1 
       12.85         4.77         1.55         4.77         4.96         1.87 
TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK TCGA-06-A7TL TCGA-08-0244 TCGA-08-0246 
        3.12         2.56         5.39         5.42        22.68         4.18 
TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 
      115.86         1.74         8.42        25.71        12.16         9.80 
TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 
       65.33         1.28         8.42        17.95        24.56        31.10 
TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 
       37.58        22.29         3.39        12.23        14.93        18.02 
TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0512 TCGA-08-0514 
       15.35        13.97         0.72        12.56        42.15        11.08 
TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 
       19.59        58.68        19.33        10.75         4.80         7.27 
TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 
       18.41         7.56        15.35        14.73        12.99        34.92 
TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 
       10.45         7.59        94.78         0.10        38.17        25.97 
TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 
       26.66        12.13         3.65        20.38        28.41        15.06 
TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 
       53.85        43.23         7.63        14.93        14.86        91.76 
TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 TCGA-12-0827 TCGA-12-0828 
       24.79        18.48        10.62        23.51        38.76         8.94 
TCGA-12-0829 TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 
       20.58         5.82         7.59        33.21        21.73        15.98 
TCGA-12-1094 TCGA-12-1095 TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 TCGA-12-1598 
       12.23        15.85        14.53         3.98         4.14        15.65 
TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 
       25.68        14.73         6.77        59.77        44.02        26.93 
TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 
       15.22        10.95        12.69        34.92        14.53        14.93 
TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 TCGA-14-0783 
        3.22         2.04        15.12        11.97         0.95         6.21 
TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 TCGA-14-0813 TCGA-14-0862 
       23.05         2.24        11.24        13.78         1.35         2.89 
TCGA-14-0865 TCGA-14-0866 TCGA-14-0867 TCGA-14-0871 TCGA-14-1034 TCGA-14-1037 
       16.50        26.33         2.04        28.93        15.95        19.30 
TCGA-14-1043 TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 
        0.79         1.38         1.12         3.75        32.05        58.78 
TCGA-14-1451 TCGA-14-1452 TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 
       23.11         7.10        30.18         0.92        40.96         6.67 
TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 TCGA-14-1823 TCGA-14-1825 
       12.43         0.99         1.97        17.79        17.85         7.63 
TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-3477 TCGA-15-0742 
        5.88         7.17        17.49         7.96         3.78        13.78 
TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 TCGA-16-0848 TCGA-16-0849 
       50.53        19.10        53.19        13.28        17.59        26.07 
TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 
        4.31        29.03         4.57        10.29        14.01         9.14 
TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 
       21.24        13.97         6.41        11.77        21.90         8.61 
TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 
        0.66        14.27         3.39        10.75         9.07         5.95 
TCGA-19-1388 TCGA-19-1389 TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 
       12.95         4.64         3.65         7.17        12.66         3.25 
TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 
        0.13         9.67         4.87         1.08         7.53         0.16 
TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 
        4.08        24.23         7.00         6.64        17.19         8.02 
TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 
       18.90         4.73        12.10         1.78        22.49        14.07 
TCGA-19-5959 TCGA-19-A60I TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1440 TCGA-26-1442 
       16.80        17.79         3.98        28.54         9.73        31.33 
TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 
        7.13         9.37         9.40         5.49         8.88        18.97 
TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-26-A7UX TCGA-27-1831 TCGA-27-1832 
        1.58         7.92         2.33        19.33        16.60         9.86 
TCGA-27-1833 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-2518 TCGA-27-2519 
       24.23        21.30        30.05        14.04        24.76        10.39 
TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 
       10.39        16.08         7.59         2.86        14.40        15.78 
TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 
        0.20         2.53         9.21         7.63         8.48         1.22 
TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 TCGA-28-2502 TCGA-28-2506 TCGA-28-2509 
        1.55         2.83         0.13         0.66         6.74         4.77 
TCGA-28-2513 TCGA-28-5204 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5214 
        7.30        14.93        17.88        14.53        11.77        23.44 
TCGA-28-5215 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 
       11.01         5.16        22.68        12.76         5.42        15.39 
TCGA-32-1973 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 
       21.07         0.10        15.85        19.50         1.18         4.67 
TCGA-32-1986 TCGA-32-1987 TCGA-32-1991 TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 
       12.69        14.86        16.93        20.78        15.02        15.95 
TCGA-32-2616 TCGA-32-2632 TCGA-32-2638 TCGA-32-4208 TCGA-32-4211 TCGA-32-4213 
        7.36         8.84        25.18        21.14        12.59        19.86 
TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 
       10.85        19.23         0.85        13.35         8.94         9.53 
TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9T 
        4.44        11.84         0.20        15.12        12.46        14.76 
TCGA-74-6573 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 TCGA-76-4926 
        3.45         4.34        14.33         8.22         7.50         4.54 
TCGA-76-4928 TCGA-76-4931 TCGA-76-4934 TCGA-76-4935 TCGA-76-6192 TCGA-76-6193 
        3.09         9.17         2.53        10.78         3.29         2.70 
TCGA-76-6280 TCGA-76-6282 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 
       11.38        17.06         4.83         5.03         0.23         9.27 
TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-87-5896 TCGA-OX-A56R TCGA-RR-A6KA 
        7.73         7.79         1.61        26.30         5.92         6.28 
TCGA-RR-A6KC 
       20.55 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              0.49               0.10 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            127.59             120.56 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            11.985             11.840 
[1] "0.5 - 127.6 (12.0)" "0.1 - 120.6 (11.8)"
[1] "hr=" "1.2"
D73V2, continuous
D73V3, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    25  45
  18P LOSS WILD-TYPE 199 301
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     25   45
  18P LOSS WILD-TYPE  199  301
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE               25                199
  MALE                 45                301
[1] 2 2
[1] FALSE
D73V4, continuous
                    vv
clus                 GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  18P LOSS MUTATED                               4                   3
  18P LOSS WILD-TYPE                            23                  15
                    vv
clus                 UNTREATED PRIMARY (DE NOVO) GBM
  18P LOSS MUTATED                                63
  18P LOSS WILD-TYPE                             462
D73V5, multiclass
                                 clus
vv                                18P LOSS MUTATED 18P LOSS WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                  4                 23
  TREATED PRIMARY GBM                            3                 15
  UNTREATED PRIMARY (DE NOVO) GBM               63                462
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V6, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    47  23
  18P LOSS WILD-TYPE 335 165
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     47   23
  18P LOSS WILD-TYPE  335  165
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  NO                47                335
  YES               23                165
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18P LOSS MUTATED       3                         7    57
  18P LOSS WILD-TYPE    10                        42   428
D73V7, multiclass
                           clus
vv                          18P LOSS MUTATED 18P LOSS WILD-TYPE
  ASIAN                                    3                 10
  BLACK OR AFRICAN AMERICAN                7                 42
  WHITE                                   57                428
[1] 3 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
  18P LOSS MUTATED     2  57
  18P LOSS WILD-TYPE  10 415
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      2   57
  18P LOSS WILD-TYPE   10  415
                        clus
vv                       18P LOSS MUTATED 18P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                 10
  NOT HISPANIC OR LATINO               57                415
[1] 2 2
[1] FALSE

Clustering(74) Variable = 18Q LOSS MUTATION ANALYSIS
D74V1, survival
                    sevent
clus2                  0   1
  18Q LOSS MUTATED    14  48
  18Q LOSS WILD-TYPE  90 417
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                62                507 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                48                417 
$`18Q LOSS MUTATED`
TCGA-02-0006 TCGA-02-0011 TCGA-02-0075 TCGA-02-0079 TCGA-02-0106 TCGA-02-0111 
       18.35        20.71        20.84        27.25        11.67        23.18 
TCGA-02-0113 TCGA-02-0324 TCGA-06-0129 TCGA-06-0151 TCGA-06-0173 TCGA-06-0206 
       92.65         7.73        33.67        46.59         4.47         7.66 
TCGA-06-0213 TCGA-06-0237 TCGA-06-0648 TCGA-06-0649 TCGA-06-0749 TCGA-06-1086 
        0.53        13.64         9.80         2.10         2.70         6.84 
TCGA-06-1800 TCGA-06-1806 TCGA-06-2559 TCGA-06-5859 TCGA-06-6694 TCGA-06-A5U0 
       26.79        15.32         4.93         4.57         7.36         4.70 
TCGA-08-0245 TCGA-08-0359 TCGA-08-0510 TCGA-08-0525 TCGA-12-0776 TCGA-12-0826 
       37.84         3.39         4.27        15.98         9.73        27.78 
TCGA-12-1088 TCGA-12-1096 TCGA-14-0812 TCGA-14-0817 TCGA-16-0846 TCGA-19-0962 
      127.59         9.11         3.25         5.39         3.91         0.66 
TCGA-19-1390 TCGA-19-2619 TCGA-19-4065 TCGA-19-5960 TCGA-26-1438 TCGA-26-1439 
       25.38         9.67         7.04        14.96        10.03        13.87 
TCGA-26-5133 TCGA-27-1834 TCGA-27-1838 TCGA-28-1750 TCGA-28-2514 TCGA-28-5207 
       14.86        40.54        11.51         8.35         5.26        11.28 
TCGA-28-5213 TCGA-28-5216 TCGA-32-1973 TCGA-32-1976 TCGA-32-1987 TCGA-32-2491 
       31.27        13.64        21.07         0.49        14.86        12.23 
TCGA-32-2634 TCGA-32-4210 TCGA-41-3392 TCGA-4W-AA9S TCGA-76-4925 TCGA-76-6285 
       22.78         3.72         0.99         4.14         4.80         8.35 
TCGA-76-6286 TCGA-81-5911 
       20.98        17.72 

$`18Q LOSS WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 TCGA-02-0014 
       11.77         4.73        23.18        10.59        35.41        82.59 
TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0024 TCGA-02-0025 
       20.61        87.06        77.65        20.12        53.10        42.74 
TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 
       24.59        12.16        90.58         2.83        14.14         3.62 
TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 TCGA-02-0048 
       10.72        10.52        18.31         6.87        14.73         3.22 
TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 TCGA-02-0055 TCGA-02-0057 TCGA-02-0058 
       15.09        12.59         6.54         2.50        19.86         8.35 
TCGA-02-0059 TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 TCGA-02-0069 TCGA-02-0070 
        9.57         6.02        19.73        26.43        28.70        25.05 
TCGA-02-0071 TCGA-02-0074 TCGA-02-0080 TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 
        5.49        10.19        89.72        22.72        12.62        51.32 
TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 TCGA-02-0104 
        8.81        57.76        16.96         3.48        27.02        65.00 
TCGA-02-0107 TCGA-02-0114 TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 
       17.65        99.98        15.65        48.95        16.54        16.93 
TCGA-02-0266 TCGA-02-0269 TCGA-02-0271 TCGA-02-0281 TCGA-02-0285 TCGA-02-0289 
       17.72        10.75        14.47         3.98        13.87        14.20 
TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 
       15.95        12.23         9.90        10.62         7.33        15.91 
TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 
       25.71         4.37        25.12        10.59        12.39        14.50 
TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 
       10.55        47.11        11.34         9.27        16.21         3.35 
TCGA-02-2466 TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 
       16.80        12.92        15.32        15.45        20.32         2.70 
TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 
        6.15        20.38        47.61         6.94         3.98        22.72 
TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 
       12.95        25.35        14.30        26.70        24.23        11.90 
TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 
        0.20        10.29         2.20        11.74         2.33        20.09 
TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0152 TCGA-06-0154 
       17.79        10.09         8.61        19.46        12.33        13.94 
TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 
       10.45         3.19        10.82         9.44        11.80         3.42 
TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 
       56.91        10.65         5.85        19.66         3.29        13.12 
TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 
        3.22         4.04        91.00         4.18        88.14        20.25 
TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 
        3.65        69.90        73.84        27.22        44.58        15.42 
TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 
       10.42        38.96         4.67         7.40         5.56         0.39 
TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0214 TCGA-06-0216 
        8.42         7.63         7.40        11.84        15.02        24.16 
TCGA-06-0219 TCGA-06-0221 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 
        0.72        19.82        13.32        20.42        48.69        10.82 
TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 
        9.01         0.26        72.36         4.70         9.57         3.16 
TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0650 TCGA-06-0686 
       35.11        12.62         5.75         5.75        23.57        14.20 
TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0750 TCGA-06-0875 
       26.40        46.88         7.86         2.70         0.92        43.46 
TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 
       46.19         5.65         7.17        40.41        16.57        20.78 
TCGA-06-0939 TCGA-06-1084 TCGA-06-1087 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 
       26.76        23.93         4.04        11.84        15.32        13.61 
TCGA-06-1805 TCGA-06-2557 TCGA-06-2558 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 
       33.90         1.08        12.49        17.65        12.56        30.64 
TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 
        5.95        16.64         5.98         4.37         0.43        31.50 
TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 
       11.74         3.55         8.35         4.54         8.81         8.98 
TCGA-06-5415 TCGA-06-5416 TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 TCGA-06-6388 
        8.55         6.71         2.73         3.75         6.15         5.23 
TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6695 TCGA-06-6697 
        7.79         5.39         1.48       120.56         8.32        12.85 
TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U1 TCGA-06-A6S0 
        4.77         1.55         4.77         4.96         1.87         3.12 
TCGA-06-A6S1 TCGA-06-A7TK TCGA-06-A7TL TCGA-08-0244 TCGA-08-0246 TCGA-08-0344 
        2.56         5.39         5.42        22.68         4.18       115.86 
TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 
        1.74         8.42        25.71        12.16         9.80        29.23 
TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 
       65.33         1.28         8.42        17.95        24.56        31.10 
TCGA-08-0357 TCGA-08-0358 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 
       37.58        22.29        12.23        14.93        18.02        15.35 
TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 
       13.97         0.72        12.56        42.15        11.08        19.59 
TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0529 
       58.68        19.33        10.75         4.80         7.27        18.41 
TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 
        7.56        15.35        14.73        12.99        34.92        10.45 
TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 
        7.59        94.78         0.10        38.17        25.97        26.66 
TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 
       12.13         3.65        20.38        28.41        15.06        53.85 
TCGA-12-0773 TCGA-12-0775 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 
       43.23         7.63        14.93        14.86        91.76        24.79 
TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 
       18.48        10.62        23.51        38.76         8.94        20.58 
TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 
        5.82         7.59        33.21        21.73        15.98        12.23 
TCGA-12-1095 TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 TCGA-12-1598 TCGA-12-1599 
       15.85        14.53         3.98         4.14        15.65        25.68 
TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 
       14.73         6.77        59.77        44.02        26.93        15.22 
TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 
       10.95        12.69        34.92        14.53        14.93         3.22 
TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 
        2.04        15.12        11.97         0.95         6.21        23.05 
TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 TCGA-14-0813 TCGA-14-0862 TCGA-14-0865 
        2.24        11.24        13.78         1.35         2.89        16.50 
TCGA-14-0866 TCGA-14-0867 TCGA-14-0871 TCGA-14-1034 TCGA-14-1037 TCGA-14-1043 
       26.33         2.04        28.93        15.95        19.30         0.79 
TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 
        1.38         1.12         3.75        32.05        58.78        23.11 
TCGA-14-1452 TCGA-14-1453 TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 
        7.10         1.15        30.18         0.92        40.96         6.67 
TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 TCGA-14-1823 TCGA-14-1825 
       12.43         0.99         1.97        17.79        17.85         7.63 
TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-3477 TCGA-14-4157 
        5.88         7.17        17.49         7.96         3.78         3.42 
TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 TCGA-16-0848 
       13.78        50.53        19.10        53.19        13.28        17.59 
TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 
       26.07        16.37         4.31        29.03         4.57        10.29 
TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 
       14.01         9.14        21.24        13.97         6.41        11.77 
TCGA-19-0957 TCGA-19-0960 TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 
       21.90         8.61        14.27         3.39        10.75         9.07 
TCGA-19-1387 TCGA-19-1388 TCGA-19-1389 TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 
        5.95        12.95         4.64         3.65         7.17        12.66 
TCGA-19-1789 TCGA-19-1791 TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 
        3.25         0.13         4.87         1.08         7.53         0.16 
TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 
        4.08        24.23         7.00         6.64        17.19         8.02 
TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 
       18.90         4.73        12.10         1.78        22.49        14.07 
TCGA-19-5959 TCGA-19-A60I TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1440 TCGA-26-1442 
       16.80        17.79         3.98        28.54         9.73        31.33 
TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 
        7.13         9.37         9.40         5.49         8.88        18.97 
TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 
        1.58         7.92         2.33        19.33         5.06        16.60 
TCGA-27-1832 TCGA-27-1833 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-2518 
        9.86        24.23        21.30        30.05        14.04        24.76 
TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 
       10.39        10.39        16.08         7.59         2.86        14.40 
TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 TCGA-28-1751 TCGA-28-1752 
       15.78         0.20         2.53         9.21         7.63         8.48 
TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 TCGA-28-2502 TCGA-28-2506 
        1.22         1.55         2.83         0.13         0.66         6.74 
TCGA-28-2509 TCGA-28-2513 TCGA-28-5204 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 
        4.77         7.30        14.93        17.88        14.53        11.77 
TCGA-28-5214 TCGA-28-5215 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 
       23.44        11.01         5.16        22.68        12.76         5.42 
TCGA-32-1970 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 
       15.39         0.10        15.85        19.50         1.18         4.67 
TCGA-32-1986 TCGA-32-1991 TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 TCGA-32-2616 
       12.69        16.93        20.78        15.02        15.95         7.36 
TCGA-32-2632 TCGA-32-2638 TCGA-32-4208 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 
        8.84        25.18        21.14        12.59        19.86        10.85 
TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3393 
       19.23         0.85        13.35         8.94         9.53         4.44 
TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9T TCGA-74-6573 
       11.84         0.20        15.12        12.46        14.76         3.45 
TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 TCGA-76-4926 
       20.91         4.34        14.33         8.22         7.50         4.54 
TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 
        3.09         3.65         9.17         2.53        10.78        16.70 
TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 TCGA-76-6656 TCGA-76-6657 
        3.29         2.70        11.38        17.06         4.83         5.03 
TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-87-5896 
        0.23         9.27         7.73         7.79         1.61        26.30 
TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC 
        5.92         6.28        20.55 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              0.49               0.10 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            127.59             120.56 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            10.655             12.100 
[1] "0.5 - 127.6 (10.7)" "0.1 - 120.6 (12.1)"
[1] "hr=" "1.1"
D74V2, continuous
D74V3, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED    23  39
  18Q LOSS WILD-TYPE 201 307
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     23   39
  18Q LOSS WILD-TYPE  201  307
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE               23                201
  MALE                 39                307
[1] 2 2
[1] FALSE
D74V4, continuous
                    vv
clus                 GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  18Q LOSS MUTATED                               4                   1
  18Q LOSS WILD-TYPE                            23                  17
                    vv
clus                 UNTREATED PRIMARY (DE NOVO) GBM
  18Q LOSS MUTATED                                57
  18Q LOSS WILD-TYPE                             468
D74V5, multiclass
                                 clus
vv                                18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                  4                 23
  TREATED PRIMARY GBM                            1                 17
  UNTREATED PRIMARY (DE NOVO) GBM               57                468
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V6, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED    37  25
  18Q LOSS WILD-TYPE 345 163
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     37   25
  18Q LOSS WILD-TYPE  345  163
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  NO                37                345
  YES               25                163
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18Q LOSS MUTATED       3                         7    50
  18Q LOSS WILD-TYPE    10                        42   435
D74V7, multiclass
                           clus
vv                          18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  ASIAN                                    3                 10
  BLACK OR AFRICAN AMERICAN                7                 42
  WHITE                                   50                435
[1] 3 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
  18Q LOSS MUTATED     3  52
  18Q LOSS WILD-TYPE   9 420
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      3   52
  18Q LOSS WILD-TYPE    9  420
                        clus
vv                       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  9
  NOT HISPANIC OR LATINO               52                420
[1] 2 2
[1] FALSE

Clustering(75) Variable = 19P LOSS MUTATION ANALYSIS
D75V1, survival
                    sevent
clus2                  0   1
  19P LOSS MUTATED     5  22
  19P LOSS WILD-TYPE  99 443
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                27                542 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                22                443 
$`19P LOSS MUTATED`
TCGA-02-0026 TCGA-02-0055 TCGA-02-0456 TCGA-02-2466 TCGA-06-0875 TCGA-06-2569 
       24.59         2.50         3.35        16.80        43.46         0.43 
TCGA-06-5411 TCGA-06-6389 TCGA-08-0344 TCGA-08-0349 TCGA-08-0358 TCGA-12-0619 
        8.35         7.79       115.86         9.80        22.29        34.92 
TCGA-12-1095 TCGA-14-0740 TCGA-14-0865 TCGA-14-1458 TCGA-14-3477 TCGA-15-1444 
       15.85        11.97        16.50         6.67         3.78        50.53 
TCGA-16-0850 TCGA-26-5136 TCGA-27-1834 TCGA-27-2519 TCGA-32-1976 TCGA-32-4210 
       16.37        18.97        40.54        10.39         0.49         3.72 
TCGA-76-4925 TCGA-76-4929 TCGA-76-4931 
        4.80         3.65         9.17 

$`19P LOSS WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 
       11.77         4.73        18.35        23.18        10.59        35.41 
TCGA-02-0011 TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 
       20.71        82.59        20.61        87.06        77.65        20.12 
TCGA-02-0024 TCGA-02-0025 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 
       53.10        42.74        12.16        90.58         2.83        14.14 
TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 
        3.62        10.72        10.52        18.31         6.87        14.73 
TCGA-02-0048 TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 TCGA-02-0057 TCGA-02-0058 
        3.22        15.09        12.59         6.54        19.86         8.35 
TCGA-02-0059 TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 TCGA-02-0069 TCGA-02-0070 
        9.57         6.02        19.73        26.43        28.70        25.05 
TCGA-02-0071 TCGA-02-0074 TCGA-02-0075 TCGA-02-0079 TCGA-02-0080 TCGA-02-0083 
        5.49        10.19        20.84        27.25        89.72        22.72 
TCGA-02-0084 TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 
       12.62        51.32         8.81        57.76        16.96         3.48 
TCGA-02-0102 TCGA-02-0104 TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 TCGA-02-0113 
       27.02        65.00        11.67        17.65        23.18        92.65 
TCGA-02-0114 TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 TCGA-02-0266 
       99.98        15.65        48.95        16.54        16.93        17.72 
TCGA-02-0269 TCGA-02-0271 TCGA-02-0281 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 
       10.75        14.47         3.98        13.87        14.20        15.95 
TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 
       12.23         9.90         7.73        10.62         7.33        15.91 
TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 
       25.71         4.37        25.12        10.59        12.39        14.50 
TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 TCGA-02-2470 
       10.55        47.11        11.34         9.27        16.21        12.92 
TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 
       15.32        15.45        20.32         2.70         6.15        20.38 
TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 
       47.61         6.94         3.98        22.72        33.67        12.95 
TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 
       25.35        14.30        26.70        24.23        11.90         0.20 
TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 
       10.29         2.20        11.74         2.33        20.09        17.79 
TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 
       10.09         8.61        19.46        46.59        12.33        13.94 
TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 
       10.45         3.19        10.82         9.44        11.80         3.42 
TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 
       56.91        10.65         5.85        19.66         3.29        13.12 
TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 
        4.47         3.22         4.04        91.00         4.18        88.14 
TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 
       20.25         3.65        69.90        73.84        27.22        44.58 
TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 
       15.42        10.42        38.96         4.67         7.40         5.56 
TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 
        0.39         7.66         8.42         7.63         7.40        11.84 
TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 
        0.53        15.02        24.16         0.72        19.82        13.64 
TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 
       13.32        20.42        48.69        10.82         9.01         0.26 
TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 
       72.36         4.70         9.57         3.16        35.11        12.62 
TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 
        5.75         5.75         9.80         2.10        23.57        14.20 
TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 
       26.40        46.88         7.86         2.70         2.70         0.92 
TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 
       46.19         5.65         7.17        40.41        16.57        20.78 
TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 
       26.76        23.93         6.84         4.04        26.79        11.84 
TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 TCGA-06-2557 TCGA-06-2558 
       15.32        13.61        33.90        15.32         1.08        12.49 
TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 
        4.93        17.65        12.56        30.64         5.95        16.64 
TCGA-06-2566 TCGA-06-2567 TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 TCGA-06-5412 
        5.98         4.37        31.50        11.74         3.55         4.54 
TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 TCGA-06-5418 TCGA-06-5856 
        8.81         8.98         8.55         6.71         2.73         3.75 
TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 
        6.15         4.57         5.23         5.39         1.48       120.56 
TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 
        7.36         8.32        12.85         4.77         1.55         4.77 
TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK 
        4.96         4.70         1.87         3.12         2.56         5.39 
TCGA-06-A7TL TCGA-08-0244 TCGA-08-0245 TCGA-08-0246 TCGA-08-0345 TCGA-08-0346 
        5.42        22.68        37.84         4.18         1.74         8.42 
TCGA-08-0347 TCGA-08-0348 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 
       25.71        12.16        29.23        65.33         1.28         8.42 
TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0359 TCGA-08-0375 
       17.95        24.56        31.10        37.58         3.39        12.23 
TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 
       14.93        18.02        15.35        13.97         0.72        12.56 
TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 
        4.27        42.15        11.08        19.59        58.68        19.33 
TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 
       10.75         4.80         7.27        15.98        18.41         7.56 
TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 
       15.35        14.73        12.99        10.45         7.59        94.78 
TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 
        0.10        38.17        25.97        26.66        12.13         3.65 
TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 
       20.38        28.41        15.06        53.85        43.23         7.63 
TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 
        9.73        14.93        14.86        91.76        24.79        18.48 
TCGA-12-0821 TCGA-12-0822 TCGA-12-0826 TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 
       10.62        23.51        27.78        38.76         8.94        20.58 
TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 
      127.59         5.82         7.59        33.21        21.73        15.98 
TCGA-12-1094 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 TCGA-12-1598 
       12.23         9.11        14.53         3.98         4.14        15.65 
TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 
       25.68        14.73         6.77        59.77        44.02        26.93 
TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 
       15.22        10.95        12.69        34.92        14.53        14.93 
TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 
        3.22         2.04        15.12         0.95         6.21        23.05 
TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 TCGA-14-0812 TCGA-14-0813 TCGA-14-0817 
        2.24        11.24        13.78         3.25         1.35         5.39 
TCGA-14-0862 TCGA-14-0866 TCGA-14-0867 TCGA-14-0871 TCGA-14-1034 TCGA-14-1037 
        2.89        26.33         2.04        28.93        15.95        19.30 
TCGA-14-1043 TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 
        0.79         1.38         1.12         3.75        32.05        58.78 
TCGA-14-1451 TCGA-14-1452 TCGA-14-1453 TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 
       23.11         7.10         1.15        30.18         0.92        40.96 
TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 TCGA-14-1823 TCGA-14-1825 
       12.43         0.99         1.97        17.79        17.85         7.63 
TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-4157 TCGA-15-0742 
        5.88         7.17        17.49         7.96         3.42        13.78 
TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 
       19.10        53.19        13.28         3.91        17.59        26.07 
TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 
        4.31        29.03         4.57        10.29        14.01         9.14 
TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 
       21.24        13.97         6.41        11.77        21.90         8.61 
TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 
        0.66        14.27         3.39        10.75         9.07         5.95 
TCGA-19-1388 TCGA-19-1389 TCGA-19-1390 TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 
       12.95         4.64        25.38         3.65         7.17        12.66 
TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 
        3.25         0.13         9.67         4.87         1.08         7.53 
TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 
        0.16         4.08        24.23         7.00         7.04         6.64 
TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 
       17.19         8.02        18.90         4.73        12.10         1.78 
TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J4 
       22.49        14.07        16.80        14.96        17.79         3.98 
TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 
       28.54        10.03        13.87         9.73        31.33         7.13 
TCGA-26-1799 TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 TCGA-26-5139 
        9.37         9.40        14.86         5.49         8.88         1.58 
TCGA-26-6173 TCGA-26-6174 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 
        7.92         2.33        19.33         5.06        16.60         9.86 
TCGA-27-1833 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 
       24.23        21.30        30.05        14.04        11.51        24.76 
TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 
       10.39        16.08         7.59         2.86        14.40        15.78 
TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 TCGA-28-1752 
        0.20         2.53         9.21         8.35         7.63         8.48 
TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 TCGA-28-2502 TCGA-28-2506 
        1.22         1.55         2.83         0.13         0.66         6.74 
TCGA-28-2509 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 
        4.77         7.30         5.26        14.93        11.28        17.88 
TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 
       14.53        11.77        31.27        23.44        11.01        13.64 
TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 
        5.16        22.68        12.76         5.42        15.39        21.07 
TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 
        0.10        15.85        19.50         1.18         4.67        12.69 
TCGA-32-1987 TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 
       14.86        16.93        12.23        20.78        15.02        15.95 
TCGA-32-2616 TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4211 
        7.36         8.84        22.78        25.18        21.14        12.59 
TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 
       19.86        10.85        19.23         0.85        13.35         8.94 
TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 
        9.53         0.99         4.44        11.84         0.20        15.12 
TCGA-41-6646 TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 
       12.46         4.14        14.76         3.45        20.91         4.34 
TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 TCGA-76-4926 TCGA-76-4928 TCGA-76-4934 
       14.33         8.22         7.50         4.54         3.09         2.53 
TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 
       10.78        16.70         3.29         2.70        11.38        17.06 
TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 
        8.35        20.98         4.83         5.03         0.23         9.27 
TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R 
        7.73         7.79         1.61        17.72        26.30         5.92 
TCGA-RR-A6KA TCGA-RR-A6KC 
        6.28        20.55 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              0.43               0.10 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
            115.86             127.59 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             10.39              11.87 
[1] "0.4 - 115.9 (10.4)" "0.1 - 127.6 (11.9)"
[1] "hr=" "1.1"
D75V2, continuous
D75V3, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    11  16
  19P LOSS WILD-TYPE 213 330
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     11   16
  19P LOSS WILD-TYPE  213  330
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE               11                213
  MALE                 16                330
[1] 2 2
[1] FALSE
D75V4, continuous
                    vv
clus                 GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  19P LOSS MUTATED                               1                   1
  19P LOSS WILD-TYPE                            26                  17
                    vv
clus                 UNTREATED PRIMARY (DE NOVO) GBM
  19P LOSS MUTATED                                25
  19P LOSS WILD-TYPE                             500
D75V5, multiclass
                                 clus
vv                                19P LOSS MUTATED 19P LOSS WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                  1                 26
  TREATED PRIMARY GBM                            1                 17
  UNTREATED PRIMARY (DE NOVO) GBM               25                500
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V6, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    19   8
  19P LOSS WILD-TYPE 363 180
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     19    8
  19P LOSS WILD-TYPE  363  180
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  NO                19                363
  YES                8                180
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19P LOSS MUTATED       0                         2    24
  19P LOSS WILD-TYPE    13                        47   461
D75V7, multiclass
                           clus
vv                          19P LOSS MUTATED 19P LOSS WILD-TYPE
  ASIAN                                    0                 13
  BLACK OR AFRICAN AMERICAN                2                 47
  WHITE                                   24                461
[1] 3 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
  19P LOSS MUTATED     0  23
  19P LOSS WILD-TYPE  12 449
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      0   23
  19P LOSS WILD-TYPE   12  449
                        clus
vv                       19P LOSS MUTATED 19P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 12
  NOT HISPANIC OR LATINO               23                449
[1] 2 2
[1] FALSE

Clustering(76) Variable = 19Q LOSS MUTATION ANALYSIS
D76V1, survival
                    sevent
clus2                  0   1
  19Q LOSS MUTATED     3  32
  19Q LOSS WILD-TYPE 101 433
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                35                534 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                32                433 
$`19Q LOSS MUTATED`
TCGA-02-0026 TCGA-02-0028 TCGA-02-0055 TCGA-02-0060 TCGA-02-0258 TCGA-02-0432 
       24.59        90.58         2.50         6.02        16.54        47.11 
TCGA-02-0456 TCGA-02-2466 TCGA-06-0875 TCGA-06-2561 TCGA-06-2569 TCGA-06-5411 
        3.35        16.80        43.46        17.65         0.43         8.35 
TCGA-06-A6S1 TCGA-08-0344 TCGA-08-0349 TCGA-08-0358 TCGA-12-0619 TCGA-12-1095 
        2.56       115.86         9.80        22.29        34.92        15.85 
TCGA-12-1598 TCGA-14-0740 TCGA-14-0862 TCGA-14-0865 TCGA-14-1458 TCGA-15-1444 
       15.65        11.97         2.89        16.50         6.67        50.53 
TCGA-16-0850 TCGA-19-1388 TCGA-26-5136 TCGA-27-1834 TCGA-27-2519 TCGA-32-1976 
       16.37        12.95        18.97        40.54        10.39         0.49 
TCGA-32-2491 TCGA-32-4210 TCGA-76-4925 TCGA-76-4929 TCGA-76-4931 
       12.23         3.72         4.80         3.65         9.17 

$`19Q LOSS WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 
       11.77         4.73        18.35        23.18        10.59        35.41 
TCGA-02-0011 TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 
       20.71        82.59        20.61        87.06        77.65        20.12 
TCGA-02-0024 TCGA-02-0025 TCGA-02-0027 TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 
       53.10        42.74        12.16         2.83        14.14         3.62 
TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 TCGA-02-0048 
       10.72        10.52        18.31         6.87        14.73         3.22 
TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 TCGA-02-0057 TCGA-02-0058 TCGA-02-0059 
       15.09        12.59         6.54        19.86         8.35         9.57 
TCGA-02-0064 TCGA-02-0068 TCGA-02-0069 TCGA-02-0070 TCGA-02-0071 TCGA-02-0074 
       19.73        26.43        28.70        25.05         5.49        10.19 
TCGA-02-0075 TCGA-02-0079 TCGA-02-0080 TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 
       20.84        27.25        89.72        22.72        12.62        51.32 
TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 TCGA-02-0104 
        8.81        57.76        16.96         3.48        27.02        65.00 
TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 TCGA-02-0113 TCGA-02-0114 TCGA-02-0115 
       11.67        17.65        23.18        92.65        99.98        15.65 
TCGA-02-0116 TCGA-02-0260 TCGA-02-0266 TCGA-02-0269 TCGA-02-0271 TCGA-02-0281 
       48.95        16.93        17.72        10.75        14.47         3.98 
TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 
       13.87        14.20        15.95        12.23         9.90         7.73 
TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 
       10.62         7.33        15.91        25.71         4.37        25.12 
TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 TCGA-02-0440 TCGA-02-0446 
       10.59        12.39        14.50        10.55        11.34         9.27 
TCGA-02-0451 TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 
       16.21        12.92        15.32        15.45        20.32         2.70 
TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 
        6.15        20.38        47.61         6.94         3.98        22.72 
TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 
       33.67        12.95        25.35        14.30        26.70        24.23 
TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 
       11.90         0.20        10.29         2.20        11.74         2.33 
TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 
       20.09        17.79        10.09         8.61        19.46        46.59 
TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 
       12.33        13.94        10.45         3.19        10.82         9.44 
TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 
       11.80         3.42        56.91        10.65         5.85        19.66 
TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 
        3.29        13.12         4.47         3.22         4.04        91.00 
TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 
        4.18        88.14        20.25         3.65        69.90        73.84 
TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 
       27.22        44.58        15.42        10.42        38.96         4.67 
TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 
        7.40         5.56         0.39         7.66         8.42         7.63 
TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 
        7.40        11.84         0.53        15.02        24.16         0.72 
TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 
       19.82        13.64        13.32        20.42        48.69        10.82 
TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 
        9.01         0.26        72.36         4.70         9.57         3.16 
TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 
       35.11        12.62         5.75         5.75         9.80         2.10 
TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 
       23.57        14.20        26.40        46.88         7.86         2.70 
TCGA-06-0749 TCGA-06-0750 TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 TCGA-06-0879 
        2.70         0.92        46.19         5.65         7.17        40.41 
TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 
       16.57        20.78        26.76        23.93         6.84         4.04 
TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 
       26.79        11.84        15.32        13.61        33.90        15.32 
TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 
        1.08        12.49         4.93        12.56        30.64         5.95 
TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 
       16.64         5.98         4.37        31.50        11.74         3.55 
TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 TCGA-06-5418 
        4.54         8.81         8.98         8.55         6.71         2.73 
TCGA-06-5856 TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 TCGA-06-6389 TCGA-06-6390 
        3.75         6.15         4.57         5.23         7.79         5.39 
TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 
        1.48       120.56         7.36         8.32        12.85         4.77 
TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S0 
        1.55         4.77         4.96         4.70         1.87         3.12 
TCGA-06-A7TK TCGA-06-A7TL TCGA-08-0244 TCGA-08-0245 TCGA-08-0246 TCGA-08-0345 
        5.39         5.42        22.68        37.84         4.18         1.74 
TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 
        8.42        25.71        12.16        29.23        65.33         1.28 
TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0359 
        8.42        17.95        24.56        31.10        37.58         3.39 
TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 
       12.23        14.93        18.02        15.35        13.97         0.72 
TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 
       12.56         4.27        42.15        11.08        19.59        58.68 
TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 
       19.33        10.75         4.80         7.27        15.98        18.41 
TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0620 TCGA-12-0654 
        7.56        15.35        14.73        12.99        10.45         7.59 
TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 
       94.78         0.10        38.17        25.97        26.66        12.13 
TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 
        3.65        20.38        28.41        15.06        53.85        43.23 
TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 
        7.63         9.73        14.93        14.86        91.76        24.79 
TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 TCGA-12-0826 TCGA-12-0827 TCGA-12-0828 
       18.48        10.62        23.51        27.78        38.76         8.94 
TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 TCGA-12-1092 
       20.58       127.59         5.82         7.59        33.21        21.73 
TCGA-12-1093 TCGA-12-1094 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 
       15.98        12.23         9.11        14.53         3.98         4.14 
TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 
       25.68        14.73         6.77        59.77        44.02        26.93 
TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 
       15.22        10.95        12.69        34.92        14.53        14.93 
TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 
        3.22         2.04        15.12         0.95         6.21        23.05 
TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 TCGA-14-0812 TCGA-14-0813 TCGA-14-0817 
        2.24        11.24        13.78         3.25         1.35         5.39 
TCGA-14-0866 TCGA-14-0867 TCGA-14-0871 TCGA-14-1034 TCGA-14-1037 TCGA-14-1043 
       26.33         2.04        28.93        15.95        19.30         0.79 
TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 
        1.38         1.12         3.75        32.05        58.78        23.11 
TCGA-14-1452 TCGA-14-1453 TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1459 
        7.10         1.15        30.18         0.92        40.96        12.43 
TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 TCGA-14-1823 TCGA-14-1825 TCGA-14-1827 
        0.99         1.97        17.79        17.85         7.63         5.88 
TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-3477 TCGA-14-4157 TCGA-15-0742 
        7.17        17.49         7.96         3.78         3.42        13.78 
TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 
       19.10        53.19        13.28         3.91        17.59        26.07 
TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 
        4.31        29.03         4.57        10.29        14.01         9.14 
TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 
       21.24        13.97         6.41        11.77        21.90         8.61 
TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 
        0.66        14.27         3.39        10.75         9.07         5.95 
TCGA-19-1389 TCGA-19-1390 TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 
        4.64        25.38         3.65         7.17        12.66         3.25 
TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 
        0.13         9.67         4.87         1.08         7.53         0.16 
TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 
        4.08        24.23         7.00         7.04         6.64        17.19 
TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 
        8.02        18.90         4.73        12.10         1.78        22.49 
TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J4 TCGA-19-A6J5 
       14.07        16.80        14.96        17.79         3.98        28.54 
TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 
       10.03        13.87         9.73        31.33         7.13         9.37 
TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 TCGA-26-5139 TCGA-26-6173 
        9.40        14.86         5.49         8.88         1.58         7.92 
TCGA-26-6174 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 
        2.33        19.33         5.06        16.60         9.86        24.23 
TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2521 
       21.30        30.05        14.04        11.51        24.76        10.39 
TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1746 
       16.08         7.59         2.86        14.40        15.78         0.20 
TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 
        2.53         9.21         8.35         7.63         8.48         1.22 
TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 TCGA-28-2502 TCGA-28-2506 TCGA-28-2509 
        1.55         2.83         0.13         0.66         6.74         4.77 
TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 
        7.30         5.26        14.93        11.28        17.88        14.53 
TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 
       11.77        31.27        23.44        11.01        13.64         5.16 
TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 TCGA-32-1977 
       22.68        12.76         5.42        15.39        21.07         0.10 
TCGA-32-1978 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 
       15.85        19.50         1.18         4.67        12.69        14.86 
TCGA-32-1991 TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 TCGA-32-2616 TCGA-32-2632 
       16.93        20.78        15.02        15.95         7.36         8.84 
TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 
       22.78        25.18        21.14        12.59        19.86        10.85 
TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 
       19.23         0.85        13.35         8.94         9.53         0.99 
TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9S 
        4.44        11.84         0.20        15.12        12.46         4.14 
TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 
       14.76         3.45        20.91         4.34        14.33         8.22 
TCGA-74-6584 TCGA-76-4926 TCGA-76-4928 TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 
        7.50         4.54         3.09         2.53        10.78        16.70 
TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 
        3.29         2.70        11.38        17.06         8.35        20.98 
TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 
        4.83         5.03         0.23         9.27         7.73         7.79 
TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC 
        1.61        17.72        26.30         5.92         6.28        20.55 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              0.43               0.10 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
            115.86             127.59 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             12.95              11.82 
[1] "0.4 - 115.9 (12.9)" "0.1 - 127.6 (11.8)"
[1] "hr=" "1.1"
D76V2, continuous
D76V3, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    14  21
  19Q LOSS WILD-TYPE 210 325
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     14   21
  19Q LOSS WILD-TYPE  210  325
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE               14                210
  MALE                 21                325
[1] 2 2
[1] FALSE
D76V4, continuous
                    vv
clus                 GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  19Q LOSS MUTATED                               2                   2
  19Q LOSS WILD-TYPE                            25                  16
                    vv
clus                 UNTREATED PRIMARY (DE NOVO) GBM
  19Q LOSS MUTATED                                31
  19Q LOSS WILD-TYPE                             494
D76V5, multiclass
                                 clus
vv                                19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                  2                 25
  TREATED PRIMARY GBM                            2                 16
  UNTREATED PRIMARY (DE NOVO) GBM               31                494
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V6, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    24  11
  19Q LOSS WILD-TYPE 358 177
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     24   11
  19Q LOSS WILD-TYPE  358  177
     clus
vv    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  NO                24                358
  YES               11                177
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19Q LOSS MUTATED       1                         2    31
  19Q LOSS WILD-TYPE    12                        47   454
D76V7, multiclass
                           clus
vv                          19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  ASIAN                                    1                 12
  BLACK OR AFRICAN AMERICAN                2                 47
  WHITE                                   31                454
[1] 3 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
  19Q LOSS MUTATED     0  30
  19Q LOSS WILD-TYPE  12 442
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      0   30
  19Q LOSS WILD-TYPE   12  442
                        clus
vv                       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 12
  NOT HISPANIC OR LATINO               30                442
[1] 2 2
[1] FALSE

Clustering(77) Variable = 20P LOSS MUTATION ANALYSIS
D77V1, survival
                    sevent
clus2                  0   1
  20P LOSS MUTATED     3  15
  20P LOSS WILD-TYPE 101 450
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                18                551 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                15                450 
$`20P LOSS MUTATED`
TCGA-02-0001 TCGA-02-0011 TCGA-02-0051 TCGA-02-0060 TCGA-02-0281 TCGA-06-0188 
       11.77        20.71        15.09         6.02         3.98        44.58 
TCGA-06-0414 TCGA-06-0686 TCGA-08-0245 TCGA-12-1099 TCGA-14-0867 TCGA-14-3477 
       35.11        14.20        37.84         4.14         2.04         3.78 
TCGA-19-1390 TCGA-19-2629 TCGA-27-2521 TCGA-28-1750 TCGA-76-4934 TCGA-76-6286 
       25.38        24.23        10.39         8.35         2.53        20.98 

$`20P LOSS WILD-TYPE`
TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 TCGA-02-0014 
        4.73        18.35        23.18        10.59        35.41        82.59 
TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0024 TCGA-02-0025 
       20.61        87.06        77.65        20.12        53.10        42.74 
TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 
       24.59        12.16        90.58         2.83        14.14         3.62 
TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 TCGA-02-0048 
       10.72        10.52        18.31         6.87        14.73         3.22 
TCGA-02-0052 TCGA-02-0054 TCGA-02-0055 TCGA-02-0057 TCGA-02-0058 TCGA-02-0059 
       12.59         6.54         2.50        19.86         8.35         9.57 
TCGA-02-0064 TCGA-02-0068 TCGA-02-0069 TCGA-02-0070 TCGA-02-0071 TCGA-02-0074 
       19.73        26.43        28.70        25.05         5.49        10.19 
TCGA-02-0075 TCGA-02-0079 TCGA-02-0080 TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 
       20.84        27.25        89.72        22.72        12.62        51.32 
TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 TCGA-02-0104 
        8.81        57.76        16.96         3.48        27.02        65.00 
TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 TCGA-02-0113 TCGA-02-0114 TCGA-02-0115 
       11.67        17.65        23.18        92.65        99.98        15.65 
TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 TCGA-02-0266 TCGA-02-0269 TCGA-02-0271 
       48.95        16.54        16.93        17.72        10.75        14.47 
TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 
       13.87        14.20        15.95        12.23         9.90         7.73 
TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 
       10.62         7.33        15.91        25.71         4.37        25.12 
TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 
       10.59        12.39        14.50        10.55        47.11        11.34 
TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 TCGA-02-2466 TCGA-02-2470 TCGA-02-2483 
        9.27        16.21         3.35        16.80        12.92        15.32 
TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 
       15.45        20.32         2.70         6.15        20.38        47.61 
TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 
        6.94         3.98        22.72        33.67        12.95        25.35 
TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 
       14.30        26.70        24.23        11.90         0.20        10.29 
TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 
        2.20        11.74         2.33        20.09        17.79        10.09 
TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 
        8.61        19.46        46.59        12.33        13.94        10.45 
TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 
        3.19        10.82         9.44        11.80         3.42        56.91 
TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 
       10.65         5.85        19.66         3.29        13.12         4.47 
TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 
        3.22         4.04        91.00         4.18        88.14        20.25 
TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0189 TCGA-06-0190 
        3.65        69.90        73.84        27.22        15.42        10.42 
TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 
       38.96         4.67         7.40         5.56         0.39         7.66 
TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 
        8.42         7.63         7.40        11.84         0.53        15.02 
TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 
       24.16         0.72        19.82        13.64        13.32        20.42 
TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 
       48.69        10.82         9.01         0.26        72.36         4.70 
TCGA-06-0412 TCGA-06-0413 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 
        9.57         3.16        12.62         5.75         5.75         9.80 
TCGA-06-0649 TCGA-06-0650 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 
        2.10        23.57        26.40        46.88         7.86         2.70 
TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 
        2.70         0.92        43.46        46.19         5.65         7.17 
TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 
       40.41        16.57        20.78        26.76        23.93         6.84 
TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 
        4.04        26.79        11.84        15.32        13.61        33.90 
TCGA-06-1806 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 
       15.32         1.08        12.49         4.93        17.65        12.56 
TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 
       30.64         5.95        16.64         5.98         4.37         0.43 
TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 
       31.50        11.74         3.55         8.35         4.54         8.81 
TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 
        8.98         8.55         6.71         2.73         3.75         6.15 
TCGA-06-5859 TCGA-06-6388 TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 
        4.57         5.23         7.79         5.39         1.48       120.56 
TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 
        7.36         8.32        12.85         4.77         1.55         4.77 
TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK 
        4.96         4.70         1.87         3.12         2.56         5.39 
TCGA-06-A7TL TCGA-08-0244 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 
        5.42        22.68         4.18       115.86         1.74         8.42 
TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 
       25.71        12.16         9.80        29.23        65.33         1.28 
TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 
        8.42        17.95        24.56        31.10        37.58        22.29 
TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 
        3.39        12.23        14.93        18.02        15.35        13.97 
TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 
        0.72        12.56         4.27        42.15        11.08        19.59 
TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 
       58.68        19.33        10.75         4.80         7.27        15.98 
TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 
       18.41         7.56        15.35        14.73        12.99        34.92 
TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 
       10.45         7.59        94.78         0.10        38.17        25.97 
TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 
       26.66        12.13         3.65        20.38        28.41        15.06 
TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 
       53.85        43.23         7.63         9.73        14.93        14.86 
TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 TCGA-12-0826 
       91.76        24.79        18.48        10.62        23.51        27.78 
TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 
       38.76         8.94        20.58       127.59         5.82         7.59 
TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 
       33.21        21.73        15.98        12.23        15.85         9.11 
TCGA-12-1097 TCGA-12-1098 TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 
       14.53         3.98        15.65        25.68        14.73         6.77 
TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 
       59.77        44.02        26.93        15.22        10.95        12.69 
TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 
       34.92        14.53        14.93         3.22         2.04        15.12 
TCGA-14-0740 TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 
       11.97         0.95         6.21        23.05         2.24        11.24 
TCGA-14-0790 TCGA-14-0812 TCGA-14-0813 TCGA-14-0817 TCGA-14-0862 TCGA-14-0865 
       13.78         3.25         1.35         5.39         2.89        16.50 
TCGA-14-0866 TCGA-14-0871 TCGA-14-1034 TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 
       26.33        28.93        15.95        19.30         0.79         1.38 
TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 TCGA-14-1452 
        1.12         3.75        32.05        58.78        23.11         7.10 
TCGA-14-1453 TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 
        1.15        30.18         0.92        40.96         6.67        12.43 
TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 TCGA-14-1823 TCGA-14-1825 TCGA-14-1827 
        0.99         1.97        17.79        17.85         7.63         5.88 
TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-4157 TCGA-15-0742 TCGA-15-1444 
        7.17        17.49         7.96         3.42        13.78        50.53 
TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 
       19.10        53.19        13.28         3.91        17.59        26.07 
TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 
       16.37         4.31        29.03         4.57        10.29        14.01 
TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 
        9.14        21.24        13.97         6.41        11.77        21.90 
TCGA-19-0960 TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 
        8.61         0.66        14.27         3.39        10.75         9.07 
TCGA-19-1387 TCGA-19-1388 TCGA-19-1389 TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 
        5.95        12.95         4.64         3.65         7.17        12.66 
TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 
        3.25         0.13         9.67         4.87         1.08         7.53 
TCGA-19-2624 TCGA-19-2625 TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 
        0.16         4.08         7.00         7.04         6.64        17.19 
TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 
        8.02        18.90         4.73        12.10         1.78        22.49 
TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J4 TCGA-19-A6J5 
       14.07        16.80        14.96        17.79         3.98        28.54 
TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 
       10.03        13.87         9.73        31.33         7.13         9.37 
TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 
        9.40        14.86         5.49         8.88        18.97         1.58 
TCGA-26-6173 TCGA-26-6174 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 
        7.92         2.33        19.33         5.06        16.60         9.86 
TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 
       24.23        40.54        21.30        30.05        14.04        11.51 
TCGA-27-2518 TCGA-27-2519 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 
       24.76        10.39        16.08         7.59         2.86        14.40 
TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 TCGA-28-1751 TCGA-28-1752 
       15.78         0.20         2.53         9.21         7.63         8.48 
TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 TCGA-28-2502 TCGA-28-2506 
        1.22         1.55         2.83         0.13         0.66         6.74 
TCGA-28-2509 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 
        4.77         7.30         5.26        14.93        11.28        17.88 
TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 
       14.53        11.77        31.27        23.44        11.01        13.64 
TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 
        5.16        22.68        12.76         5.42        15.39        21.07 
TCGA-32-1976 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 
        0.49         0.10        15.85        19.50         1.18         4.67 
TCGA-32-1986 TCGA-32-1987 TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 
       12.69        14.86        16.93        12.23        20.78        15.02 
TCGA-32-2615 TCGA-32-2616 TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 
       15.95         7.36         8.84        22.78        25.18        21.14 
TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 
        3.72        12.59        19.86        10.85        19.23         0.85 
TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 
       13.35         8.94         9.53         0.99         4.44        11.84 
TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 
        0.20        15.12        12.46         4.14        14.76         3.45 
TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 TCGA-76-4925 
       20.91         4.34        14.33         8.22         7.50         4.80 
TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-4935 TCGA-76-6191 
        4.54         3.09         3.65         9.17        10.78        16.70 
TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 TCGA-76-6656 
        3.29         2.70        11.38        17.06         8.35         4.83 
TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 
        5.03         0.23         9.27         7.73         7.79         1.61 
TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC 
       17.72        26.30         5.92         6.28        20.55 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
              2.04               0.10 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             44.58             127.59 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
            12.985             11.840 
[1] "2.0 - 44.6 (13.0)"  "0.1 - 127.6 (11.8)"
[1] "hr=" "1"  
D77V2, continuous
D77V3, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    10   8
  20P LOSS WILD-TYPE 214 338
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     10    8
  20P LOSS WILD-TYPE  214  338
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  FEMALE               10                214
  MALE                  8                338
[1] 2 2
[1] FALSE
D77V4, continuous
                    vv
clus                 GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  20P LOSS MUTATED                               0                   0
  20P LOSS WILD-TYPE                            27                  18
                    vv
clus                 UNTREATED PRIMARY (DE NOVO) GBM
  20P LOSS MUTATED                                18
  20P LOSS WILD-TYPE                             507
D77V5, multiclass
                                 clus
vv                                20P LOSS MUTATED 20P LOSS WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                  0                 27
  TREATED PRIMARY GBM                            0                 18
  UNTREATED PRIMARY (DE NOVO) GBM               18                507
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V6, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    12   6
  20P LOSS WILD-TYPE 370 182
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     12    6
  20P LOSS WILD-TYPE  370  182
     clus
vv    20P LOSS MUTATED 20P LOSS WILD-TYPE
  NO                12                370
  YES                6                182
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20P LOSS MUTATED       1                         2    15
  20P LOSS WILD-TYPE    12                        47   470
D77V7, multiclass
                           clus
vv                          20P LOSS MUTATED 20P LOSS WILD-TYPE
  ASIAN                                    1                 12
  BLACK OR AFRICAN AMERICAN                2                 47
  WHITE                                   15                470
[1] 3 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
  20P LOSS MUTATED     1  15
  20P LOSS WILD-TYPE  11 457
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      1   15
  20P LOSS WILD-TYPE   11  457
                        clus
vv                       20P LOSS MUTATED 20P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 11
  NOT HISPANIC OR LATINO               15                457
[1] 2 2
[1] FALSE

Clustering(78) Variable = 20Q LOSS MUTATION ANALYSIS
D78V1, survival
                    sevent
clus2                  0   1
  20Q LOSS MUTATED     2  14
  20Q LOSS WILD-TYPE 102 451
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                16                553 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                14                451 
$`20Q LOSS MUTATED`
TCGA-02-0001 TCGA-02-0051 TCGA-02-0281 TCGA-06-0188 TCGA-06-0414 TCGA-06-0686 
       11.77        15.09         3.98        44.58        35.11        14.20 
TCGA-08-0245 TCGA-12-1099 TCGA-14-0867 TCGA-14-3477 TCGA-19-1390 TCGA-19-2629 
       37.84         4.14         2.04         3.78        25.38        24.23 
TCGA-28-1750 TCGA-32-2494 TCGA-76-6285 TCGA-76-6286 
        8.35        20.78         8.35        20.98 

$`20Q LOSS WILD-TYPE`
TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 TCGA-02-0011 
        4.73        18.35        23.18        10.59        35.41        20.71 
TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0024 
       82.59        20.61        87.06        77.65        20.12        53.10 
TCGA-02-0025 TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 
       42.74        24.59        12.16        90.58         2.83        14.14 
TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 
        3.62        10.72        10.52        18.31         6.87        14.73 
TCGA-02-0048 TCGA-02-0052 TCGA-02-0054 TCGA-02-0055 TCGA-02-0057 TCGA-02-0058 
        3.22        12.59         6.54         2.50        19.86         8.35 
TCGA-02-0059 TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 TCGA-02-0069 TCGA-02-0070 
        9.57         6.02        19.73        26.43        28.70        25.05 
TCGA-02-0071 TCGA-02-0074 TCGA-02-0075 TCGA-02-0079 TCGA-02-0080 TCGA-02-0083 
        5.49        10.19        20.84        27.25        89.72        22.72 
TCGA-02-0084 TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 
       12.62        51.32         8.81        57.76        16.96         3.48 
TCGA-02-0102 TCGA-02-0104 TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 TCGA-02-0113 
       27.02        65.00        11.67        17.65        23.18        92.65 
TCGA-02-0114 TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 TCGA-02-0266 
       99.98        15.65        48.95        16.54        16.93        17.72 
TCGA-02-0269 TCGA-02-0271 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 
       10.75        14.47        13.87        14.20        15.95        12.23 
TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 
        9.90         7.73        10.62         7.33        15.91        25.71 
TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 
        4.37        25.12        10.59        12.39        14.50        10.55 
TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 TCGA-02-2466 
       47.11        11.34         9.27        16.21         3.35        16.80 
TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 
       12.92        15.32        15.45        20.32         2.70         6.15 
TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 
       20.38        47.61         6.94         3.98        22.72        33.67 
TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 
       12.95        25.35        14.30        26.70        24.23        11.90 
TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 
        0.20        10.29         2.20        11.74         2.33        20.09 
TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 
       17.79        10.09         8.61        19.46        46.59        12.33 
TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 
       13.94        10.45         3.19        10.82         9.44        11.80 
TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 
        3.42        56.91        10.65         5.85        19.66         3.29 
TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 
       13.12         4.47         3.22         4.04        91.00         4.18 
TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 
       88.14        20.25         3.65        69.90        73.84        27.22 
TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 
       15.42        10.42        38.96         4.67         7.40         5.56 
TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 
        0.39         7.66         8.42         7.63         7.40        11.84 
TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 
        0.53        15.02        24.16         0.72        19.82        13.64 
TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 
       13.32        20.42        48.69        10.82         9.01         0.26 
TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0644 TCGA-06-0645 
       72.36         4.70         9.57         3.16        12.62         5.75 
TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0743 TCGA-06-0744 
        5.75         9.80         2.10        23.57        26.40        46.88 
TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 
        7.86         2.70         2.70         0.92        43.46        46.19 
TCGA-06-0877 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 
        5.65         7.17        40.41        16.57        20.78        26.76 
TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 
       23.93         6.84         4.04        26.79        11.84        15.32 
TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 
       13.61        33.90        15.32         1.08        12.49         4.93 
TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 
       17.65        12.56        30.64         5.95        16.64         5.98 
TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 
        4.37         0.43        31.50        11.74         3.55         8.35 
TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 TCGA-06-5418 
        4.54         8.81         8.98         8.55         6.71         2.73 
TCGA-06-5856 TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 TCGA-06-6389 TCGA-06-6390 
        3.75         6.15         4.57         5.23         7.79         5.39 
TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 
        1.48       120.56         7.36         8.32        12.85         4.77 
TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S0 
        1.55         4.77         4.96         4.70         1.87         3.12 
TCGA-06-A6S1 TCGA-06-A7TK TCGA-06-A7TL TCGA-08-0244 TCGA-08-0246 TCGA-08-0344 
        2.56         5.39         5.42        22.68         4.18       115.86 
TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 
        1.74         8.42        25.71        12.16         9.80        29.23 
TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 
       65.33         1.28         8.42        17.95        24.56        31.10 
TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 
       37.58        22.29         3.39        12.23        14.93        18.02 
TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 
       15.35        13.97         0.72        12.56         4.27        42.15 
TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 
       11.08        19.59        58.68        19.33        10.75         4.80 
TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 
        7.27        15.98        18.41         7.56        15.35        14.73 
TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 
       12.99        34.92        10.45         7.59        94.78         0.10 
TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 
       38.17        25.97        26.66        12.13         3.65        20.38 
TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 
       28.41        15.06        53.85        43.23         7.63         9.73 
TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 
       14.93        14.86        91.76        24.79        18.48        10.62 
TCGA-12-0822 TCGA-12-0826 TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 
       23.51        27.78        38.76         8.94        20.58       127.59 
TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 
        5.82         7.59        33.21        21.73        15.98        12.23 
TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1598 TCGA-12-1599 
       15.85         9.11        14.53         3.98        15.65        25.68 
TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 
       14.73         6.77        59.77        44.02        26.93        15.22 
TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 
       10.95        12.69        34.92        14.53        14.93         3.22 
TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 
        2.04        15.12        11.97         0.95         6.21        23.05 
TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 TCGA-14-0812 TCGA-14-0813 TCGA-14-0817 
        2.24        11.24        13.78         3.25         1.35         5.39 
TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 TCGA-14-0871 TCGA-14-1034 TCGA-14-1037 
        2.89        16.50        26.33        28.93        15.95        19.30 
TCGA-14-1043 TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 
        0.79         1.38         1.12         3.75        32.05        58.78 
TCGA-14-1451 TCGA-14-1452 TCGA-14-1453 TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 
       23.11         7.10         1.15        30.18         0.92        40.96 
TCGA-14-1458 TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 TCGA-14-1823 
        6.67        12.43         0.99         1.97        17.79        17.85 
TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-4157 
        7.63         5.88         7.17        17.49         7.96         3.42 
TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 TCGA-16-0846 
       13.78        50.53        19.10        53.19        13.28         3.91 
TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 
       17.59        26.07        16.37         4.31        29.03         4.57 
TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 
       10.29        14.01         9.14        21.24        13.97         6.41 
TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 
       11.77        21.90         8.61         0.66        14.27         3.39 
TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 TCGA-19-1388 TCGA-19-1389 TCGA-19-1392 
       10.75         9.07         5.95        12.95         4.64         3.65 
TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 
        7.17        12.66         3.25         0.13         9.67         4.87 
TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 TCGA-19-2631 TCGA-19-4065 
        1.08         7.53         0.16         4.08         7.00         7.04 
TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 
        6.64        17.19         8.02        18.90         4.73        12.10 
TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I 
        1.78        22.49        14.07        16.80        14.96        17.79 
TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 
        3.98        28.54        10.03        13.87         9.73        31.33 
TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 
        7.13         9.37         9.40        14.86         5.49         8.88 
TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-26-A7UX TCGA-27-1830 
       18.97         1.58         7.92         2.33        19.33         5.06 
TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 
       16.60         9.86        24.23        40.54        21.30        30.05 
TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 
       14.04        11.51        24.76        10.39        10.39        16.08 
TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 
        7.59         2.86        14.40        15.78         0.20         2.53 
TCGA-28-1749 TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 
        9.21         7.63         8.48         1.22         1.55         2.83 
TCGA-28-1757 TCGA-28-2502 TCGA-28-2506 TCGA-28-2509 TCGA-28-2513 TCGA-28-2514 
        0.13         0.66         6.74         4.77         7.30         5.26 
TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 
       14.93        11.28        17.88        14.53        11.77        31.27 
TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 
       23.44        11.01        13.64         5.16        22.68        12.76 
TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 TCGA-32-1978 
        5.42        15.39        21.07         0.49         0.10        15.85 
TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 TCGA-32-1991 
       19.50         1.18         4.67        12.69        14.86        16.93 
TCGA-32-2491 TCGA-32-2495 TCGA-32-2615 TCGA-32-2616 TCGA-32-2632 TCGA-32-2634 
       12.23        15.02        15.95         7.36         8.84        22.78 
TCGA-32-2638 TCGA-32-4208 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 
       25.18        21.14         3.72        12.59        19.86        10.85 
TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 
       19.23         0.85        13.35         8.94         9.53         0.99 
TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9S 
        4.44        11.84         0.20        15.12        12.46         4.14 
TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 
       14.76         3.45        20.91         4.34        14.33         8.22 
TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 
        7.50         4.80         4.54         3.09         3.65         9.17 
TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 
        2.53        10.78        16.70         3.29         2.70        11.38 
TCGA-76-6282 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 
       17.06         4.83         5.03         0.23         9.27         7.73 
TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R TCGA-RR-A6KA 
        7.79         1.61        17.72        26.30         5.92         6.28 
TCGA-RR-A6KC 
       20.55 

  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
              2.04               0.10 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             44.58             127.59 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
            14.645             11.840 
[1] "2.0 - 44.6 (14.6)"  "0.1 - 127.6 (11.8)"
[1] "hr=" "1.1"
D78V2, continuous
D78V3, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     9   7
  20Q LOSS WILD-TYPE 215 339
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      9    7
  20Q LOSS WILD-TYPE  215  339
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  FEMALE                9                215
  MALE                  7                339
[1] 2 2
[1] FALSE
D78V4, continuous
                    vv
clus                 GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  20Q LOSS MUTATED                               0                   0
  20Q LOSS WILD-TYPE                            27                  18
                    vv
clus                 UNTREATED PRIMARY (DE NOVO) GBM
  20Q LOSS MUTATED                                16
  20Q LOSS WILD-TYPE                             509
D78V5, multiclass
                                 clus
vv                                20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                  0                 27
  TREATED PRIMARY GBM                            0                 18
  UNTREATED PRIMARY (DE NOVO) GBM               16                509
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V6, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED    10   6
  20Q LOSS WILD-TYPE 372 182
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED     10    6
  20Q LOSS WILD-TYPE  372  182
     clus
vv    20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  NO                10                372
  YES                6                182
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20Q LOSS MUTATED       0                         2    14
  20Q LOSS WILD-TYPE    13                        47   471
D78V7, multiclass
                           clus
vv                          20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  ASIAN                                    0                 13
  BLACK OR AFRICAN AMERICAN                2                 47
  WHITE                                   14                471
[1] 3 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
  20Q LOSS MUTATED     0  14
  20Q LOSS WILD-TYPE  12 458
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      0   14
  20Q LOSS WILD-TYPE   12  458
                        clus
vv                       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 12
  NOT HISPANIC OR LATINO               14                458
[1] 2 2
[1] FALSE

Clustering(79) Variable = 21Q LOSS MUTATION ANALYSIS
D79V1, survival
                    sevent
clus2                  0   1
  21Q LOSS MUTATED     7  35
  21Q LOSS WILD-TYPE  97 430
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                42                527 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                35                430 
$`21Q LOSS MUTATED`
TCGA-02-0011 TCGA-02-0015 TCGA-02-0051 TCGA-02-0106 TCGA-02-0114 TCGA-02-0266 
       20.71        20.61        15.09        11.67        99.98        17.72 
TCGA-02-0281 TCGA-02-0339 TCGA-06-0150 TCGA-06-0209 TCGA-06-0221 TCGA-06-0402 
        3.98        12.39        19.46         7.63        19.82         0.26 
TCGA-06-0414 TCGA-06-0648 TCGA-06-0875 TCGA-06-6389 TCGA-06-6693 TCGA-06-6694 
       35.11         9.80        43.46         7.79       120.56         7.36 
TCGA-06-A7TL TCGA-08-0516 TCGA-12-0826 TCGA-12-0827 TCGA-12-1099 TCGA-12-1600 
        5.42        19.59        27.78        38.76         4.14        14.73 
TCGA-12-3653 TCGA-12-5295 TCGA-14-0740 TCGA-14-0817 TCGA-14-1823 TCGA-14-3477 
       14.53        14.93        11.97         5.39        17.85         3.78 
TCGA-15-0742 TCGA-16-0848 TCGA-16-0850 TCGA-19-0960 TCGA-19-2629 TCGA-27-2521 
       13.78        17.59        16.37         8.61        24.23        10.39 
TCGA-28-2514 TCGA-32-1978 TCGA-32-4210 TCGA-41-3392 TCGA-76-4925 TCGA-76-4934 
        5.26        15.85         3.72         0.99         4.80         2.53 

$`21Q LOSS WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 
       11.77         4.73        18.35        23.18        10.59        35.41 
TCGA-02-0014 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0024 TCGA-02-0025 
       82.59        87.06        77.65        20.12        53.10        42.74 
TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 
       24.59        12.16        90.58         2.83        14.14         3.62 
TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 TCGA-02-0048 
       10.72        10.52        18.31         6.87        14.73         3.22 
TCGA-02-0052 TCGA-02-0054 TCGA-02-0055 TCGA-02-0057 TCGA-02-0058 TCGA-02-0059 
       12.59         6.54         2.50        19.86         8.35         9.57 
TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 TCGA-02-0069 TCGA-02-0070 TCGA-02-0071 
        6.02        19.73        26.43        28.70        25.05         5.49 
TCGA-02-0074 TCGA-02-0075 TCGA-02-0079 TCGA-02-0080 TCGA-02-0083 TCGA-02-0084 
       10.19        20.84        27.25        89.72        22.72        12.62 
TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 
       51.32         8.81        57.76        16.96         3.48        27.02 
TCGA-02-0104 TCGA-02-0107 TCGA-02-0111 TCGA-02-0113 TCGA-02-0115 TCGA-02-0116 
       65.00        17.65        23.18        92.65        15.65        48.95 
TCGA-02-0258 TCGA-02-0260 TCGA-02-0269 TCGA-02-0271 TCGA-02-0285 TCGA-02-0289 
       16.54        16.93        10.75        14.47        13.87        14.20 
TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 
       15.95        12.23         9.90         7.73        10.62         7.33 
TCGA-02-0330 TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 TCGA-02-0422 
       15.91        25.71         4.37        25.12        10.59        14.50 
TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 
       10.55        47.11        11.34         9.27        16.21         3.35 
TCGA-02-2466 TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 
       16.80        12.92        15.32        15.45        20.32         2.70 
TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 
        6.15        20.38        47.61         6.94         3.98        22.72 
TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 
       33.67        12.95        25.35        14.30        26.70        24.23 
TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 
       11.90         0.20        10.29         2.20        11.74         2.33 
TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0151 TCGA-06-0152 
       20.09        17.79        10.09         8.61        46.59        12.33 
TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 
       13.94        10.45         3.19        10.82         9.44        11.80 
TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 
        3.42        56.91        10.65         5.85        19.66         3.29 
TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 
       13.12         4.47         3.22         4.04        91.00         4.18 
TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 
       88.14        20.25         3.65        69.90        73.84        27.22 
TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 
       44.58        15.42        10.42        38.96         4.67         7.40 
TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0210 TCGA-06-0211 
        5.56         0.39         7.66         8.42         7.40        11.84 
TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0237 TCGA-06-0238 
        0.53        15.02        24.16         0.72        13.64        13.32 
TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0409 TCGA-06-0410 
       20.42        48.69        10.82         9.01        72.36         4.70 
TCGA-06-0412 TCGA-06-0413 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0649 
        9.57         3.16        12.62         5.75         5.75         2.10 
TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 
       23.57        14.20        26.40        46.88         7.86         2.70 
TCGA-06-0749 TCGA-06-0750 TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 TCGA-06-0879 
        2.70         0.92        46.19         5.65         7.17        40.41 
TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 
       16.57        20.78        26.76        23.93         6.84         4.04 
TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 
       26.79        11.84        15.32        13.61        33.90        15.32 
TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 
        1.08        12.49         4.93        17.65        12.56        30.64 
TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 
        5.95        16.64         5.98         4.37         0.43        31.50 
TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 
       11.74         3.55         8.35         4.54         8.81         8.98 
TCGA-06-5415 TCGA-06-5416 TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 TCGA-06-5859 
        8.55         6.71         2.73         3.75         6.15         4.57 
TCGA-06-6388 TCGA-06-6390 TCGA-06-6391 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 
        5.23         5.39         1.48         8.32        12.85         4.77 
TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S0 
        1.55         4.77         4.96         4.70         1.87         3.12 
TCGA-06-A6S1 TCGA-06-A7TK TCGA-08-0244 TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 
        2.56         5.39        22.68        37.84         4.18       115.86 
TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 
        1.74         8.42        25.71        12.16         9.80        29.23 
TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 
       65.33         1.28         8.42        17.95        24.56        31.10 
TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 
       37.58        22.29         3.39        12.23        14.93        18.02 
TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 
       15.35        13.97         0.72        12.56         4.27        42.15 
TCGA-08-0514 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 
       11.08        58.68        19.33        10.75         4.80         7.27 
TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 
       15.98        18.41         7.56        15.35        14.73        12.99 
TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 
       34.92        10.45         7.59        94.78         0.10        38.17 
TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 
       25.97        26.66        12.13         3.65        20.38        28.41 
TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 
       15.06        53.85        43.23         7.63         9.73        14.93 
TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 
       14.86        91.76        24.79        18.48        10.62        23.51 
TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 
        8.94        20.58       127.59         5.82         7.59        33.21 
TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 
       21.73        15.98        12.23        15.85         9.11        14.53 
TCGA-12-1098 TCGA-12-1598 TCGA-12-1599 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 
        3.98        15.65        25.68         6.77        59.77        44.02 
TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-5299 
       26.93        15.22        10.95        12.69        34.92         3.22 
TCGA-12-5301 TCGA-14-0736 TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 TCGA-14-0787 
        2.04        15.12         0.95         6.21        23.05         2.24 
TCGA-14-0789 TCGA-14-0790 TCGA-14-0812 TCGA-14-0813 TCGA-14-0862 TCGA-14-0865 
       11.24        13.78         3.25         1.35         2.89        16.50 
TCGA-14-0866 TCGA-14-0867 TCGA-14-0871 TCGA-14-1034 TCGA-14-1037 TCGA-14-1043 
       26.33         2.04        28.93        15.95        19.30         0.79 
TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 
        1.38         1.12         3.75        32.05        58.78        23.11 
TCGA-14-1452 TCGA-14-1453 TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 
        7.10         1.15        30.18         0.92        40.96         6.67 
TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 TCGA-14-1825 TCGA-14-1827 
       12.43         0.99         1.97        17.79         7.63         5.88 
TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-4157 TCGA-15-1444 TCGA-15-1446 
        7.17        17.49         7.96         3.42        50.53        19.10 
TCGA-15-1447 TCGA-15-1449 TCGA-16-0846 TCGA-16-0849 TCGA-16-0861 TCGA-16-1045 
       53.19        13.28         3.91        26.07         4.31        29.03 
TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 
        4.57        10.29        14.01         9.14        21.24        13.97 
TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 
        6.41        11.77        21.90         0.66        14.27         3.39 
TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 TCGA-19-1388 TCGA-19-1389 TCGA-19-1390 
       10.75         9.07         5.95        12.95         4.64        25.38 
TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 
        3.65         7.17        12.66         3.25         0.13         9.67 
TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 TCGA-19-2631 
        4.87         1.08         7.53         0.16         4.08         7.00 
TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 
        7.04         6.64        17.19         8.02        18.90         4.73 
TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 
       12.10         1.78        22.49        14.07        16.80        14.96 
TCGA-19-A60I TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 
       17.79         3.98        28.54        10.03        13.87         9.73 
TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 
       31.33         7.13         9.37         9.40        14.86         5.49 
TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-26-A7UX 
        8.88        18.97         1.58         7.92         2.33        19.33 
TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 
        5.06        16.60         9.86        24.23        40.54        21.30 
TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2523 
       30.05        14.04        11.51        24.76        10.39        16.08 
TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 
        7.59         2.86        14.40        15.78         0.20         2.53 
TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 TCGA-28-1755 
        9.21         8.35         7.63         8.48         1.22         1.55 
TCGA-28-1756 TCGA-28-1757 TCGA-28-2502 TCGA-28-2506 TCGA-28-2509 TCGA-28-2513 
        2.83         0.13         0.66         6.74         4.77         7.30 
TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 
       14.93        11.28        17.88        14.53        11.77        31.27 
TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 
       23.44        11.01        13.64         5.16        22.68        12.76 
TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 TCGA-32-1979 
        5.42        15.39        21.07         0.49         0.10        19.50 
TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 TCGA-32-1991 TCGA-32-2491 
        1.18         4.67        12.69        14.86        16.93        12.23 
TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 TCGA-32-2616 TCGA-32-2632 TCGA-32-2634 
       20.78        15.02        15.95         7.36         8.84        22.78 
TCGA-32-2638 TCGA-32-4208 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 
       25.18        21.14        12.59        19.86        10.85        19.23 
TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3393 TCGA-41-3915 
        0.85        13.35         8.94         9.53         4.44        11.84 
TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 
        0.20        15.12        12.46         4.14        14.76         3.45 
TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 TCGA-76-4926 
       20.91         4.34        14.33         8.22         7.50         4.54 
TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 
        3.09         3.65         9.17        10.78        16.70         3.29 
TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 
        2.70        11.38        17.06         8.35        20.98         4.83 
TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 
        5.03         0.23         9.27         7.73         7.79         1.61 
TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC 
       17.72        26.30         5.92         6.28        20.55 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              0.26               0.10 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            120.56             127.59 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            14.155             11.800 
[1] "0.3 - 120.6 (14.2)" "0.1 - 127.6 (11.8)"
[1] "hr=" "1.1"
D79V2, continuous
D79V3, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    19  23
  21Q LOSS WILD-TYPE 205 323
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     19   23
  21Q LOSS WILD-TYPE  205  323
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE               19                205
  MALE                 23                323
[1] 2 2
[1] FALSE
D79V4, continuous
                    vv
clus                 GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  21Q LOSS MUTATED                               2                   1
  21Q LOSS WILD-TYPE                            25                  17
                    vv
clus                 UNTREATED PRIMARY (DE NOVO) GBM
  21Q LOSS MUTATED                                39
  21Q LOSS WILD-TYPE                             486
D79V5, multiclass
                                 clus
vv                                21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                  2                 25
  TREATED PRIMARY GBM                            1                 17
  UNTREATED PRIMARY (DE NOVO) GBM               39                486
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V6, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    25  17
  21Q LOSS WILD-TYPE 357 171
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     25   17
  21Q LOSS WILD-TYPE  357  171
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  NO                25                357
  YES               17                171
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  21Q LOSS MUTATED       1                         3    37
  21Q LOSS WILD-TYPE    12                        46   448
D79V7, multiclass
                           clus
vv                          21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  ASIAN                                    1                 12
  BLACK OR AFRICAN AMERICAN                3                 46
  WHITE                                   37                448
[1] 3 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
  21Q LOSS MUTATED     2  36
  21Q LOSS WILD-TYPE  10 436
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      2   36
  21Q LOSS WILD-TYPE   10  436
                        clus
vv                       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                 10
  NOT HISPANIC OR LATINO               36                436
[1] 2 2
[1] FALSE

Clustering(80) Variable = 22Q LOSS MUTATION ANALYSIS
D80V1, survival
                    sevent
clus2                  0   1
  22Q LOSS MUTATED    28 153
  22Q LOSS WILD-TYPE  76 312
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               181                388 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               153                312 
$`22Q LOSS MUTATED`
TCGA-02-0007 TCGA-02-0010 TCGA-02-0015 TCGA-02-0016 TCGA-02-0027 TCGA-02-0039 
       23.18        35.41        20.61        87.06        12.16        10.52 
TCGA-02-0043 TCGA-02-0054 TCGA-02-0057 TCGA-02-0059 TCGA-02-0060 TCGA-02-0075 
       18.31         6.54        19.86         9.57         6.02        20.84 
TCGA-02-0086 TCGA-02-0099 TCGA-02-0113 TCGA-02-0260 TCGA-02-0266 TCGA-02-0269 
        8.81         3.48        92.65        16.93        17.72        10.75 
TCGA-02-0321 TCGA-02-0325 TCGA-02-0326 TCGA-02-0333 TCGA-02-0456 TCGA-02-2466 
        9.90        10.62         7.33         4.37         3.35        16.80 
TCGA-02-2483 TCGA-02-2486 TCGA-06-0129 TCGA-06-0140 TCGA-06-0141 TCGA-06-0147 
       15.32        20.32        33.67         0.20        10.29        17.79 
TCGA-06-0152 TCGA-06-0158 TCGA-06-0159 TCGA-06-0162 TCGA-06-0164 TCGA-06-0166 
       12.33        10.82         9.44         3.42        56.91         5.85 
TCGA-06-0168 TCGA-06-0175 TCGA-06-0182 TCGA-06-0185 TCGA-06-0188 TCGA-06-0189 
       19.66         4.04         3.65        73.84        44.58        15.42 
TCGA-06-0194 TCGA-06-0197 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 
        4.67         5.56        24.16         0.72        19.82        13.64 
TCGA-06-0241 TCGA-06-0397 TCGA-06-0402 TCGA-06-0410 TCGA-06-0744 TCGA-06-0745 
       48.69         9.01         0.26         4.70        46.88         7.86 
TCGA-06-0747 TCGA-06-0875 TCGA-06-0878 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 
        2.70        43.46         7.17        20.78        26.76        23.93 
TCGA-06-1804 TCGA-06-1806 TCGA-06-2558 TCGA-06-2562 TCGA-06-2567 TCGA-06-5408 
       13.61        15.32        12.49        12.56         4.37        11.74 
TCGA-06-5411 TCGA-06-5413 TCGA-06-5418 TCGA-06-5856 TCGA-06-6389 TCGA-06-6390 
        8.35         8.81         2.73         3.75         7.79         5.39 
TCGA-06-6693 TCGA-06-6697 TCGA-06-6698 TCGA-06-A5U1 TCGA-06-A6S1 TCGA-08-0244 
      120.56        12.85         4.77         1.87         2.56        22.68 
TCGA-08-0245 TCGA-08-0246 TCGA-08-0349 TCGA-08-0350 TCGA-08-0354 TCGA-08-0386 
       37.84         4.18         9.80        29.23        17.95        18.02 
TCGA-08-0389 TCGA-08-0392 TCGA-08-0512 TCGA-08-0516 TCGA-08-0520 TCGA-12-0619 
       15.35         0.72        42.15        19.59        10.75        34.92 
TCGA-12-0620 TCGA-12-0656 TCGA-12-0662 TCGA-12-0670 TCGA-12-0776 TCGA-12-0821 
       10.45        94.78        38.17        25.97         9.73        10.62 
TCGA-12-0826 TCGA-12-1088 TCGA-12-1091 TCGA-12-1096 TCGA-12-1097 TCGA-12-1598 
       27.78       127.59        33.21         9.11        14.53        15.65 
TCGA-12-1600 TCGA-12-3646 TCGA-12-3651 TCGA-12-3653 TCGA-12-5295 TCGA-14-0736 
       14.73        44.02        12.69        14.53        14.93        15.12 
TCGA-14-0783 TCGA-14-0862 TCGA-14-0865 TCGA-14-0867 TCGA-14-1034 TCGA-14-1402 
        6.21         2.89        16.50         2.04        15.95        32.05 
TCGA-14-1450 TCGA-14-1454 TCGA-14-1794 TCGA-14-1821 TCGA-14-3477 TCGA-15-0742 
       58.78        30.18         0.99        17.79         3.78        13.78 
TCGA-15-1444 TCGA-15-1447 TCGA-16-1056 TCGA-19-0962 TCGA-19-0964 TCGA-19-1385 
       50.53        53.19        14.01         0.66         3.39        10.75 
TCGA-19-1389 TCGA-19-1392 TCGA-19-1791 TCGA-19-2620 TCGA-19-2623 TCGA-19-2625 
        4.64         3.65         0.13         4.87         7.53         4.08 
TCGA-19-2629 TCGA-19-2631 TCGA-19-5947 TCGA-19-5956 TCGA-19-5958 TCGA-19-5960 
       24.23         7.00         6.64        22.49        14.07        14.96 
TCGA-19-A60I TCGA-19-A6J4 TCGA-26-5132 TCGA-26-5136 TCGA-26-6173 TCGA-27-1830 
       17.79         3.98         9.40        18.97         7.92         5.06 
TCGA-27-1832 TCGA-27-1834 TCGA-27-1835 TCGA-27-2519 TCGA-27-2523 TCGA-27-2527 
        9.86        40.54        21.30        10.39        16.08        14.40 
TCGA-28-1752 TCGA-28-2506 TCGA-28-2509 TCGA-28-5207 TCGA-28-5208 TCGA-28-5213 
        8.48         6.74         4.77        11.28        17.88        31.27 
TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-1978 TCGA-32-1980 TCGA-32-1986 
       15.39        21.07         0.49        15.85         1.18        12.69 
TCGA-32-2491 TCGA-32-2615 TCGA-32-2632 TCGA-32-2634 TCGA-41-2573 TCGA-41-2575 
       12.23        15.95         8.84        22.78         8.94         9.53 
TCGA-41-3915 TCGA-41-4097 TCGA-41-6646 TCGA-4W-AA9S TCGA-74-6581 TCGA-76-4925 
       11.84         0.20        12.46         4.14         8.22         4.80 
TCGA-76-4926 TCGA-76-4929 TCGA-76-4934 TCGA-76-6280 TCGA-76-6657 TCGA-87-5896 
        4.54         3.65         2.53        11.38         5.03        26.30 
TCGA-OX-A56R 
        5.92 

$`22Q LOSS WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0009 TCGA-02-0011 TCGA-02-0014 
       11.77         4.73        18.35        10.59        20.71        82.59 
TCGA-02-0021 TCGA-02-0023 TCGA-02-0024 TCGA-02-0025 TCGA-02-0026 TCGA-02-0028 
       77.65        20.12        53.10        42.74        24.59        90.58 
TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 TCGA-02-0046 TCGA-02-0047 
        2.83        14.14         3.62        10.72         6.87        14.73 
TCGA-02-0048 TCGA-02-0051 TCGA-02-0052 TCGA-02-0055 TCGA-02-0058 TCGA-02-0064 
        3.22        15.09        12.59         2.50         8.35        19.73 
TCGA-02-0068 TCGA-02-0069 TCGA-02-0070 TCGA-02-0071 TCGA-02-0074 TCGA-02-0079 
       26.43        28.70        25.05         5.49        10.19        27.25 
TCGA-02-0080 TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 TCGA-02-0087 TCGA-02-0089 
       89.72        22.72        12.62        51.32        57.76        16.96 
TCGA-02-0102 TCGA-02-0104 TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 TCGA-02-0114 
       27.02        65.00        11.67        17.65        23.18        99.98 
TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 TCGA-02-0271 TCGA-02-0281 TCGA-02-0285 
       15.65        48.95        16.54        14.47         3.98        13.87 
TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 TCGA-02-0324 TCGA-02-0330 TCGA-02-0332 
       14.20        15.95        12.23         7.73        15.91        25.71 
TCGA-02-0337 TCGA-02-0338 TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 
       25.12        10.59        12.39        14.50        10.55        47.11 
TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 TCGA-02-2470 TCGA-02-2485 TCGA-06-0119 
       11.34         9.27        16.21        12.92        15.45         2.70 
TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 
        6.15        20.38        47.61         6.94         3.98        22.72 
TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 
       12.95        25.35        14.30        26.70        24.23        11.90 
TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0148 TCGA-06-0149 
        2.20        11.74         2.33        20.09        10.09         8.61 
TCGA-06-0150 TCGA-06-0151 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0160 
       19.46        46.59        13.94        10.45         3.19        11.80 
TCGA-06-0165 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0176 
       10.65         3.29        13.12         4.47         3.22        91.00 
TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0184 TCGA-06-0187 TCGA-06-0190 
        4.18        88.14        20.25        69.90        27.22        10.42 
TCGA-06-0192 TCGA-06-0195 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 
       38.96         7.40         0.39         7.66         8.42         7.63 
TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0238 TCGA-06-0240 
        7.40        11.84         0.53        15.02        13.32        20.42 
TCGA-06-0394 TCGA-06-0409 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 
       10.82        72.36         9.57         3.16        35.11        12.62 
TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 
        5.75         5.75         9.80         2.10        23.57        14.20 
TCGA-06-0743 TCGA-06-0749 TCGA-06-0750 TCGA-06-0876 TCGA-06-0877 TCGA-06-0879 
       26.40         2.70         0.92        46.19         5.65        40.41 
TCGA-06-0881 TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 
       16.57         6.84         4.04        26.79        11.84        15.32 
TCGA-06-1805 TCGA-06-2557 TCGA-06-2559 TCGA-06-2561 TCGA-06-2563 TCGA-06-2564 
       33.90         1.08         4.93        17.65        30.64         5.95 
TCGA-06-2565 TCGA-06-2566 TCGA-06-2569 TCGA-06-2570 TCGA-06-5410 TCGA-06-5412 
       16.64         5.98         0.43        31.50         3.55         4.54 
TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 
        8.98         8.55         6.71         6.15         4.57         5.23 
TCGA-06-6391 TCGA-06-6694 TCGA-06-6695 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 
        1.48         7.36         8.32         1.55         4.77         4.96 
TCGA-06-A5U0 TCGA-06-A6S0 TCGA-06-A7TK TCGA-06-A7TL TCGA-08-0344 TCGA-08-0345 
        4.70         3.12         5.39         5.42       115.86         1.74 
TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 
        8.42        25.71        12.16        65.33         1.28         8.42 
TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 
       24.56        31.10        37.58        22.29         3.39        12.23 
TCGA-08-0380 TCGA-08-0390 TCGA-08-0509 TCGA-08-0510 TCGA-08-0514 TCGA-08-0517 
       14.93        13.97        12.56         4.27        11.08        58.68 
TCGA-08-0518 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 
       19.33         4.80         7.27        15.98        18.41         7.56 
TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0654 TCGA-12-0657 TCGA-12-0688 
       15.35        14.73        12.99         7.59         0.10        26.66 
TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 
       12.13         3.65        20.38        28.41        15.06        53.85 
TCGA-12-0773 TCGA-12-0775 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 
       43.23         7.63        14.93        14.86        91.76        24.79 
TCGA-12-0820 TCGA-12-0822 TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 TCGA-12-1089 
       18.48        23.51        38.76         8.94        20.58         5.82 
TCGA-12-1090 TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1098 
        7.59        21.73        15.98        12.23        15.85         3.98 
TCGA-12-1099 TCGA-12-1599 TCGA-12-1602 TCGA-12-3644 TCGA-12-3648 TCGA-12-3649 
        4.14        25.68         6.77        59.77        26.93        15.22 
TCGA-12-3650 TCGA-12-3652 TCGA-12-5299 TCGA-12-5301 TCGA-14-0740 TCGA-14-0781 
       10.95        34.92         3.22         2.04        11.97         0.95 
TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 TCGA-14-0812 TCGA-14-0813 
       23.05         2.24        11.24        13.78         3.25         1.35 
TCGA-14-0817 TCGA-14-0866 TCGA-14-0871 TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 
        5.39        26.33        28.93        19.30         0.79         1.38 
TCGA-14-1396 TCGA-14-1401 TCGA-14-1451 TCGA-14-1452 TCGA-14-1453 TCGA-14-1455 
        1.12         3.75        23.11         7.10         1.15         0.92 
TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 TCGA-14-1795 TCGA-14-1823 TCGA-14-1825 
       40.96         6.67        12.43         1.97        17.85         7.63 
TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-4157 TCGA-15-1446 
        5.88         7.17        17.49         7.96         3.42        19.10 
TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 
       13.28         3.91        17.59        26.07        16.37         4.31 
TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 
       29.03         4.57        10.29         9.14        21.24        13.97 
TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 TCGA-19-0963 TCGA-19-1386 
        6.41        11.77        21.90         8.61        14.27         9.07 
TCGA-19-1387 TCGA-19-1388 TCGA-19-1390 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 
        5.95        12.95        25.38         7.17        12.66         3.25 
TCGA-19-2619 TCGA-19-2621 TCGA-19-2624 TCGA-19-4065 TCGA-19-5950 TCGA-19-5951 
        9.67         1.08         0.16         7.04        17.19         8.02 
TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5959 TCGA-19-A6J5 
       18.90         4.73        12.10         1.78        16.80        28.54 
TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 
       10.03        13.87         9.73        31.33         7.13         9.37 
TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 TCGA-26-5139 TCGA-26-6174 TCGA-26-A7UX 
       14.86         5.49         8.88         1.58         2.33        19.33 
TCGA-27-1831 TCGA-27-1833 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 
       16.60        24.23        30.05        14.04        11.51        24.76 
TCGA-27-2521 TCGA-27-2524 TCGA-27-2526 TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 
       10.39         7.59         2.86        15.78         0.20         2.53 
TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 
        9.21         8.35         7.63         1.22         1.55         2.83 
TCGA-28-1757 TCGA-28-2502 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5209 
        0.13         0.66         7.30         5.26        14.93        14.53 
TCGA-28-5211 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 
       11.77        23.44        11.01        13.64         5.16        22.68 
TCGA-28-5220 TCGA-28-6450 TCGA-32-1977 TCGA-32-1979 TCGA-32-1982 TCGA-32-1987 
       12.76         5.42         0.10        19.50         4.67        14.86 
TCGA-32-1991 TCGA-32-2494 TCGA-32-2495 TCGA-32-2616 TCGA-32-2638 TCGA-32-4208 
       16.93        20.78        15.02         7.36        25.18        21.14 
TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 
        3.72        12.59        19.86        10.85        19.23         0.85 
TCGA-41-2572 TCGA-41-3392 TCGA-41-3393 TCGA-41-5651 TCGA-4W-AA9T TCGA-74-6573 
       13.35         0.99         4.44        15.12        14.76         3.45 
TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6584 TCGA-76-4928 TCGA-76-4931 
       20.91         4.34        14.33         7.50         3.09         9.17 
TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6282 TCGA-76-6285 
       10.78        16.70         3.29         2.70        17.06         8.35 
TCGA-76-6286 TCGA-76-6656 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 
       20.98         4.83         0.23         9.27         7.73         7.79 
TCGA-81-5910 TCGA-81-5911 TCGA-RR-A6KA TCGA-RR-A6KC 
        1.61        17.72         6.28        20.55 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              0.13               0.10 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            127.59             115.86 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             12.16              11.84 
[1] "0.1 - 127.6 (12.2)" "0.1 - 115.9 (11.8)"
[1] "hr=" "1"  
D80V2, continuous
D80V3, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    70 111
  22Q LOSS WILD-TYPE 154 235
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     70  111
  22Q LOSS WILD-TYPE  154  235
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE               70                154
  MALE                111                235
[1] 2 2
[1] FALSE
D80V4, continuous
                    vv
clus                 GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  22Q LOSS MUTATED                              10                   6
  22Q LOSS WILD-TYPE                            17                  12
                    vv
clus                 UNTREATED PRIMARY (DE NOVO) GBM
  22Q LOSS MUTATED                               165
  22Q LOSS WILD-TYPE                             360
D80V5, multiclass
                                 clus
vv                                22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                 10                 17
  TREATED PRIMARY GBM                            6                 12
  UNTREATED PRIMARY (DE NOVO) GBM              165                360
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V6, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED   120  61
  22Q LOSS WILD-TYPE 262 127
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED    120   61
  22Q LOSS WILD-TYPE  262  127
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  NO               120                262
  YES               61                127
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  22Q LOSS MUTATED       4                        13   158
  22Q LOSS WILD-TYPE     9                        36   327
D80V7, multiclass
                           clus
vv                          22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  ASIAN                                    4                  9
  BLACK OR AFRICAN AMERICAN               13                 36
  WHITE                                  158                327
[1] 3 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
  22Q LOSS MUTATED     4 158
  22Q LOSS WILD-TYPE   8 314
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      4  158
  22Q LOSS WILD-TYPE    8  314
                        clus
vv                       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  8
  NOT HISPANIC OR LATINO              158                314
[1] 2 2
[1] FALSE

Clustering(81) Variable = XP LOSS MUTATION ANALYSIS
D81V1, survival
                   sevent
clus2                 0   1
  XP LOSS MUTATED    25  88
  XP LOSS WILD-TYPE  79 377
  XP LOSS MUTATED XP LOSS WILD-TYPE 
              113               456 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               88               377 
$`XP LOSS MUTATED`
TCGA-02-0007 TCGA-02-0010 TCGA-02-0011 TCGA-02-0026 TCGA-02-0039 TCGA-02-0048 
       23.18        35.41        20.71        24.59        10.52         3.22 
TCGA-02-0058 TCGA-02-0099 TCGA-02-0330 TCGA-02-0339 TCGA-02-0432 TCGA-02-2466 
        8.35         3.48        15.91        12.39        47.11        16.80 
TCGA-02-2483 TCGA-06-0129 TCGA-06-0152 TCGA-06-0158 TCGA-06-0162 TCGA-06-0171 
       15.32        33.67        12.33        10.82         3.42        13.12 
TCGA-06-0184 TCGA-06-0185 TCGA-06-0214 TCGA-06-0219 TCGA-06-0221 TCGA-06-0743 
       69.90        73.84        15.02         0.72        19.82        26.40 
TCGA-06-0875 TCGA-06-1800 TCGA-06-2558 TCGA-06-2564 TCGA-06-2569 TCGA-06-2570 
       43.46        26.79        12.49         5.95         0.43        31.50 
TCGA-06-5408 TCGA-06-5416 TCGA-06-5418 TCGA-06-5856 TCGA-06-5859 TCGA-06-6693 
       11.74         6.71         2.73         3.75         4.57       120.56 
TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S1 TCGA-06-A7TL TCGA-08-0245 TCGA-08-0348 
        4.70         1.87         2.56         5.42        37.84        12.16 
TCGA-08-0354 TCGA-08-0355 TCGA-08-0389 TCGA-08-0392 TCGA-08-0512 TCGA-08-0517 
       17.95        24.56        15.35         0.72        42.15        58.68 
TCGA-08-0520 TCGA-08-0525 TCGA-12-0615 TCGA-12-0821 TCGA-12-0827 TCGA-12-1091 
       10.75        15.98        15.35        10.62        38.76        33.21 
TCGA-12-3644 TCGA-12-3646 TCGA-12-3652 TCGA-12-5295 TCGA-14-0736 TCGA-14-0740 
       59.77        44.02        34.92        14.93        15.12        11.97 
TCGA-14-0787 TCGA-14-0862 TCGA-14-0865 TCGA-14-0871 TCGA-14-1453 TCGA-14-3477 
        2.24         2.89        16.50        28.93         1.15         3.78 
TCGA-15-0742 TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 TCGA-19-1388 TCGA-19-1390 
       13.78        16.37         4.31        29.03        12.95        25.38 
TCGA-19-1392 TCGA-19-1786 TCGA-19-2619 TCGA-19-2621 TCGA-19-2623 TCGA-19-2625 
        3.65         7.17         9.67         1.08         7.53         4.08 
TCGA-19-2629 TCGA-19-5947 TCGA-19-5956 TCGA-19-5960 TCGA-26-1439 TCGA-26-1440 
       24.23         6.64        22.49        14.96        13.87         9.73 
TCGA-26-5133 TCGA-27-2524 TCGA-28-1750 TCGA-28-2514 TCGA-28-5204 TCGA-28-5220 
       14.86         7.59         8.35         5.26        14.93        12.76 
TCGA-32-1973 TCGA-32-1977 TCGA-32-1978 TCGA-32-2494 TCGA-32-2615 TCGA-32-2634 
       21.07         0.10        15.85        20.78        15.95        22.78 
TCGA-32-4208 TCGA-32-4210 TCGA-32-4213 TCGA-32-4719 TCGA-41-2572 TCGA-41-2575 
       21.14         3.72        19.86        10.85        13.35         9.53 
TCGA-41-3392 TCGA-74-6575 TCGA-76-4925 TCGA-76-4926 TCGA-76-4929 TCGA-76-4931 
        0.99        20.91         4.80         4.54         3.65         9.17 
TCGA-76-4934 TCGA-76-4935 TCGA-76-6285 TCGA-76-6286 TCGA-OX-A56R 
        2.53        10.78         8.35        20.98         5.92 

$`XP LOSS WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0009 TCGA-02-0014 TCGA-02-0015 
       11.77         4.73        18.35        10.59        82.59        20.61 
TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0024 TCGA-02-0025 TCGA-02-0027 
       87.06        77.65        20.12        53.10        42.74        12.16 
TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 TCGA-02-0043 
       90.58         2.83        14.14         3.62        10.72        18.31 
TCGA-02-0046 TCGA-02-0047 TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 TCGA-02-0055 
        6.87        14.73        15.09        12.59         6.54         2.50 
TCGA-02-0057 TCGA-02-0059 TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 TCGA-02-0069 
       19.86         9.57         6.02        19.73        26.43        28.70 
TCGA-02-0070 TCGA-02-0071 TCGA-02-0074 TCGA-02-0075 TCGA-02-0079 TCGA-02-0080 
       25.05         5.49        10.19        20.84        27.25        89.72 
TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 TCGA-02-0089 
       22.72        12.62        51.32         8.81        57.76        16.96 
TCGA-02-0102 TCGA-02-0104 TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 TCGA-02-0113 
       27.02        65.00        11.67        17.65        23.18        92.65 
TCGA-02-0114 TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 TCGA-02-0260 TCGA-02-0266 
       99.98        15.65        48.95        16.54        16.93        17.72 
TCGA-02-0269 TCGA-02-0271 TCGA-02-0281 TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 
       10.75        14.47         3.98        13.87        14.20        15.95 
TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 TCGA-02-0332 
       12.23         9.90         7.73        10.62         7.33        25.71 
TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 TCGA-02-0422 TCGA-02-0430 TCGA-02-0440 
        4.37        25.12        10.59        14.50        10.55        11.34 
TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 TCGA-02-2470 TCGA-02-2485 TCGA-02-2486 
        9.27        16.21         3.35        12.92        15.45        20.32 
TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 
        2.70         6.15        20.38        47.61         6.94         3.98 
TCGA-06-0128 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 
       22.72        12.95        25.35        14.30        26.70        24.23 
TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 
       11.90         0.20        10.29         2.20        11.74         2.33 
TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 
       20.09        17.79        10.09         8.61        19.46        46.59 
TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0159 TCGA-06-0160 TCGA-06-0164 
       13.94        10.45         3.19         9.44        11.80        56.91 
TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0173 TCGA-06-0174 
       10.65         5.85        19.66         3.29         4.47         3.22 
TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 
        4.04        91.00         4.18        88.14        20.25         3.65 
TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 
       27.22        44.58        15.42        10.42        38.96         4.67 
TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 
        7.40         5.56         0.39         7.66         8.42         7.63 
TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0216 TCGA-06-0237 TCGA-06-0238 
        7.40        11.84         0.53        24.16        13.64        13.32 
TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 
       20.42        48.69        10.82         9.01         0.26        72.36 
TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 
        4.70         9.57         3.16        35.11        12.62         5.75 
TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0744 
        5.75         9.80         2.10        23.57        14.20        46.88 
TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0876 TCGA-06-0877 
        7.86         2.70         2.70         0.92        46.19         5.65 
TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 
        7.17        40.41        16.57        20.78        26.76        23.93 
TCGA-06-1086 TCGA-06-1087 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 
        6.84         4.04        11.84        15.32        13.61        33.90 
TCGA-06-1806 TCGA-06-2557 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 
       15.32         1.08         4.93        17.65        12.56        30.64 
TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 
       16.64         5.98         4.37         3.55         8.35         4.54 
TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5858 TCGA-06-6388 TCGA-06-6389 
        8.81         8.98         8.55         6.15         5.23         7.79 
TCGA-06-6390 TCGA-06-6391 TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 
        5.39         1.48         7.36         8.32        12.85         4.77 
TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-06-A6S0 TCGA-06-A7TK TCGA-08-0244 
        1.55         4.77         4.96         3.12         5.39        22.68 
TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0349 
        4.18       115.86         1.74         8.42        25.71         9.80 
TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0356 TCGA-08-0357 
       29.23        65.33         1.28         8.42        31.10        37.58 
TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0390 
       22.29         3.39        12.23        14.93        18.02        13.97 
TCGA-08-0509 TCGA-08-0510 TCGA-08-0514 TCGA-08-0516 TCGA-08-0518 TCGA-08-0521 
       12.56         4.27        11.08        19.59        19.33         4.80 
TCGA-08-0524 TCGA-08-0529 TCGA-08-0531 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 
        7.27        18.41         7.56        14.73        12.99        34.92 
TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 
       10.45         7.59        94.78         0.10        38.17        25.97 
TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 
       26.66        12.13         3.65        20.38        28.41        15.06 
TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 
       53.85        43.23         7.63         9.73        14.93        14.86 
TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0822 TCGA-12-0826 TCGA-12-0828 
       91.76        24.79        18.48        23.51        27.78         8.94 
TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1092 TCGA-12-1093 
       20.58       127.59         5.82         7.59        21.73        15.98 
TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 
       12.23        15.85         9.11        14.53         3.98         4.14 
TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 TCGA-12-3648 TCGA-12-3649 
       15.65        25.68        14.73         6.77        26.93        15.22 
TCGA-12-3650 TCGA-12-3651 TCGA-12-3653 TCGA-12-5299 TCGA-12-5301 TCGA-14-0781 
       10.95        12.69        14.53         3.22         2.04         0.95 
TCGA-14-0783 TCGA-14-0786 TCGA-14-0789 TCGA-14-0790 TCGA-14-0812 TCGA-14-0813 
        6.21        23.05        11.24        13.78         3.25         1.35 
TCGA-14-0817 TCGA-14-0866 TCGA-14-0867 TCGA-14-1034 TCGA-14-1037 TCGA-14-1043 
        5.39        26.33         2.04        15.95        19.30         0.79 
TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 
        1.38         1.12         3.75        32.05        58.78        23.11 
TCGA-14-1452 TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 
        7.10        30.18         0.92        40.96         6.67        12.43 
TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 TCGA-14-1823 TCGA-14-1825 TCGA-14-1827 
        0.99         1.97        17.79        17.85         7.63         5.88 
TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-4157 TCGA-15-1444 TCGA-15-1446 
        7.17        17.49         7.96         3.42        50.53        19.10 
TCGA-15-1447 TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 TCGA-16-1047 
       53.19        13.28         3.91        17.59        26.07         4.57 
TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 
       10.29        14.01         9.14        21.24        13.97         6.41 
TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 
       11.77        21.90         8.61         0.66        14.27         3.39 
TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 TCGA-19-1389 TCGA-19-1787 TCGA-19-1789 
       10.75         9.07         5.95         4.64        12.66         3.25 
TCGA-19-1791 TCGA-19-2620 TCGA-19-2624 TCGA-19-2631 TCGA-19-4065 TCGA-19-5950 
        0.13         4.87         0.16         7.00         7.04        17.19 
TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5958 
        8.02        18.90         4.73        12.10         1.78        14.07 
TCGA-19-5959 TCGA-19-A60I TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1442 
       16.80        17.79         3.98        28.54        10.03        31.33 
TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 
        7.13         9.37         9.40         5.49         8.88        18.97 
TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 
        1.58         7.92         2.33        19.33         5.06        16.60 
TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 
        9.86        24.23        40.54        21.30        30.05        14.04 
TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 TCGA-27-2526 
       11.51        24.76        10.39        10.39        16.08         2.86 
TCGA-27-2527 TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 TCGA-28-1751 
       14.40        15.78         0.20         2.53         9.21         7.63 
TCGA-28-1752 TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 TCGA-28-2502 
        8.48         1.22         1.55         2.83         0.13         0.66 
TCGA-28-2506 TCGA-28-2509 TCGA-28-2513 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 
        6.74         4.77         7.30        11.28        17.88        14.53 
TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 
       11.77        31.27        23.44        11.01        13.64         5.16 
TCGA-28-5219 TCGA-28-6450 TCGA-32-1970 TCGA-32-1976 TCGA-32-1979 TCGA-32-1980 
       22.68         5.42        15.39         0.49        19.50         1.18 
TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 TCGA-32-1991 TCGA-32-2491 TCGA-32-2495 
        4.67        12.69        14.86        16.93        12.23        15.02 
TCGA-32-2616 TCGA-32-2632 TCGA-32-2638 TCGA-32-4211 TCGA-32-5222 TCGA-41-2571 
        7.36         8.84        25.18        12.59        19.23         0.85 
TCGA-41-2573 TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 
        8.94         4.44        11.84         0.20        15.12        12.46 
TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 
        4.14        14.76         3.45         4.34        14.33         8.22 
TCGA-74-6584 TCGA-76-4928 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 
        7.50         3.09        16.70         3.29         2.70        11.38 
TCGA-76-6282 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 
       17.06         4.83         5.03         0.23         9.27         7.73 
TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-RR-A6KA TCGA-RR-A6KC 
        7.79         1.61        17.72        26.30         6.28        20.55 

  XP LOSS MUTATED XP LOSS WILD-TYPE 
              0.1               0.1 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
           120.56            127.59 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
           12.950            11.755 
[1] "0.1 - 120.6 (12.9)" "0.1 - 127.6 (11.8)"
[1] "hr=" "1.2"
D81V2, continuous
D81V3, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    49  64
  XP LOSS WILD-TYPE 175 282
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     49   64
  XP LOSS WILD-TYPE  175  282
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  FEMALE              49               175
  MALE                64               282
[1] 2 2
[1] FALSE
D81V4, continuous
                   vv
clus                GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  XP LOSS MUTATED                               5                   4
  XP LOSS WILD-TYPE                            22                  14
                   vv
clus                UNTREATED PRIMARY (DE NOVO) GBM
  XP LOSS MUTATED                               104
  XP LOSS WILD-TYPE                             421
D81V5, multiclass
                                 clus
vv                                XP LOSS MUTATED XP LOSS WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                 5                22
  TREATED PRIMARY GBM                           4                14
  UNTREATED PRIMARY (DE NOVO) GBM             104               421
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V6, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    78  35
  XP LOSS WILD-TYPE 304 153
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     78   35
  XP LOSS WILD-TYPE  304  153
     clus
vv    XP LOSS MUTATED XP LOSS WILD-TYPE
  NO               78               304
  YES              35               153
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XP LOSS MUTATED       5                        12    92
  XP LOSS WILD-TYPE     8                        37   393
D81V7, multiclass
                           clus
vv                          XP LOSS MUTATED XP LOSS WILD-TYPE
  ASIAN                                   5                 8
  BLACK OR AFRICAN AMERICAN              12                37
  WHITE                                  92               393
[1] 3 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
  XP LOSS MUTATED     3  94
  XP LOSS WILD-TYPE   9 378
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      3   94
  XP LOSS WILD-TYPE    9  378
                        clus
vv                       XP LOSS MUTATED XP LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                 9
  NOT HISPANIC OR LATINO              94               378
[1] 2 2
[1] FALSE

Clustering(82) Variable = XQ LOSS MUTATION ANALYSIS
D82V1, survival
                   sevent
clus2                 0   1
  XQ LOSS MUTATED    25  80
  XQ LOSS WILD-TYPE  79 385
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
              105               464 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               80               385 
$`XQ LOSS MUTATED`
TCGA-02-0007 TCGA-02-0011 TCGA-02-0026 TCGA-02-0039 TCGA-02-0048 TCGA-02-0099 
       23.18        20.71        24.59        10.52         3.22         3.48 
TCGA-02-0330 TCGA-02-0339 TCGA-02-2466 TCGA-06-0129 TCGA-06-0152 TCGA-06-0162 
       15.91        12.39        16.80        33.67        12.33         3.42 
TCGA-06-0171 TCGA-06-0184 TCGA-06-0185 TCGA-06-0214 TCGA-06-0219 TCGA-06-0221 
       13.12        69.90        73.84        15.02         0.72        19.82 
TCGA-06-0875 TCGA-06-1800 TCGA-06-2558 TCGA-06-2564 TCGA-06-2569 TCGA-06-2570 
       43.46        26.79        12.49         5.95         0.43        31.50 
TCGA-06-5408 TCGA-06-5416 TCGA-06-5418 TCGA-06-5856 TCGA-06-5859 TCGA-06-6693 
       11.74         6.71         2.73         3.75         4.57       120.56 
TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S1 TCGA-06-A7TL TCGA-08-0245 TCGA-08-0348 
        4.70         1.87         2.56         5.42        37.84        12.16 
TCGA-08-0354 TCGA-08-0355 TCGA-08-0389 TCGA-08-0392 TCGA-08-0512 TCGA-08-0517 
       17.95        24.56        15.35         0.72        42.15        58.68 
TCGA-08-0520 TCGA-08-0525 TCGA-12-0615 TCGA-12-0821 TCGA-12-0827 TCGA-12-1091 
       10.75        15.98        15.35        10.62        38.76        33.21 
TCGA-12-3644 TCGA-12-3646 TCGA-12-3652 TCGA-12-5295 TCGA-14-0736 TCGA-14-0740 
       59.77        44.02        34.92        14.93        15.12        11.97 
TCGA-14-0787 TCGA-14-0862 TCGA-14-0865 TCGA-14-1453 TCGA-14-3477 TCGA-15-0742 
        2.24         2.89        16.50         1.15         3.78        13.78 
TCGA-15-1447 TCGA-16-0861 TCGA-16-1045 TCGA-19-1388 TCGA-19-1390 TCGA-19-1392 
       53.19         4.31        29.03        12.95        25.38         3.65 
TCGA-19-1786 TCGA-19-2619 TCGA-19-2621 TCGA-19-2623 TCGA-19-2625 TCGA-19-2629 
        7.17         9.67         1.08         7.53         4.08        24.23 
TCGA-19-5947 TCGA-19-5956 TCGA-19-5960 TCGA-26-1439 TCGA-26-1440 TCGA-26-5133 
        6.64        22.49        14.96        13.87         9.73        14.86 
TCGA-27-2524 TCGA-28-1750 TCGA-28-2514 TCGA-28-5204 TCGA-28-5220 TCGA-32-1973 
        7.59         8.35         5.26        14.93        12.76        21.07 
TCGA-32-1977 TCGA-32-1978 TCGA-32-2494 TCGA-32-2615 TCGA-32-2634 TCGA-32-4208 
        0.10        15.85        20.78        15.95        22.78        21.14 
TCGA-32-4213 TCGA-32-4719 TCGA-41-2572 TCGA-41-2575 TCGA-41-3392 TCGA-74-6575 
       19.86        10.85        13.35         9.53         0.99        20.91 
TCGA-76-4925 TCGA-76-4926 TCGA-76-4929 TCGA-76-4931 TCGA-76-4934 TCGA-76-4935 
        4.80         4.54         3.65         9.17         2.53        10.78 
TCGA-76-6285 TCGA-76-6286 TCGA-OX-A56R 
        8.35        20.98         5.92 

$`XQ LOSS WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0009 TCGA-02-0010 TCGA-02-0014 
       11.77         4.73        18.35        10.59        35.41        82.59 
TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 TCGA-02-0024 TCGA-02-0025 
       20.61        87.06        77.65        20.12        53.10        42.74 
TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 
       12.16        90.58         2.83        14.14         3.62        10.72 
TCGA-02-0043 TCGA-02-0046 TCGA-02-0047 TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 
       18.31         6.87        14.73        15.09        12.59         6.54 
TCGA-02-0055 TCGA-02-0057 TCGA-02-0058 TCGA-02-0059 TCGA-02-0060 TCGA-02-0064 
        2.50        19.86         8.35         9.57         6.02        19.73 
TCGA-02-0068 TCGA-02-0069 TCGA-02-0070 TCGA-02-0071 TCGA-02-0074 TCGA-02-0075 
       26.43        28.70        25.05         5.49        10.19        20.84 
TCGA-02-0079 TCGA-02-0080 TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 TCGA-02-0086 
       27.25        89.72        22.72        12.62        51.32         8.81 
TCGA-02-0087 TCGA-02-0089 TCGA-02-0102 TCGA-02-0104 TCGA-02-0106 TCGA-02-0107 
       57.76        16.96        27.02        65.00        11.67        17.65 
TCGA-02-0111 TCGA-02-0113 TCGA-02-0114 TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 
       23.18        92.65        99.98        15.65        48.95        16.54 
TCGA-02-0260 TCGA-02-0266 TCGA-02-0269 TCGA-02-0271 TCGA-02-0281 TCGA-02-0285 
       16.93        17.72        10.75        14.47         3.98        13.87 
TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 
       14.20        15.95        12.23         9.90         7.73        10.62 
TCGA-02-0326 TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 TCGA-02-0422 
        7.33        25.71         4.37        25.12        10.59        14.50 
TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 
       10.55        47.11        11.34         9.27        16.21         3.35 
TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 
       12.92        15.32        15.45        20.32         2.70         6.15 
TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0130 
       20.38        47.61         6.94         3.98        22.72        12.95 
TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 
       25.35        14.30        26.70        24.23        11.90         0.20 
TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 
       10.29         2.20        11.74         2.33        20.09        17.79 
TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0154 TCGA-06-0155 
       10.09         8.61        19.46        46.59        13.94        10.45 
TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0164 TCGA-06-0165 
        3.19        10.82         9.44        11.80        56.91        10.65 
TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 
        5.85        19.66         3.29         4.47         3.22         4.04 
TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0187 
       91.00         4.18        88.14        20.25         3.65        27.22 
TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 
       44.58        15.42        10.42        38.96         4.67         7.40 
TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 
        5.56         0.39         7.66         8.42         7.63         7.40 
TCGA-06-0211 TCGA-06-0213 TCGA-06-0216 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 
       11.84         0.53        24.16        13.64        13.32        20.42 
TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 
       48.69        10.82         9.01         0.26        72.36         4.70 
TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 
        9.57         3.16        35.11        12.62         5.75         5.75 
TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 
        9.80         2.10        23.57        14.20        26.40        46.88 
TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0876 TCGA-06-0877 
        7.86         2.70         2.70         0.92        46.19         5.65 
TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 
        7.17        40.41        16.57        20.78        26.76        23.93 
TCGA-06-1086 TCGA-06-1087 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 
        6.84         4.04        11.84        15.32        13.61        33.90 
TCGA-06-1806 TCGA-06-2557 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 
       15.32         1.08         4.93        17.65        12.56        30.64 
TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 
       16.64         5.98         4.37         3.55         8.35         4.54 
TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5858 TCGA-06-6388 TCGA-06-6389 
        8.81         8.98         8.55         6.15         5.23         7.79 
TCGA-06-6390 TCGA-06-6391 TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 
        5.39         1.48         7.36         8.32        12.85         4.77 
TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-06-A6S0 TCGA-06-A7TK TCGA-08-0244 
        1.55         4.77         4.96         3.12         5.39        22.68 
TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0349 
        4.18       115.86         1.74         8.42        25.71         9.80 
TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0356 TCGA-08-0357 
       29.23        65.33         1.28         8.42        31.10        37.58 
TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0390 
       22.29         3.39        12.23        14.93        18.02        13.97 
TCGA-08-0509 TCGA-08-0510 TCGA-08-0514 TCGA-08-0516 TCGA-08-0518 TCGA-08-0521 
       12.56         4.27        11.08        19.59        19.33         4.80 
TCGA-08-0524 TCGA-08-0529 TCGA-08-0531 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 
        7.27        18.41         7.56        14.73        12.99        34.92 
TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 
       10.45         7.59        94.78         0.10        38.17        25.97 
TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 
       26.66        12.13         3.65        20.38        28.41        15.06 
TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 
       53.85        43.23         7.63         9.73        14.93        14.86 
TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0822 TCGA-12-0826 TCGA-12-0828 
       91.76        24.79        18.48        23.51        27.78         8.94 
TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1092 TCGA-12-1093 
       20.58       127.59         5.82         7.59        21.73        15.98 
TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 
       12.23        15.85         9.11        14.53         3.98         4.14 
TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 TCGA-12-3648 TCGA-12-3649 
       15.65        25.68        14.73         6.77        26.93        15.22 
TCGA-12-3650 TCGA-12-3651 TCGA-12-3653 TCGA-12-5299 TCGA-12-5301 TCGA-14-0781 
       10.95        12.69        14.53         3.22         2.04         0.95 
TCGA-14-0783 TCGA-14-0786 TCGA-14-0789 TCGA-14-0790 TCGA-14-0812 TCGA-14-0813 
        6.21        23.05        11.24        13.78         3.25         1.35 
TCGA-14-0817 TCGA-14-0866 TCGA-14-0867 TCGA-14-0871 TCGA-14-1034 TCGA-14-1037 
        5.39        26.33         2.04        28.93        15.95        19.30 
TCGA-14-1043 TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 
        0.79         1.38         1.12         3.75        32.05        58.78 
TCGA-14-1451 TCGA-14-1452 TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 
       23.11         7.10        30.18         0.92        40.96         6.67 
TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 TCGA-14-1823 TCGA-14-1825 
       12.43         0.99         1.97        17.79        17.85         7.63 
TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-4157 TCGA-15-1444 
        5.88         7.17        17.49         7.96         3.42        50.53 
TCGA-15-1446 TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 
       19.10        13.28         3.91        17.59        26.07        16.37 
TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 
        4.57        10.29        14.01         9.14        21.24        13.97 
TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 TCGA-19-0962 TCGA-19-0963 
        6.41        11.77        21.90         8.61         0.66        14.27 
TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 TCGA-19-1389 TCGA-19-1787 
        3.39        10.75         9.07         5.95         4.64        12.66 
TCGA-19-1789 TCGA-19-1791 TCGA-19-2620 TCGA-19-2624 TCGA-19-2631 TCGA-19-4065 
        3.25         0.13         4.87         0.16         7.00         7.04 
TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 
       17.19         8.02        18.90         4.73        12.10         1.78 
TCGA-19-5958 TCGA-19-5959 TCGA-19-A60I TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 
       14.07        16.80        17.79         3.98        28.54        10.03 
TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5134 TCGA-26-5135 
       31.33         7.13         9.37         9.40         5.49         8.88 
TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-26-A7UX TCGA-27-1830 
       18.97         1.58         7.92         2.33        19.33         5.06 
TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 
       16.60         9.86        24.23        40.54        21.30        30.05 
TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 
       14.04        11.51        24.76        10.39        10.39        16.08 
TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 
        2.86        14.40        15.78         0.20         2.53         9.21 
TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 
        7.63         8.48         1.22         1.55         2.83         0.13 
TCGA-28-2502 TCGA-28-2506 TCGA-28-2509 TCGA-28-2513 TCGA-28-5207 TCGA-28-5208 
        0.66         6.74         4.77         7.30        11.28        17.88 
TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 
       14.53        11.77        31.27        23.44        11.01        13.64 
TCGA-28-5218 TCGA-28-5219 TCGA-28-6450 TCGA-32-1970 TCGA-32-1976 TCGA-32-1979 
        5.16        22.68         5.42        15.39         0.49        19.50 
TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 TCGA-32-1991 TCGA-32-2491 
        1.18         4.67        12.69        14.86        16.93        12.23 
TCGA-32-2495 TCGA-32-2616 TCGA-32-2632 TCGA-32-2638 TCGA-32-4210 TCGA-32-4211 
       15.02         7.36         8.84        25.18         3.72        12.59 
TCGA-32-5222 TCGA-41-2571 TCGA-41-2573 TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 
       19.23         0.85         8.94         4.44        11.84         0.20 
TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6577 
       15.12        12.46         4.14        14.76         3.45         4.34 
TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 TCGA-76-4928 TCGA-76-6191 TCGA-76-6192 
       14.33         8.22         7.50         3.09        16.70         3.29 
TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 
        2.70        11.38        17.06         4.83         5.03         0.23 
TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
        9.27         7.73         7.79         1.61        17.72        26.30 
TCGA-RR-A6KA TCGA-RR-A6KC 
        6.28        20.55 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
              0.1               0.1 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           120.56            127.59 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            12.76             11.77 
[1] "0.1 - 120.6 (12.8)" "0.1 - 127.6 (11.8)"
[1] "hr=" "1.2"
D82V2, continuous
D82V3, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    46  59
  XQ LOSS WILD-TYPE 178 287
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     46   59
  XQ LOSS WILD-TYPE  178  287
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE              46               178
  MALE                59               287
[1] 2 2
[1] FALSE
D82V4, continuous
                   vv
clus                GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  XQ LOSS MUTATED                               5                   2
  XQ LOSS WILD-TYPE                            22                  16
                   vv
clus                UNTREATED PRIMARY (DE NOVO) GBM
  XQ LOSS MUTATED                                98
  XQ LOSS WILD-TYPE                             427
D82V5, multiclass
                                 clus
vv                                XQ LOSS MUTATED XQ LOSS WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                 5                22
  TREATED PRIMARY GBM                           2                16
  UNTREATED PRIMARY (DE NOVO) GBM              98               427
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V6, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    72  33
  XQ LOSS WILD-TYPE 310 155
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     72   33
  XQ LOSS WILD-TYPE  310  155
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  NO               72               310
  YES              33               155
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XQ LOSS MUTATED       4                        12    85
  XQ LOSS WILD-TYPE     9                        37   400
D82V7, multiclass
                           clus
vv                          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  ASIAN                                   4                 9
  BLACK OR AFRICAN AMERICAN              12                37
  WHITE                                  85               400
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V8, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     3  86
  XQ LOSS WILD-TYPE   9 386
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      3   86
  XQ LOSS WILD-TYPE    9  386
                        clus
vv                       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                 9
  NOT HISPANIC OR LATINO              86               386
[1] 2 2
[1] FALSE
