[1] "terrence_modification_tag"
[1] TRUE
[1] "nver"         "-nVNozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[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/10005922/GBM-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/GBM-TP/10015648/transformed.cor.cli.txt"

nPatients in clinical file=582, in cluster file=571, common to both=560
[1]  80 560
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               81               479 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               81               479 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               87               473 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               87               473 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               36               524 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               36               524 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               35               525 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               35               525 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               56               504 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               56               504 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               61               499 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               61               499 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               36               524 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               36               524 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               33               527 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               33               527 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               49               511 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               49               511 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               41               519 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               41               519 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               23               537 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               23               537 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               22               538 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               22               538 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              454               106 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              454               106 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              459               101 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              459               101 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               52               508 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               52               508 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               59               501 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               59               501 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               47               513 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               47               513 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               71               489 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               71               489 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                12                548 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                12                548 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 3                557 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 3                557 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                17                543 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                17                543 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                14                546 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                14                546 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                58                502 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                58                502 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                47                513 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                47                513 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                10                550 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                10                550 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                22                538 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                22                538 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                24                536 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                24                536 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                38                522 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                38                522 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                37                523 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                37                523 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                47                513 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                47                513 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                58                502 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                58                502 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                57                503 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                57                503 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                57                503 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                57                503 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
               218                342 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
               218                342 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
               193                367 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
               193                367 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               216                344 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               216                344 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               214                346 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               214                346 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                62                498 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                62                498 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                34                526 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                34                526 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               16               544 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               16               544 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               15               545 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               15               545 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               14               546 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               14               546 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               32               528 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               32               528 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               32               528 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               32               528 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               40               520 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               40               520 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               34               526 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               34               526 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               53               507 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               53               507 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               53               507 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               53               507 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               42               518 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               42               518 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               43               517 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               43               517 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               86               474 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               86               474 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              123               437 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              123               437 
[1] "7P LOSS MUTATION ANALYSIS"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                8               552 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                8               552 
[1] "7Q LOSS MUTATION ANALYSIS"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                6               554 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                6               554 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               58               502 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               58               502 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               42               518 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               42               518 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              195               365 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              195               365 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               90               470 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               90               470 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               466                 94 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               466                 94 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               478                 82 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               478                 82 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                97                463 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                97                463 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                92                468 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                92                468 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                59                501 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                59                501 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                58                502 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                58                502 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               181                379 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               181                379 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               145                415 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               145                415 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               101                459 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               101                459 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                63                497 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                63                497 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                82                478 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                82                478 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                61                499 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                61                499 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                40                520 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                40                520 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                68                492 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                68                492 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                60                500 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                60                500 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                25                535 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                25                535 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                33                527 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                33                527 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                18                542 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                18                542 
[1] "20Q LOSS MUTATION ANALYSIS"
[1] 3
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                16                544 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                16                544 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                40                520 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                40                520 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               178                382 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               178                382 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
              104               456 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
              104               456 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDESEASE"                  
 [6] "DCCUPLOADDATE"                         
 [7] "GENDER"                                
 [8] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
 [9] "RADIATIONTHERAPY"                      
[10] "KARNOFSKYPERFORMANCESCORE"             
[11] "HISTOLOGICALTYPE"                      
[12] "RADIATIONS.RADIATION.REGIMENINDICATION"
[13] "RACE"                                  
[14] "ETHNICITY"                             
[15] "BATCHNUMBER"                           

Input Data has 15 rows and 560 columns.

[1] "Batch" "15"   
[1] "Last Follow UP"
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 
         279          144          558          705          322         1077 
TCGA-02-0011 TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 TCGA-02-0023 
         630         2512          627         1699         2362          612 
TCGA-02-0024 TCGA-02-0025 TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 
        1615         1300          748          315         2755           86 
TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 
         430          110          326          320          557          209 
TCGA-02-0047 TCGA-02-0048 TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 TCGA-02-0055 
         448           98          459          383          199           76 
TCGA-02-0057 TCGA-02-0058 TCGA-02-0059 TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 
         604          254          291          183          600          804 
TCGA-02-0069 TCGA-02-0070 TCGA-02-0071 TCGA-02-0074 TCGA-02-0075 TCGA-02-0079 
         873          762          167          310          634          829 
TCGA-02-0080 TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 
        2729          691            7         1561          268         1757 
TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 TCGA-02-0104 TCGA-02-0106 TCGA-02-0107 
         516          106          822         1977          355          537 
TCGA-02-0111 TCGA-02-0113 TCGA-02-0114 TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 
         705         2818         3041          476         1489          503 
TCGA-02-0260 TCGA-02-0266 TCGA-02-0269 TCGA-02-0271 TCGA-02-0281 TCGA-02-0285 
         515          539          327          440          121          422 
TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 
         432          485          372          301          235          323 
TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 
           5          484          782          133          764          322 
TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 TCGA-02-0440 TCGA-02-0446 
         377          441          321         1433          345          282 
TCGA-02-0451 TCGA-02-0456 TCGA-02-2466 TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 
         493          102          511          393          466          470 
TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 
         493           NA            8          123         1439            3 
TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 
         109          691          989          320          570          428 
TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 
         702          674          327           NA          280           NA 
TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 
         357           71          611          508          298          239 
TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 
          NA           NA          359          389          263           97 
TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 
         166           NA           NA           78         1730           NA 
TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 
         161          579           95          396            7           67 
TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 
          83         2768           61         1642          578           77 
TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 
        1228         2246          801          866          454          313 
TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 
         557          142          214           79           12          197 
TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 
         167          119          151          360            6          378 
TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 
         684           11          548          315          359           NA 
TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 
         455          314          168            8         2145          143 
TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 
         245            5         1065          375           98          136 
TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 
         294           62          717          286          679          595 
TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 
         164           82           66           28         1322         1405 
TCGA-06-0877 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 
         204          218          699          178          165          637 
TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 
         226          193          109          815          263          240 
TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 
         414         1031           NA           33           23          150 
TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 
         282           86          932          181          207          182 
TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 
         133           13          958          342          108          254 
TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 TCGA-06-5418 
         138          268          273          260          204           83 
TCGA-06-5856 TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 TCGA-06-6389 TCGA-06-6390 
         114          187          139          120          237          164 
TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 
          45           15          224          253          391          145 
TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 
          47          145          151           NA           NA           NA 
TCGA-08-0244 TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 
         690         1057          119         3310           53          132 
TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 
         419          316          231          104         1637           39 
TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 
         195          458          685          447         1084          594 
TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 
          29          279          330          478           97          322 
TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 
           9           17          107          358          259          561 
TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 
        1770           39          327          146          199          486 
TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 
         527          168          426          439           50          316 
TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 
         181          218         2005            3         1161          790 
TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 
         734          186           80          551           NA          378 
TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 
        1615         1311          167          277          452          434 
TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 TCGA-12-0826 
        2791          754          562          323          715          845 
TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 
        1179          272          626         3881          177          190 
TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 
         929          658          364          346          482          277 
TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 
         442          121          104          287          769          414 
TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 
         195         1807         1315          784          351          333 
TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 
         358         1050          357          399           98           62 
TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 TCGA-14-0787 
         460          364           29          189          701           68 
TCGA-14-0789 TCGA-14-0790 TCGA-14-0812 TCGA-14-0813 TCGA-14-0817 TCGA-14-0862 
         342          419           99           41          164           88 
TCGA-14-0865 TCGA-14-0866 TCGA-14-0867 TCGA-14-0871 TCGA-14-1034 TCGA-14-1037 
         502          801           62          880          485          587 
TCGA-14-1043 TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 
          24           42           34          114          975         1788 
TCGA-14-1451 TCGA-14-1452 TCGA-14-1453 TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 
         703          216           35          918           28         1246 
TCGA-14-1458 TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 TCGA-14-1823 
         187          378           30           60          541          543 
TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-3477 
         232          179          218          532          242          115 
TCGA-14-4157 TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 
         104          300           NA          581         1618          168 
TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 
         119          302          793          496          131          883 
TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 
          25          301          406          111          556          425 
TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 TCGA-19-0962 TCGA-19-0963 
         195          358          666          262           13          434 
TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 TCGA-19-1388 TCGA-19-1389 
         103          327          276          181          394          141 
TCGA-19-1390 TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 
         772          106          218          385           99            4 
TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 
         294          148           33          229            5          124 
TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 
         501          213          214          202          343          244 
TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 
         567          144          242           54          198          164 
TCGA-19-5959 TCGA-19-5960 TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 
         161          165           NA          504          305          422 
TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5133 
         296          953          217          285          286          452 
TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 
         167          270           37           48          241           71 
TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 
         146          505           NA          555         1008          648 
TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 
         914          427          350          753          316          316 
TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1746 
         489          231           87          438          480            6 
TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 
          77          280          254          232          258           37 
TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 TCGA-28-2502 TCGA-28-2506 TCGA-28-2509 
          47           86            4           20          205          145 
TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 
         222          160          119          275          474          442 
TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 
         358          951          432          237          415          128 
TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 
         690          319          165          468          641           15 
TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 
           3          482          593           36          142          386 
TCGA-32-1987 TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 
         452          515          372          632          457          485 
TCGA-32-2616 TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4210 
         224          269          693          644          643          113 
TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 
         383          604          330          323           26          406 
TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 
         272          290           30          135          360            6 
TCGA-41-5651 TCGA-41-6646 TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 
         351          236          105          636          132          436 
TCGA-74-6581 TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 
         250          228          146          138           94          111 
TCGA-76-4931 TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 
         279           77          328          508          100           82 
TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 
         346          519          254          638          147          153 
TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 
           7          282          235          237           49          539 
TCGA-87-5896 TCGA-OX-A56R 
         800           NA 
Variable 1:'AGE':	nDistinctValues=72,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=369,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=397,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 7:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=25,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
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=19,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                                   
[2] "GENDER"                                
[3] "KARNOFSKY.PERFORMANCE.SCORE"           
[4] "HISTOLOGICAL.TYPE"                     
[5] "RADIATIONS.RADIATION.REGIMENINDICATION"
[6] "RACE"                                  
[7] "ETHNICITY"                             
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 560 columns, 1 survival variables, and 7 non-survival variables.
AGE, 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  83 396
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               81               479 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               66               396 
$`1P GAIN MUTATED`
TCGA-02-0001 TCGA-02-0052 TCGA-02-0055 TCGA-02-0106 TCGA-02-0113 TCGA-02-0266 
        9.17        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 
       10.52        14.07        11.80        19.04         2.01         2.53 
TCGA-06-0188 TCGA-06-0192 TCGA-06-0195 TCGA-06-0206 TCGA-06-0209 TCGA-06-0216 
       28.47        18.31         7.04         6.48         3.91        22.49 
TCGA-06-0237 TCGA-06-0410 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 TCGA-06-0649 
       10.36         4.70        35.01        12.33         3.22         2.04 
TCGA-06-1084 TCGA-06-1087 TCGA-06-2557 TCGA-06-5856 TCGA-06-6698 TCGA-08-0349 
        7.43         3.58         1.08         3.75         4.77         7.59 
TCGA-08-0350 TCGA-08-0386 TCGA-08-0531 TCGA-12-0619 TCGA-12-0662 TCGA-12-0773 
        3.42        15.72         5.52        10.39        38.17        43.10 
TCGA-12-0826 TCGA-12-1090 TCGA-12-1098 TCGA-12-1099 TCGA-12-1598 TCGA-12-3653 
       27.78         6.25         3.98         3.42         9.44        11.74 
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         9.86 
TCGA-15-1447 TCGA-15-1449 TCGA-19-0962 TCGA-19-1786 TCGA-19-1787 TCGA-19-2625 
       53.19         5.52         0.43         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 
        9.04        13.64        15.39        14.86        22.78         3.72 
TCGA-32-5222 TCGA-74-6584 TCGA-76-4934 
       10.62         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        55.86        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        10.36        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         0.23 
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 
        0.16         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        16.21         2.70         0.26         4.04        47.31 
TCGA-06-0126 TCGA-06-0127 TCGA-06-0129 TCGA-06-0132 TCGA-06-0137 TCGA-06-0138 
        0.10         3.58        32.52        18.74        23.08        22.16 
TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 
       10.75         0.20         9.21         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        16.70         9.80         7.86        19.46        46.59 
TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 
       12.79         8.65         3.19         5.46         9.44        11.80 
TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0169 TCGA-06-0171 
        2.56        56.88        10.65         5.29         3.12        13.02 
TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0178 TCGA-06-0179 
        0.23         2.20         2.73        91.00        53.98        19.00 
TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0189 TCGA-06-0190 TCGA-06-0194 
       40.37        73.84        26.33        14.93        10.29         4.67 
TCGA-06-0197 TCGA-06-0201 TCGA-06-0208 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 
        2.60         0.39         5.49         4.96        11.84         0.20 
TCGA-06-0214 TCGA-06-0219 TCGA-06-0221 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 
       12.43         0.36        18.02        11.80        20.42        14.96 
TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0412 TCGA-06-0413 
       10.32         5.52         0.26        70.52         8.05         0.16 
TCGA-06-0646 TCGA-06-0648 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 
        4.47         9.67        23.57         9.40        22.32        19.56 
TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 
        5.39         2.70         2.17         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        22.98         5.85         5.42        20.94 
TCGA-06-1086 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 
        6.35        26.79         8.65         7.89        13.61        33.90 
TCGA-06-1806 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 
       15.32         0.76         4.93         9.27         2.83        30.64 
TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 
        5.95         6.81         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 
       11.24         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         3.95 
TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 
        7.79         5.39         1.48         0.49         7.36         8.32 
TCGA-06-6697 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U1 TCGA-06-A6S0 
       12.85         1.55         4.77         4.96         1.87         3.12 
TCGA-06-A6S1 TCGA-08-0244 TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 
        2.56        22.68        34.75         3.91       108.82         1.74 
TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 
        4.34        13.78        10.39        53.82         1.28         6.41 
TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 
       15.06        22.52        14.70        35.64        19.53         0.95 
TCGA-08-0375 TCGA-08-0380 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 
        9.17        10.85         3.19        10.59         0.30         0.56 
TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 
        3.52        11.77         8.52        18.44        58.19         1.28 
TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-12-0615 
       10.75         4.80         6.54        15.98        17.33        14.01 
TCGA-12-0616 TCGA-12-0618 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 
       14.43         1.64         5.95         7.17        65.92         0.10 
TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 
       25.97        24.13         6.12         2.63        18.12        28.41 
TCGA-12-0769 TCGA-12-0772 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 
       12.43        53.10         5.49         9.11        14.86        14.27 
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-12-1091 TCGA-12-1092 
        8.94        20.58       127.59         5.82        30.54        21.63 
TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1599 
       11.97        11.38        15.85         9.11        14.53        25.28 
TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 
       13.61         6.41        59.41        43.23        25.78        11.54 
TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 
       10.95        11.77        34.52        13.12         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-14-0862 TCGA-14-0865 TCGA-14-0866 TCGA-14-0871 
       13.78         3.25         2.89        16.50        26.33        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-14-1453 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 
       58.78        23.11         1.15         0.92        40.96         6.15 
TCGA-14-1459 TCGA-14-1795 TCGA-14-1821 TCGA-14-1825 TCGA-14-1829 TCGA-14-2554 
       12.43         1.97        17.79         7.63         7.17        17.49 
TCGA-14-2555 TCGA-14-4157 TCGA-15-1444 TCGA-15-1446 TCGA-16-0846 TCGA-16-0848 
        7.96         3.42        50.53        19.10         3.91         9.93 
TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 
       26.07        16.31         4.31        29.03         0.82         9.90 
TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 
       13.35         3.65        18.28        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-19-1392 TCGA-19-1789 
        5.95        12.95         4.64        25.38         3.48         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-19-2629 TCGA-19-2631 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 
       16.47         7.00         6.64        11.28         8.02        18.64 
TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 
        4.73         7.96         1.78         6.51         5.39         5.29 
TCGA-19-5960 TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1442 
        5.42         3.98        16.57        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         1.22 
TCGA-26-5139 TCGA-26-6174 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 
        1.58         2.33         4.80        16.60         9.86        18.25 
TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 
       33.14        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-28-1753 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-28-5208 TCGA-28-5209 TCGA-28-5211 
        7.30         5.26         3.91        15.58        14.53        11.77 
TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 
       31.27        14.20         7.79         4.21        22.68        10.49 
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-32-2632 TCGA-32-2638 TCGA-32-4208 
       15.02        15.95         7.36         8.84        21.17        21.14 
TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 
       12.59        19.86        10.85         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        11.54 
TCGA-41-6646 TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 
        7.76         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 
        7.79         1.61        17.72        26.30         5.92 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             0.43              0.10 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            92.65            127.59 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             9.04             10.39 
[1] "0.4 - 92.7 (9.0)"   "0.1 - 127.6 (10.4)"
[1] "hr=" "1.2"
D1V2, continuous
D1V3, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    34  47
  1P GAIN WILD-TYPE 186 293
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     34   47
  1P GAIN WILD-TYPE  186  293
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE              34               186
  MALE                47               293
[1] 2 2
[1] FALSE
D1V4, continuous
                   vv
clus                GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  1P GAIN MUTATED                               0                   1
  1P GAIN WILD-TYPE                            17                  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                17
  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 323 156
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     59   22
  1P GAIN WILD-TYPE  323  156
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  NO               59               323
  YES              22               156
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1P GAIN MUTATED       2                         6    68
  1P GAIN WILD-TYPE    11                        33   417
D1V7, multiclass
                           clus
vv                          1P GAIN MUTATED 1P GAIN WILD-TYPE
  ASIAN                                   2                11
  BLACK OR AFRICAN AMERICAN               6                33
  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  10 400
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      2   62
  1P GAIN WILD-TYPE   10  400
                        clus
vv                       1P GAIN MUTATED 1P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                10
  NOT HISPANIC OR LATINO              62               400
[1] 2 2
[1] FALSE

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                 0   1
  1Q GAIN MUTATED    17  70
  1Q GAIN WILD-TYPE  81 392
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               87               473 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               70               392 
$`1Q GAIN MUTATED`
TCGA-02-0001 TCGA-02-0024 TCGA-02-0052 TCGA-02-0055 TCGA-02-0106 TCGA-02-0113 
        9.17        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 
       10.52        14.07        11.80        19.04         2.01         2.53 
TCGA-06-0188 TCGA-06-0192 TCGA-06-0195 TCGA-06-0206 TCGA-06-0209 TCGA-06-0216 
       28.47        18.31         7.04         6.48         3.91        22.49 
TCGA-06-0237 TCGA-06-0409 TCGA-06-0410 TCGA-06-0414 TCGA-06-0645 TCGA-06-0649 
       10.36        70.52         4.70        35.01         3.22         2.04 
TCGA-06-1084 TCGA-06-1087 TCGA-06-2557 TCGA-06-2569 TCGA-06-5856 TCGA-06-6698 
        7.43         3.58         1.08         0.43         3.75         4.77 
TCGA-08-0349 TCGA-08-0350 TCGA-08-0386 TCGA-08-0524 TCGA-08-0531 TCGA-12-0619 
        7.59         3.42        15.72         6.54         5.52        10.39 
TCGA-12-0662 TCGA-12-0773 TCGA-12-0826 TCGA-12-0827 TCGA-12-1090 TCGA-12-1098 
       38.17        43.10        27.78        38.76         6.25         3.98 
TCGA-12-1099 TCGA-12-1598 TCGA-12-3653 TCGA-14-0783 TCGA-14-0813 TCGA-14-0817 
        3.42         9.44        11.74         6.21         1.35         5.39 
TCGA-14-0865 TCGA-14-0867 TCGA-14-0871 TCGA-14-1452 TCGA-14-1454 TCGA-14-1794 
       16.50         2.04        28.93         7.10        30.18         0.99 
TCGA-14-1823 TCGA-14-3477 TCGA-15-0742 TCGA-15-1447 TCGA-15-1449 TCGA-19-0962 
       17.85         3.78         9.86        53.19         5.52         0.43 
TCGA-19-1786 TCGA-19-1791 TCGA-19-2625 TCGA-19-4065 TCGA-26-1440 TCGA-26-5132 
        7.17         0.13         4.08         7.04         9.73         9.40 
TCGA-26-6173 TCGA-28-1752 TCGA-28-2509 TCGA-28-5207 TCGA-28-5216 TCGA-28-5218 
        7.92         8.48         4.77         9.04        13.64         4.21 
TCGA-32-1970 TCGA-32-1987 TCGA-32-2632 TCGA-32-2634 TCGA-32-4210 TCGA-32-5222 
       15.39        14.86         8.84        22.78         3.72        10.62 
TCGA-41-5651 TCGA-74-6584 TCGA-76-4934 
       11.54         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        55.86        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        10.36        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         0.23        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         0.16 
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        16.21         2.70         0.26         4.04        47.31 
TCGA-06-0126 TCGA-06-0127 TCGA-06-0129 TCGA-06-0132 TCGA-06-0137 TCGA-06-0138 
        0.10         3.58        32.52        18.74        23.08        22.16 
TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 
       10.75         0.20         9.21         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        16.70         9.80         7.86        19.46        46.59 
TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 
       12.79         8.65         3.19         5.46         9.44        11.80 
TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0169 TCGA-06-0171 
        2.56        56.88        10.65         5.29         3.12        13.02 
TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0178 TCGA-06-0179 
        0.23         2.20         2.73        91.00        53.98        19.00 
TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0189 TCGA-06-0190 TCGA-06-0194 
       40.37        73.84        26.33        14.93        10.29         4.67 
TCGA-06-0197 TCGA-06-0201 TCGA-06-0208 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 
        2.60         0.39         5.49         4.96        11.84         0.20 
TCGA-06-0214 TCGA-06-0219 TCGA-06-0221 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 
       12.43         0.36        18.02        11.80        20.42        14.96 
TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0412 TCGA-06-0413 TCGA-06-0644 
       10.32         5.52         0.26         8.05         0.16        12.33 
TCGA-06-0646 TCGA-06-0648 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 
        4.47         9.67        23.57         9.40        22.32        19.56 
TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 
        5.39         2.70         2.17         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        22.98         5.85         5.42        20.94 
TCGA-06-1086 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 
        6.35        26.79         8.65         7.89        13.61        33.90 
TCGA-06-1806 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 
       15.32         0.76         4.93         9.27         2.83        30.64 
TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2570 TCGA-06-5408 
        5.95         6.81         5.98         4.37        31.50        11.24 
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         3.95         7.79 
TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 
        5.39         1.48         0.49         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-08-0244 TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 
       22.68        34.75         3.91       108.82         1.74         4.34 
TCGA-08-0347 TCGA-08-0348 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 
       13.78        10.39        53.82         1.28         6.41        15.06 
TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 
       22.52        14.70        35.64        19.53         0.95         9.17 
TCGA-08-0380 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 
       10.85         3.19        10.59         0.30         0.56         3.52 
TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 
       11.77         8.52        18.44        58.19         1.28        10.75 
TCGA-08-0521 TCGA-08-0525 TCGA-08-0529 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 
        4.80        15.98        17.33        14.01        14.43         1.64 
TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0670 TCGA-12-0688 
        5.95         7.17        65.92         0.10        25.97        24.13 
TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 
        6.12         2.63        18.12        28.41        12.43        53.10 
TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 
        5.49         9.11        14.86        14.27        91.76        24.79 
TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 
       18.48        10.62        23.51         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        30.54        21.63        11.97        11.38        15.85 
TCGA-12-1096 TCGA-12-1097 TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 
        9.11        14.53        25.28        13.61         6.41        59.41 
TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 
       43.23        25.78        11.54        10.95        11.77        34.52 
TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 
       13.12         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-14-0866 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-14-1453 TCGA-14-1455 
        3.75        32.05        58.78        23.11         1.15         0.92 
TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 TCGA-14-1795 TCGA-14-1821 TCGA-14-1825 
       40.96         6.15        12.43         1.97        17.79         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-16-0846 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 
       19.10         3.91         9.93        26.07        16.31         4.31 
TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 
       29.03         0.82         9.90        13.35         3.65        18.28 
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-19-1787 TCGA-19-1789 TCGA-19-2619 TCGA-19-2620 
       25.38         3.48        12.66         3.25         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        16.47         7.00         6.64 
TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 
       11.28         8.02        18.64         4.73         7.96         1.78 
TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A6J4 TCGA-19-A6J5 
        6.51         5.39         5.29         5.42         3.98        16.57 
TCGA-26-1438 TCGA-26-1439 TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 TCGA-26-5133 
       10.03        13.87        31.33         7.13         9.37        14.86 
TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 TCGA-26-6174 TCGA-27-1830 
        5.49         8.88         1.22         1.58         2.33         4.80 
TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 
       16.60         9.86        18.25        33.14        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-28-2513 TCGA-28-2514 TCGA-28-5204 
        0.13         0.66         6.74         7.30         5.26         3.91 
TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 
       15.58        14.53        11.77        31.27        14.20         7.79 
TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 
       22.68        10.49         5.42        21.07         0.49         0.10 
TCGA-32-1978 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1991 
       15.85        19.50         1.18         4.67        12.69        16.93 
TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 TCGA-32-2616 TCGA-32-2638 
       12.23        20.78        15.02        15.95         7.36        21.17 
TCGA-32-4208 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-41-2571 TCGA-41-2572 
       21.14        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-41-6646 TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 
        7.76         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 
        7.79         1.61        17.72        26.30         5.92 

  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 
             8.84             10.39 
[1] "0.1 - 92.7 (8.8)"   "0.1 - 127.6 (10.4)"
[1] "hr=" "1.1"
D2V2, continuous
D2V3, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    38  49
  1Q GAIN WILD-TYPE 182 291
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     38   49
  1Q GAIN WILD-TYPE  182  291
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE              38               182
  MALE                49               291
[1] 2 2
[1] FALSE
D2V4, continuous
                   vv
clus                GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  1Q GAIN MUTATED                               0                   2
  1Q GAIN WILD-TYPE                            17                  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)                 0                17
  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  24
  1Q GAIN WILD-TYPE 319 154
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     63   24
  1Q GAIN WILD-TYPE  319  154
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  NO               63               319
  YES              24               154
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1Q GAIN MUTATED       2                         8    73
  1Q GAIN WILD-TYPE    11                        31   412
D2V7, multiclass
                           clus
vv                          1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  ASIAN                                   2                11
  BLACK OR AFRICAN AMERICAN               8                31
  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  67
  1Q GAIN WILD-TYPE  10 395
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      2   67
  1Q GAIN WILD-TYPE   10  395
                        clus
vv                       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                10
  NOT HISPANIC OR LATINO              67               395
[1] 2 2
[1] FALSE

Clustering(3) Variable = 2P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                 0   1
  2P GAIN MUTATED     5  31
  2P GAIN WILD-TYPE  93 431
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               36               524 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               31               431 
$`2P GAIN MUTATED`
TCGA-02-0001 TCGA-02-0106 TCGA-02-0113 TCGA-02-0281 TCGA-06-0133 TCGA-06-0151 
        9.17        11.67        92.65         3.98        14.07        46.59 
TCGA-06-0192 TCGA-06-0216 TCGA-06-0649 TCGA-06-0877 TCGA-06-1086 TCGA-06-2557 
       18.31        22.49         2.04         5.65         6.35         1.08 
TCGA-06-2569 TCGA-06-6391 TCGA-08-0346 TCGA-08-0386 TCGA-08-0510 TCGA-08-0517 
        0.43         1.48         4.34        15.72         3.52        58.19 
TCGA-08-0524 TCGA-12-0778 TCGA-12-1099 TCGA-12-3653 TCGA-14-0817 TCGA-14-0871 
        6.54        14.86         3.42        11.74         5.39        28.93 
TCGA-14-1453 TCGA-14-1823 TCGA-14-3477 TCGA-16-0846 TCGA-19-0957 TCGA-19-1786 
        1.15        17.85         3.78         3.91        21.90         7.17 
TCGA-19-2629 TCGA-26-1439 TCGA-27-1834 TCGA-28-5218 TCGA-32-4210 TCGA-74-6584 
       16.47        13.87        33.14         4.21         3.72         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        55.86        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        10.36        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         0.23        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         0.16        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        16.21         2.70         0.26         4.04 
TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 
       47.31         0.10         3.58        22.72        32.52        10.52 
TCGA-06-0132 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 
       18.74        23.08        22.16        10.75         0.20         9.21 
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        16.70         9.80 
TCGA-06-0149 TCGA-06-0150 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 
        7.86        19.46        11.80        12.79         8.65         3.19 
TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 
        5.46         9.44        11.80         2.56        56.88        10.65 
TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 
        5.29        19.04         3.12        13.02         0.23         2.20 
TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 
        2.73        91.00         2.01        53.98        19.00         2.53 
TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 
       40.37        73.84        26.33        28.47        14.93        10.29 
TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 
        4.67         7.04         2.60         0.39         6.48         5.49 
TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0219 
        3.91         4.96        11.84         0.20        12.43         0.36 
TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 
       18.02        10.36        11.80        20.42        14.96        10.32 
TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 
        5.52         0.26        70.52         4.70         8.05         0.16 
TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0650 
       35.01        12.33         3.22         4.47         9.67        23.57 
TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 
        9.40        22.32        19.56         5.39         2.70         2.17 
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        22.98         5.85 
TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 
        5.42        20.94         7.43         3.58        26.79         8.65 
TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 TCGA-06-2558 TCGA-06-2559 
        7.89        13.61        33.90        15.32         0.76         4.93 
TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 
        9.27         2.83        30.64         5.95         6.81         5.98 
TCGA-06-2567 TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 
        4.37        31.50        11.24         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-06-6693 
        6.15         4.57         3.95         7.79         5.39         0.49 
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-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-08-0244 TCGA-08-0245 
        4.96         1.87         3.12         2.56        22.68        34.75 
TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 
        3.91       108.82         1.74        13.78        10.39         7.59 
TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 
        3.42        53.82         1.28         6.41        15.06        22.52 
TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 
       14.70        35.64        19.53         0.95         9.17        10.85 
TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0512 TCGA-08-0514 
        3.19        10.59         0.30         0.56        11.77         8.52 
TCGA-08-0516 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0525 TCGA-08-0529 
       18.44         1.28        10.75         4.80        15.98        17.33 
TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 
        5.52        14.01        14.43         1.64        10.39         5.95 
TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 
        7.17        65.92         0.10        38.17        25.97        24.13 
TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 
        6.12         2.63        18.12        28.41        12.43        53.10 
TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 
       43.10         5.49         9.11        14.27        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         6.25        30.54        21.63 
TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 
       11.97        11.38        15.85         9.11        14.53         3.98 
TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 
        9.44        25.28        13.61         6.41        59.41        43.23 
TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-5295 
       25.78        11.54        10.95        11.77        34.52        13.12 
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-14-0862 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-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 
       23.11         7.10        30.18         0.92        40.96         6.15 
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         9.86        50.53 
TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 
       19.10        53.19         5.52         9.93        26.07        16.31 
TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 
        4.31        29.03         0.82         9.90        13.35         3.65 
TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0960 TCGA-19-0962 
       18.28        13.97         6.41        11.77         8.61         0.43 
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-19-1787 TCGA-19-1789 TCGA-19-1791 
        4.64        25.38         3.48        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-19-4065 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 
        7.00         7.04         6.64        11.28         8.02        18.64 
TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 
        4.73         7.96         1.78         6.51         5.39         5.29 
TCGA-19-5960 TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1440 TCGA-26-1442 
        5.42         3.98        16.57        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-27-1830 TCGA-27-1831 
        1.22         1.58         7.92         2.33         4.80        16.60 
TCGA-27-1832 TCGA-27-1833 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 
        9.86        18.25        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         3.91 
TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 
        9.04        15.58        14.53        11.77        31.27        14.20 
TCGA-28-5215 TCGA-28-5216 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 
        7.79        13.64        22.68        10.49         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        21.17 
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        10.62         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-74-6573 TCGA-74-6575 TCGA-74-6577 
        0.20        11.54         7.76         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 
       26.30         5.92 

  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 
            7.335            10.305 
[1] "0.4 - 92.7 (7.3)"   "0.1 - 127.6 (10.3)"
[1] "hr=" "1.1"
D3V2, continuous
D3V3, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    19  17
  2P GAIN WILD-TYPE 201 323
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     19   17
  2P GAIN WILD-TYPE  201  323
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE              19               201
  MALE                17               323
[1] 2 2
[1] FALSE
D3V4, continuous
                   vv
clus                GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  2P GAIN MUTATED                               1                   1
  2P GAIN WILD-TYPE                            16                  17
                   vv
clus                UNTREATED PRIMARY (DE NOVO) GBM
  2P GAIN MUTATED                                34
  2P GAIN WILD-TYPE                             491
D3V5, multiclass
                                 clus
vv                                2P GAIN MUTATED 2P GAIN WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                 1                16
  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"
D3V6, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    24  12
  2P GAIN WILD-TYPE 358 166
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     24   12
  2P GAIN WILD-TYPE  358  166
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  NO               24               358
  YES              12               166
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2P GAIN MUTATED       1                         5    28
  2P GAIN WILD-TYPE    12                        34   457
D3V7, multiclass
                           clus
vv                          2P GAIN MUTATED 2P GAIN WILD-TYPE
  ASIAN                                   1                12
  BLACK OR AFRICAN AMERICAN               5                34
  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"
D3V8, binary
                   cls
clus                  0   1
  2P GAIN MUTATED     0  29
  2P GAIN WILD-TYPE  12 433
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      0   29
  2P GAIN WILD-TYPE   12  433
                        clus
vv                       2P GAIN MUTATED 2P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                12
  NOT HISPANIC OR LATINO              29               433
[1] 2 2
[1] FALSE

Clustering(4) Variable = 2Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                 0   1
  2Q GAIN MUTATED     5  30
  2Q GAIN WILD-TYPE  93 432
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               35               525 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               30               432 
$`2Q GAIN MUTATED`
TCGA-02-0001 TCGA-02-0106 TCGA-02-0113 TCGA-02-0281 TCGA-06-0128 TCGA-06-0133 
        9.17        11.67        92.65         3.98        22.72        14.07 
TCGA-06-0151 TCGA-06-0192 TCGA-06-0216 TCGA-06-0649 TCGA-06-0877 TCGA-06-1086 
       46.59        18.31        22.49         2.04         5.65         6.35 
TCGA-06-2557 TCGA-06-2569 TCGA-08-0346 TCGA-08-0386 TCGA-08-0510 TCGA-08-0524 
        1.08         0.43         4.34        15.72         3.52         6.54 
TCGA-12-0778 TCGA-12-1099 TCGA-12-3653 TCGA-14-0740 TCGA-14-0817 TCGA-14-0871 
       14.86         3.42        11.74        11.97         5.39        28.93 
TCGA-14-1453 TCGA-14-1823 TCGA-14-3477 TCGA-16-0846 TCGA-19-0957 TCGA-19-1786 
        1.15        17.85         3.78         3.91        21.90         7.17 
TCGA-26-1439 TCGA-27-1834 TCGA-28-5218 TCGA-32-4210 TCGA-74-6584 
       13.87        33.14         4.21         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        55.86        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        10.36        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         0.23        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         0.16        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        16.21         2.70         0.26         4.04 
TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 
       47.31         0.10         3.58        32.52        10.52        18.74 
TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 
       23.08        22.16        10.75         0.20         9.21         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        16.70         9.80         7.86 
TCGA-06-0150 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 
       19.46        11.80        12.79         8.65         3.19         5.46 
TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 
        9.44        11.80         2.56        56.88        10.65         5.29 
TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 
       19.04         3.12        13.02         0.23         2.20         2.73 
TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 
       91.00         2.01        53.98        19.00         2.53        40.37 
TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0194 
       73.84        26.33        28.47        14.93        10.29         4.67 
TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 
        7.04         2.60         0.39         6.48         5.49         3.91 
TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0219 TCGA-06-0221 
        4.96        11.84         0.20        12.43         0.36        18.02 
TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 
       10.36        11.80        20.42        14.96        10.32         5.52 
TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 
        0.26        70.52         4.70         8.05         0.16        35.01 
TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0650 TCGA-06-0686 
       12.33         3.22         4.47         9.67        23.57         9.40 
TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 
       22.32        19.56         5.39         2.70         2.17         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        22.98         5.85         5.42 
TCGA-06-0939 TCGA-06-1084 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 
       20.94         7.43         3.58        26.79         8.65         7.89 
TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 
       13.61        33.90        15.32         0.76         4.93         9.27 
TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 
        2.83        30.64         5.95         6.81         5.98         4.37 
TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 
       31.50        11.24         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         3.95         7.79         5.39         1.48         0.49 
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-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-08-0244 TCGA-08-0245 
        4.96         1.87         3.12         2.56        22.68        34.75 
TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 
        3.91       108.82         1.74        13.78        10.39         7.59 
TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 
        3.42        53.82         1.28         6.41        15.06        22.52 
TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 
       14.70        35.64        19.53         0.95         9.17        10.85 
TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0512 TCGA-08-0514 
        3.19        10.59         0.30         0.56        11.77         8.52 
TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0525 
       18.44        58.19         1.28        10.75         4.80        15.98 
TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 
       17.33         5.52        14.01        14.43         1.64        10.39 
TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 
        5.95         7.17        65.92         0.10        38.17        25.97 
TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 
       24.13         6.12         2.63        18.12        28.41        12.43 
TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0780 TCGA-12-0818 
       53.10        43.10         5.49         9.11        14.27        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         6.25        30.54 
TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 
       21.63        11.97        11.38        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         9.44        25.28        13.61         6.41        59.41 
TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 
       43.23        25.78        11.54        10.95        11.77        34.52 
TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0781 TCGA-14-0783 
       13.12         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-14-0862 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-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 
       23.11         7.10        30.18         0.92        40.96         6.15 
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         9.86        50.53 
TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 
       19.10        53.19         5.52         9.93        26.07        16.31 
TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 
        4.31        29.03         0.82         9.90        13.35         3.65 
TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0960 TCGA-19-0962 
       18.28        13.97         6.41        11.77         8.61         0.43 
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-19-1787 TCGA-19-1789 TCGA-19-1791 
        4.64        25.38         3.48        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 
       16.47         7.00         7.04         6.64        11.28         8.02 
TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 
       18.64         4.73         7.96         1.78         6.51         5.39 
TCGA-19-5959 TCGA-19-5960 TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1440 
        5.29         5.42         3.98        16.57        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-27-1830 
        8.88         1.22         1.58         7.92         2.33         4.80 
TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 
       16.60         9.86        18.25        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 
        3.91         9.04        15.58        14.53        11.77        31.27 
TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 
       14.20         7.79        13.64        22.68        10.49         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-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 
       21.17        21.14        12.59        19.86        10.85        10.62 
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-74-6573 TCGA-74-6575 
       11.84         0.20        11.54         7.76         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 
       17.72        26.30         5.92 

  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 
             7.50             10.29 
[1] "0.4 - 92.7 (7.5)"   "0.1 - 127.6 (10.3)"
[1] "hr=" "1.1"
D4V2, continuous
D4V3, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    17  18
  2Q GAIN WILD-TYPE 203 322
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     17   18
  2Q GAIN WILD-TYPE  203  322
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE              17               203
  MALE                18               322
[1] 2 2
[1] FALSE
D4V4, continuous
                   vv
clus                GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  2Q GAIN MUTATED                               1                   1
  2Q GAIN WILD-TYPE                            16                  17
                   vv
clus                UNTREATED PRIMARY (DE NOVO) GBM
  2Q GAIN MUTATED                                33
  2Q GAIN WILD-TYPE                             492
D4V5, multiclass
                                 clus
vv                                2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                 1                16
  TREATED PRIMARY GBM                           1                17
  UNTREATED PRIMARY (DE NOVO) GBM              33               492
[1] 3 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  11
  2Q GAIN WILD-TYPE 358 167
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     24   11
  2Q GAIN WILD-TYPE  358  167
     clus
vv    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  NO               24               358
  YES              11               167
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2Q GAIN MUTATED       1                         5    27
  2Q GAIN WILD-TYPE    12                        34   458
D4V7, multiclass
                           clus
vv                          2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  ASIAN                                   1                12
  BLACK OR AFRICAN AMERICAN               5                34
  WHITE                                  27               458
[1] 3 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  27
  2Q GAIN WILD-TYPE  12 435
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      0   27
  2Q GAIN WILD-TYPE   12  435
                        clus
vv                       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                12
  NOT HISPANIC OR LATINO              27               435
[1] 2 2
[1] FALSE

Clustering(5) Variable = 3P GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                 0   1
  3P GAIN MUTATED     9  47
  3P GAIN WILD-TYPE  89 415
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               56               504 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               47               415 
$`3P GAIN MUTATED`
TCGA-02-0001 TCGA-02-0028 TCGA-02-0069 TCGA-02-0074 TCGA-02-0281 TCGA-02-0324 
        9.17        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         5.29        28.47        18.31        11.84 
TCGA-06-0237 TCGA-06-0410 TCGA-06-0413 TCGA-06-0414 TCGA-06-0648 TCGA-06-0649 
       10.36         4.70         0.16        35.01         9.67         2.04 
TCGA-06-0686 TCGA-06-0743 TCGA-06-1087 TCGA-06-2557 TCGA-08-0345 TCGA-08-0346 
        9.40        22.32         3.58         1.08         1.74         4.34 
TCGA-08-0510 TCGA-12-0615 TCGA-12-0619 TCGA-12-0822 TCGA-12-0829 TCGA-12-1088 
        3.52        14.01        10.39        23.51        20.58       127.59 
TCGA-12-1099 TCGA-12-1598 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-14-0867 
        3.42         9.44         6.41        59.41        43.23         2.04 
TCGA-14-1794 TCGA-14-1825 TCGA-19-2629 TCGA-19-4065 TCGA-26-1440 TCGA-26-6174 
        0.99         7.63        16.47         7.04         9.73         2.33 
TCGA-27-1834 TCGA-27-2521 TCGA-28-2506 TCGA-28-2509 TCGA-28-5207 TCGA-28-5215 
       33.14        10.39         6.74         4.77         9.04         7.79 
TCGA-28-5216 TCGA-28-5219 TCGA-28-6450 TCGA-32-2632 TCGA-41-3915 TCGA-41-4097 
       13.64        22.68         5.42         8.84        11.84         0.20 
TCGA-76-4934 TCGA-76-6285 
        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        55.86        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        10.36         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         0.23        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         0.16 
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        16.21         2.70 
TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 
        0.26         4.04        47.31         0.10         3.58        22.72 
TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 
       32.52        10.52        18.74        14.07        23.08        22.16 
TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 
       10.75         0.20         9.21         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        16.70         9.80         7.86        19.46        46.59 
TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 
       11.80        12.79         8.65         3.19         5.46         9.44 
TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0168 TCGA-06-0169 
       11.80         2.56        56.88        10.65        19.04         3.12 
TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 
       13.02         0.23         2.20         2.73        91.00         2.01 
TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 
       53.98        19.00         2.53        40.37        73.84        26.33 
TCGA-06-0189 TCGA-06-0190 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 
       14.93        10.29         4.67         7.04         2.60         0.39 
TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0213 TCGA-06-0214 
        6.48         5.49         3.91         4.96         0.20        12.43 
TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 
       22.49         0.36        18.02        11.80        20.42        14.96 
TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0412 TCGA-06-0644 
       10.32         5.52         0.26        70.52         8.05        12.33 
TCGA-06-0645 TCGA-06-0646 TCGA-06-0650 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 
        3.22         4.47        23.57        19.56         5.39         2.70 
TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 
        2.17         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 
       22.98         5.85         5.42        20.94         7.43         6.35 
TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 
       26.79         8.65         7.89        13.61        33.90        15.32 
TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 
        0.76         4.93         9.27         2.83        30.64         5.95 
TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-5408 
        6.81         5.98         4.37         0.43        31.50        11.24 
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         3.95 
TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 
        7.79         5.39         1.48         0.49         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-08-0244 TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 
        3.12         2.56        22.68        34.75         3.91       108.82 
TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 
       13.78        10.39         7.59         3.42        53.82         1.28 
TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 
        6.41        15.06        22.52        14.70        35.64        19.53 
TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 
        0.95         9.17        10.85        15.72         3.19        10.59 
TCGA-08-0392 TCGA-08-0509 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 
        0.30         0.56        11.77         8.52        18.44        58.19 
TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 
        1.28        10.75         4.80         6.54        15.98        17.33 
TCGA-08-0531 TCGA-12-0616 TCGA-12-0618 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 
        5.52        14.43         1.64         5.95         7.17        65.92 
TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 
        0.10        38.17        25.97        24.13         6.12         2.63 
TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 
       18.12        28.41        12.43        53.10        43.10         5.49 
TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 
        9.11        14.86        14.27        91.76        24.79        18.48 
TCGA-12-0821 TCGA-12-0826 TCGA-12-0827 TCGA-12-0828 TCGA-12-1089 TCGA-12-1090 
       10.62        27.78        38.76         8.94         5.82         6.25 
TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 
       30.54        21.63        11.97        11.38        15.85         9.11 
TCGA-12-1097 TCGA-12-1098 TCGA-12-1599 TCGA-12-1600 TCGA-12-3648 TCGA-12-3649 
       14.53         3.98        25.28        13.61        25.78        11.54 
TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 
       10.95        11.77        34.52        11.74        13.12         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 
        6.15        12.43         1.97        17.79        17.85         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         9.86 
TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 
       50.53        19.10        53.19         5.52         3.91         9.93 
TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 
       26.07        16.31         4.31        29.03         0.82         9.90 
TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 
       13.35         3.65        18.28        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         0.43        14.27         3.39        10.75 
TCGA-19-1386 TCGA-19-1387 TCGA-19-1388 TCGA-19-1389 TCGA-19-1390 TCGA-19-1392 
        9.07         5.95        12.95         4.64        25.38         3.48 
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-19-5947 
        1.08         7.53         0.16         4.08         7.00         6.64 
TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 
       11.28         8.02        18.64         4.73         7.96         1.78 
TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A6J4 TCGA-19-A6J5 
        6.51         5.39         5.29         5.42         3.98        16.57 
TCGA-26-1438 TCGA-26-1439 TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 
       10.03        13.87        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         1.22         1.58         7.92 
TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1835 TCGA-27-1836 
        4.80        16.60         9.86        18.25        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-28-1755 TCGA-28-1756 
        8.35         7.63         8.48         1.22         1.55         2.83 
TCGA-28-1757 TCGA-28-2502 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5208 
        0.13         0.66         7.30         5.26         3.91        15.58 
TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5218 TCGA-28-5220 
       14.53        11.77        31.27        14.20         4.21        10.49 
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        21.17 
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        10.62 
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-41-5651 TCGA-41-6646 TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 
       11.54         7.76         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 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             0.16              0.10 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
           127.59            108.82 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            9.285            10.390 
[1] "0.2 - 127.6 (9.3)"  "0.1 - 108.8 (10.4)"
[1] "hr=" "1"  
D5V2, continuous
D5V3, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    25  31
  3P GAIN WILD-TYPE 195 309
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     25   31
  3P GAIN WILD-TYPE  195  309
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE              25               195
  MALE                31               309
[1] 2 2
[1] FALSE
D5V4, continuous
                   vv
clus                GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  3P GAIN MUTATED                               0                   1
  3P GAIN WILD-TYPE                            17                  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)                 0                17
  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  18
  3P GAIN WILD-TYPE 344 160
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     38   18
  3P GAIN WILD-TYPE  344  160
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  NO               38               344
  YES              18               160
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3P GAIN MUTATED       1                         3    48
  3P GAIN WILD-TYPE    12                        36   437
D5V7, multiclass
                           clus
vv                          3P GAIN MUTATED 3P GAIN WILD-TYPE
  ASIAN                                   1                12
  BLACK OR AFRICAN AMERICAN               3                36
  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  44
  3P GAIN WILD-TYPE  11 418
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      1   44
  3P GAIN WILD-TYPE   11  418
                        clus
vv                       3P GAIN MUTATED 3P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                11
  NOT HISPANIC OR LATINO              44               418
[1] 2 2
[1] FALSE

Clustering(6) Variable = 3Q GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                 0   1
  3Q GAIN MUTATED    11  50
  3Q GAIN WILD-TYPE  87 412
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               61               499 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               50               412 
$`3Q GAIN MUTATED`
TCGA-02-0001 TCGA-02-0028 TCGA-02-0047 TCGA-02-0074 TCGA-02-0106 TCGA-02-0281 
        9.17        90.58        14.73        10.19        11.67         3.98 
TCGA-02-0324 TCGA-02-0325 TCGA-02-0332 TCGA-06-0166 TCGA-06-0188 TCGA-06-0192 
        7.73        10.62        25.71         5.29        28.47        18.31 
TCGA-06-0211 TCGA-06-0237 TCGA-06-0410 TCGA-06-0413 TCGA-06-0414 TCGA-06-0648 
       11.84        10.36         4.70         0.16        35.01         9.67 
TCGA-06-0649 TCGA-06-0686 TCGA-06-0743 TCGA-06-1087 TCGA-06-2557 TCGA-06-5416 
        2.04         9.40        22.32         3.58         1.08         6.71 
TCGA-08-0345 TCGA-08-0346 TCGA-08-0510 TCGA-12-0615 TCGA-12-0619 TCGA-12-0827 
        1.74         4.34         3.52        14.01        10.39        38.76 
TCGA-12-0829 TCGA-12-1088 TCGA-12-1598 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 
       20.58       127.59         9.44         6.41        59.41        43.23 
TCGA-14-0867 TCGA-14-1794 TCGA-14-1825 TCGA-14-1829 TCGA-14-3477 TCGA-19-2629 
        2.04         0.99         7.63         7.17         3.78        16.47 
TCGA-19-4065 TCGA-26-1440 TCGA-26-6174 TCGA-27-1831 TCGA-27-1834 TCGA-27-2521 
        7.04         9.73         2.33        16.60        33.14        10.39 
TCGA-28-2506 TCGA-28-2509 TCGA-28-5207 TCGA-28-5215 TCGA-28-5216 TCGA-28-5219 
        6.74         4.77         9.04         7.79        13.64        22.68 
TCGA-28-6450 TCGA-32-1991 TCGA-32-2632 TCGA-41-3915 TCGA-41-4097 TCGA-76-4934 
        5.42        16.93         8.84        11.84         0.20         2.53 
TCGA-76-6285 
        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        55.86        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        10.36         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-02-0069 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         0.23        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-02-0326 TCGA-02-0330 
       14.20        15.95        12.23         9.90         0.16        15.91 
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        16.21         2.70         0.26 
TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 
        4.04        47.31         0.10         3.58        22.72        32.52 
TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 
       10.52        18.74        14.07        23.08        22.16        10.75 
TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 
        0.20         9.21         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 
       16.70         9.80         7.86        19.46        46.59        11.80 
TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 
       12.79         8.65         3.19         5.46         9.44        11.80 
TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 
        2.56        56.88        10.65        19.04         3.12        13.02 
TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 
        0.23         2.20         2.73        91.00         2.01        53.98 
TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0189 
       19.00         2.53        40.37        73.84        26.33        14.93 
TCGA-06-0190 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 
       10.29         4.67         7.04         2.60         0.39         6.48 
TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 
        5.49         3.91         4.96         0.20        12.43        22.49 
TCGA-06-0219 TCGA-06-0221 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 
        0.36        18.02        11.80        20.42        14.96        10.32 
TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0412 TCGA-06-0644 TCGA-06-0645 
        5.52         0.26        70.52         8.05        12.33         3.22 
TCGA-06-0646 TCGA-06-0650 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 
        4.47        23.57        19.56         5.39         2.70         2.17 
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        22.98 
TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1800 
        5.85         5.42        20.94         7.43         6.35        26.79 
TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 TCGA-06-2558 
        8.65         7.89        13.61        33.90        15.32         0.76 
TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 
        4.93         9.27         2.83        30.64         5.95         6.81 
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        11.24         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-06-6389 TCGA-06-6390 
        3.75         6.15         4.57         3.95         7.79         5.39 
TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 
        1.48         0.49         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-08-0244 TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 TCGA-08-0347 TCGA-08-0348 
       22.68        34.75         3.91       108.82        13.78        10.39 
TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 
        7.59         3.42        53.82         1.28         6.41        15.06 
TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 
       22.52        14.70        35.64        19.53         0.95         9.17 
TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 
       10.85        15.72         3.19        10.59         0.30         0.56 
TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 
       11.77         8.52        18.44        58.19         1.28        10.75 
TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0616 
        4.80         6.54        15.98        17.33         5.52        14.43 
TCGA-12-0618 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 
        1.64         5.95         7.17        65.92         0.10        38.17 
TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 
       25.97        24.13         6.12         2.63        18.12        28.41 
TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 
       12.43        53.10        43.10         5.49         9.11        14.86 
TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 
       14.27        91.76        24.79        18.48        10.62        23.51 
TCGA-12-0826 TCGA-12-0828 TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 TCGA-12-1092 
       27.78         8.94         5.82         6.25        30.54        21.63 
TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 
       11.97        11.38        15.85         9.11        14.53         3.98 
TCGA-12-1099 TCGA-12-1599 TCGA-12-1600 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 
        3.42        25.28        13.61        25.78        11.54        10.95 
TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 
       11.77        34.52        11.74        13.12         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-14-0871 TCGA-14-1034 TCGA-14-1037 TCGA-14-1043 
       16.50        26.33        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         6.15 
TCGA-14-1459 TCGA-14-1795 TCGA-14-1821 TCGA-14-1823 TCGA-14-1827 TCGA-14-2554 
       12.43         1.97        17.79        17.85         5.88        17.49 
TCGA-14-2555 TCGA-14-4157 TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 
        7.96         3.42         9.86        50.53        19.10        53.19 
TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 
        5.52         3.91         9.93        26.07        16.31         4.31 
TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 
       29.03         0.82         9.90        13.35         3.65        18.28 
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         0.43 
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         3.48         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-19-2631 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 
        4.08         7.00         6.64        11.28         8.02        18.64 
TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 
        4.73         7.96         1.78         6.51         5.39         5.29 
TCGA-19-5960 TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1442 
        5.42         3.98        16.57        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-27-1830 TCGA-27-1832 TCGA-27-1833 
        1.22         1.58         7.92         4.80         9.86        18.25 
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-28-1746 
       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-28-2513 TCGA-28-2514 
        1.55         2.83         0.13         0.66         7.30         5.26 
TCGA-28-5204 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 
        3.91        15.58        14.53        11.77        31.27        14.20 
TCGA-28-5218 TCGA-28-5220 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 
        4.21        10.49        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-32-2634 
       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 
       21.17        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 
       10.62         0.85        13.35         8.94         9.53         0.99 
TCGA-41-3393 TCGA-41-5651 TCGA-41-6646 TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 
        4.44        11.54         7.76         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-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 
       11.38        17.06        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 
        5.92 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             0.16              0.10 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
           127.59            108.82 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             9.40             10.39 
[1] "0.2 - 127.6 (9.4)"  "0.1 - 108.8 (10.4)"
[1] "hr=" "1"  
D6V2, continuous
D6V3, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    26  35
  3Q GAIN WILD-TYPE 194 305
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     26   35
  3Q GAIN WILD-TYPE  194  305
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE              26               194
  MALE                35               305
[1] 2 2
[1] FALSE
D6V4, continuous
                   vv
clus                GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  3Q GAIN MUTATED                               0                   1
  3Q GAIN WILD-TYPE                            17                  17
                   vv
clus                UNTREATED PRIMARY (DE NOVO) GBM
  3Q GAIN MUTATED                                60
  3Q GAIN WILD-TYPE                             465
D6V5, multiclass
                                 clus
vv                                3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                 0                17
  TREATED PRIMARY GBM                           1                17
  UNTREATED PRIMARY (DE NOVO) GBM              60               465
[1] 3 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    43  18
  3Q GAIN WILD-TYPE 339 160
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     43   18
  3Q GAIN WILD-TYPE  339  160
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  NO               43               339
  YES              18               160
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3Q GAIN MUTATED       0                         5    52
  3Q GAIN WILD-TYPE    13                        34   433
D6V7, multiclass
                           clus
vv                          3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  ASIAN                                   0                13
  BLACK OR AFRICAN AMERICAN               5                34
  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  48
  3Q GAIN WILD-TYPE  11 414
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      1   48
  3Q GAIN WILD-TYPE   11  414
                        clus
vv                       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                11
  NOT HISPANIC OR LATINO              48               414
[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  93 431
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               36               524 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               31               431 
$`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 
       10.52         2.20        18.31         7.04        70.52         4.70 
TCGA-06-0879 TCGA-06-5856 TCGA-06-6697 TCGA-08-0245 TCGA-08-0246 TCGA-08-0510 
       22.98         3.75        12.85        34.75         3.91         3.52 
TCGA-08-0514 TCGA-08-0516 TCGA-08-0531 TCGA-12-0616 TCGA-12-0691 TCGA-12-0826 
        8.52        18.44         5.52        14.43         6.12        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         7.79        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 
        9.17         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        55.86        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        10.36        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         0.23        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 
        0.16        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 
       16.21         2.70         0.26         4.04        47.31         0.10 
TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 
        3.58        22.72        32.52        18.74        14.07        23.08 
TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 
       22.16        10.75         0.20         9.21         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        16.70         9.80         7.86        19.46 
TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 
       46.59        11.80        12.79         8.65         3.19         5.46 
TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 
        9.44        11.80         2.56        56.88        10.65         5.29 
TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0175 TCGA-06-0176 
       19.04         3.12        13.02         0.23         2.73        91.00 
TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 
        2.01        53.98        19.00         2.53        40.37        73.84 
TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0194 TCGA-06-0197 
       26.33        28.47        14.93        10.29         4.67         2.60 
TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 
        0.39         6.48         5.49         3.91         4.96        11.84 
TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 
        0.20        12.43        22.49         0.36        18.02        10.36 
TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 
       11.80        20.42        14.96        10.32         5.52         0.26 
TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 
        8.05         0.16        35.01        12.33         3.22         4.47 
TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 
        9.67         2.04        23.57         9.40        22.32        19.56 
TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 
        5.39         2.70         2.17         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         5.85         5.42        20.94         7.43 
TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 
        6.35         3.58        26.79         8.65         7.89        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         0.76         4.93         9.27 
TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 
        2.83        30.64         5.95         6.81         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        11.24         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         3.95         7.79         5.39         1.48         0.49 
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-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-08-0244 TCGA-08-0344 TCGA-08-0345 
        1.87         3.12         2.56        22.68       108.82         1.74 
TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 
        4.34        13.78        10.39         7.59         3.42        53.82 
TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 
        1.28         6.41        15.06        22.52        14.70        35.64 
TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 
       19.53         0.95         9.17        10.85        15.72         3.19 
TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0512 TCGA-08-0517 TCGA-08-0518 
       10.59         0.30         0.56        11.77        58.19         1.28 
TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-12-0615 
       10.75         4.80         6.54        15.98        17.33        14.01 
TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 
        1.64        10.39         5.95         7.17        65.92         0.10 
TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 
       38.17        25.97        24.13         2.63        18.12        28.41 
TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 
       12.43        53.10        43.10         5.49         9.11        14.86 
TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 
       14.27        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         6.25 
TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 
       30.54        21.63        11.97        11.38        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         3.42         9.44        25.28        13.61 
TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 
        6.41        59.41        43.23        25.78        11.54        10.95 
TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 
       11.77        34.52        11.74        13.12         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-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 
       23.11         7.10        30.18         0.92        40.96         6.15 
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         9.86        50.53 
TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 
       19.10        53.19         5.52         9.93        26.07        16.31 
TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 
        4.31        29.03         0.82         9.90        13.35         3.65 
TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 
       18.28        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 
        0.43        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         3.48         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        16.47         7.00         7.04         6.64 
TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 
       11.28         8.02        18.64         4.73         7.96         1.78 
TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A6J5 TCGA-26-1438 
        6.51         5.39         5.29         5.42        16.57        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         1.22         1.58         7.92         2.33 
TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 
        4.80        16.60         9.86        18.25        33.14        21.30 
TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 
       30.05        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-28-2509 TCGA-28-2513 
        1.55         2.83         0.13         0.66         4.77         7.30 
TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 
        5.26         3.91         9.04        15.58        14.53        11.77 
TCGA-28-5213 TCGA-28-5214 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 
       31.27        14.20        13.64         4.21        22.68        10.49 
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-32-2615 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 
       21.17        21.14        12.59        19.86        10.85        10.62 
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-41-5651 TCGA-41-6646 TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 
       11.54         7.76         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 
       26.30         5.92 

  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 
            9.355            10.160 
[1] "0.2 - 92.7 (9.4)"   "0.1 - 127.6 (10.2)"
[1] "hr=" "1"  
D7V2, continuous
D7V3, binary
                   cls
clus                  0   1
  4P GAIN MUTATED    15  21
  4P GAIN WILD-TYPE 205 319
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     15   21
  4P GAIN WILD-TYPE  205  319
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE              15               205
  MALE                21               319
[1] 2 2
[1] FALSE
D7V4, continuous
                   vv
clus                GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  4P GAIN MUTATED                               1                   1
  4P GAIN WILD-TYPE                            16                  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                16
  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 356 168
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     26   10
  4P GAIN WILD-TYPE  356  168
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  NO               26               356
  YES              10               168
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4P GAIN MUTATED       1                         4    31
  4P GAIN WILD-TYPE    12                        35   454
D7V7, multiclass
                           clus
vv                          4P GAIN MUTATED 4P GAIN WILD-TYPE
  ASIAN                                   1                12
  BLACK OR AFRICAN AMERICAN               4                35
  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  11 430
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      1   32
  4P GAIN WILD-TYPE   11  430
                        clus
vv                       4P GAIN MUTATED 4P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                11
  NOT HISPANIC OR LATINO              32               430
[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  93 434
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               33               527 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               28               434 
$`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        10.52 
TCGA-06-0174 TCGA-06-0192 TCGA-06-0195 TCGA-06-0409 TCGA-06-0410 TCGA-06-0879 
        2.20        18.31         7.04        70.52         4.70        22.98 
TCGA-06-5856 TCGA-06-6697 TCGA-08-0245 TCGA-08-0246 TCGA-08-0510 TCGA-08-0514 
        3.75        12.85        34.75         3.91         3.52         8.52 
TCGA-08-0516 TCGA-08-0531 TCGA-12-0616 TCGA-12-0826 TCGA-14-1821 TCGA-14-3477 
       18.44         5.52        14.43        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         6.51         3.98        13.87         6.74         7.79 
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 
        9.17         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        55.86        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        10.36        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         0.23        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         0.16        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        16.21         2.70         0.26         4.04        47.31 
TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0132 TCGA-06-0133 
        0.10         3.58        22.72        32.52        18.74        14.07 
TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 
       23.08        22.16        10.75         0.20         9.21         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        16.70         9.80         7.86 
TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 
       19.46        46.59        11.80        12.79         8.65         3.19 
TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 
        5.46         9.44        11.80         2.56        56.88        10.65 
TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0175 
        5.29        19.04         3.12        13.02         0.23         2.73 
TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 
       91.00         2.01        53.98        19.00         2.53        40.37 
TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0194 
       73.84        26.33        28.47        14.93        10.29         4.67 
TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 
        2.60         0.39         6.48         5.49         3.91         4.96 
TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 
       11.84         0.20        12.43        22.49         0.36        18.02 
TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 
       10.36        11.80        20.42        14.96        10.32         5.52 
TCGA-06-0402 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 
        0.26         8.05         0.16        35.01        12.33         3.22 
TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 
        4.47         9.67         2.04        23.57         9.40        22.32 
TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 
       19.56         5.39         2.70         2.17         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         5.85         5.42        20.94 
TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 
        7.43         6.35         3.58        26.79         8.65         7.89 
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         0.76         4.93 
TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 
        9.27         2.83        30.64         5.95         6.81         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        11.24         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         3.95         7.79         5.39         1.48 
TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 
        0.49         7.36         8.32         4.77         1.55         4.77 
TCGA-06-6701 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-08-0244 TCGA-08-0344 
        4.96         1.87         3.12         2.56        22.68       108.82 
TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 
        1.74         4.34        13.78        10.39         7.59         3.42 
TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 
       53.82         1.28         6.41        15.06        22.52        14.70 
TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 
       35.64        19.53         0.95         9.17        10.85        15.72 
TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0512 TCGA-08-0517 
        3.19        10.59         0.30         0.56        11.77        58.19 
TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 
        1.28        10.75         4.80         6.54        15.98        17.33 
TCGA-12-0615 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 
       14.01         1.64        10.39         5.95         7.17        65.92 
TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 
        0.10        38.17        25.97        24.13         6.12         2.63 
TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 
       18.12        28.41        12.43        53.10        43.10         5.49 
TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 
        9.11        14.86        14.27        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         6.25        30.54        21.63        11.97        11.38 
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         3.42         9.44 
TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 
       25.28        13.61         6.41        59.41        43.23        25.78 
TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 
       11.54        10.95        11.77        34.52        11.74        13.12 
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-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 
        0.92        40.96         6.15        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         9.86        50.53        19.10        53.19         5.52 
TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 
        9.93        26.07        16.31         4.31        29.03         0.82 
TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 
        9.90        13.35         3.65        18.28        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         0.43        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 
        3.48         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        16.47 
TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 
        7.00         7.04         6.64        11.28         8.02        18.64 
TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 
        4.73         7.96         1.78         5.39         5.29         5.42 
TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 
       16.57        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         1.22         1.58 
TCGA-26-6173 TCGA-26-6174 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 
        7.92         2.33         4.80        16.60         9.86        18.25 
TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 
       33.14        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-28-2509 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 
        4.77         7.30         5.26         3.91         9.04        15.58 
TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5216 TCGA-28-5218 
       14.53        11.77        31.27        14.20        13.64         4.21 
TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 
       22.68        10.49         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-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 TCGA-32-2616 
       14.86        12.23        20.78        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        21.17        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        10.62         0.85        13.35         8.94         9.53 
TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 TCGA-41-5651 TCGA-41-6646 TCGA-74-6573 
        0.99         4.44        11.84        11.54         7.76         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 
        7.79         1.61        17.72        26.30         5.92 

  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 
             8.52             10.29 
[1] "0.2 - 92.7 (8.5)"   "0.1 - 127.6 (10.3)"
[1] "hr=" "1"  
D8V2, continuous
D8V3, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED    15  18
  4Q GAIN WILD-TYPE 205 322
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     15   18
  4Q GAIN WILD-TYPE  205  322
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE              15               205
  MALE                18               322
[1] 2 2
[1] FALSE
D8V4, continuous
                   vv
clus                GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  4Q GAIN MUTATED                               1                   1
  4Q GAIN WILD-TYPE                            16                  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                16
  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 357 170
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     25    8
  4Q GAIN WILD-TYPE  357  170
     clus
vv    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  NO               25               357
  YES               8               170
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4Q GAIN MUTATED       1                         4    28
  4Q GAIN WILD-TYPE    12                        35   457
D8V7, multiclass
                           clus
vv                          4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  ASIAN                                   1                12
  BLACK OR AFRICAN AMERICAN               4                35
  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  12 431
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      0   31
  4Q GAIN WILD-TYPE   12  431
                        clus
vv                       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                12
  NOT HISPANIC OR LATINO              31               431
[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  92 419
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               49               511 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               43               419 
$`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         7.04 
TCGA-06-0209 TCGA-06-0237 TCGA-06-0397 TCGA-06-0409 TCGA-06-0410 TCGA-06-0645 
        3.91        10.36         5.52        70.52         4.70         3.22 
TCGA-06-0649 TCGA-06-1806 TCGA-06-2557 TCGA-06-5856 TCGA-08-0350 TCGA-08-0510 
        2.04        15.32         1.08         3.75         3.42         3.52 
TCGA-08-0518 TCGA-08-0524 TCGA-12-0691 TCGA-12-0778 TCGA-12-0826 TCGA-12-1096 
        1.28         6.54         6.12        14.86        27.78         9.11 
TCGA-12-1098 TCGA-12-1602 TCGA-12-3646 TCGA-14-1396 TCGA-14-1823 TCGA-15-1447 
        3.98         6.41        43.23         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 
        9.17         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        55.86        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        10.36         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         0.23        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         0.16        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        16.21         2.70         0.26         4.04 
TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 
       47.31         0.10         3.58        22.72        32.52        10.52 
TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 
       18.74        14.07        23.08        22.16        10.75         0.20 
TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 
        9.21         2.20        11.74         2.33        20.09        16.70 
TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 
        9.80         7.86        19.46        11.80        12.79         8.65 
TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 
        3.19         5.46         9.44        11.80         2.56        56.88 
TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 
       10.65         5.29        19.04         3.12        13.02         0.23 
TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 
        2.20         2.73        91.00         2.01        53.98        19.00 
TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 
        2.53        40.37        73.84        26.33        28.47        14.93 
TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 
       10.29        18.31         4.67         2.60         0.39         6.48 
TCGA-06-0208 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 
        5.49         4.96        11.84         0.20        12.43        22.49 
TCGA-06-0219 TCGA-06-0221 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 
        0.36        18.02        11.80        20.42        14.96        10.32 
TCGA-06-0402 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0646 
        0.26         8.05         0.16        35.01        12.33         4.47 
TCGA-06-0648 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 
        9.67        23.57         9.40        22.32        19.56         5.39 
TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 
        2.70         2.17         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        22.98         5.85         5.42        20.94         7.43 
TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 
        6.35         3.58        26.79         8.65         7.89        13.61 
TCGA-06-1805 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 
       33.90         0.76         4.93         9.27         2.83        30.64 
TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 
        5.95         6.81         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 
       11.24         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         3.95 
TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 
        7.79         5.39         1.48         0.49         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-08-0244 TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 
        3.12         2.56        22.68        34.75         3.91       108.82 
TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0351 
        1.74         4.34        13.78        10.39         7.59        53.82 
TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 
        1.28         6.41        15.06        22.52        14.70        35.64 
TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 
       19.53         0.95         9.17        10.85        15.72         3.19 
TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 
       10.59         0.30         0.56        11.77         8.52        18.44 
TCGA-08-0517 TCGA-08-0520 TCGA-08-0521 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 
       58.19        10.75         4.80        15.98        17.33         5.52 
TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 
       14.01        14.43         1.64        10.39         5.95         7.17 
TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0692 
       65.92         0.10        38.17        25.97        24.13         2.63 
TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 
       18.12        28.41        12.43        53.10        43.10         5.49 
TCGA-12-0776 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 
        9.11        14.27        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 
        6.25        30.54        21.63        11.97        11.38        15.85 
TCGA-12-1097 TCGA-12-1099 TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 TCGA-12-3644 
       14.53         3.42         9.44        25.28        13.61        59.41 
TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 
       25.78        11.54        10.95        11.77        34.52        11.74 
TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 
       13.12         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-14-1401 
       28.93        15.95        19.30         0.79         1.38         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         6.15        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-15-1449 
        3.78         3.42         9.86        50.53        19.10         5.52 
TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 
        3.91         9.93        26.07        16.31         4.31        29.03 
TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 
        0.82         9.90        13.35         3.65        18.28        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         0.43        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         3.48 
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        16.47         7.00         7.04 
TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 
        6.64        11.28         8.02        18.64         4.73         7.96 
TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A6J5 
        1.78         6.51         5.39         5.29         5.42        16.57 
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         1.22         1.58 
TCGA-26-6173 TCGA-26-6174 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 
        7.92         2.33         4.80        16.60         9.86        18.25 
TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 
       33.14        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-28-5207 TCGA-28-5208 TCGA-28-5209 
        7.30         5.26         3.91         9.04        15.58        14.53 
TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5218 TCGA-28-5219 
       11.77        31.27        14.20         7.79         4.21        22.68 
TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1976 TCGA-32-1977 TCGA-32-1978 
       10.49         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-32-2615 TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 
       12.23        20.78        15.95        22.78        21.17        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        10.62         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-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 
       11.54         7.76         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-76-6285 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 
        5.92 

  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 
             7.73             10.36 
[1] "1.1 - 92.7 (7.7)"   "0.1 - 127.6 (10.4)"
[1] "hr=" "1"  
D9V2, continuous
D9V3, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    24  25
  5P GAIN WILD-TYPE 196 315
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     24   25
  5P GAIN WILD-TYPE  196  315
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE              24               196
  MALE                25               315
[1] 2 2
[1] FALSE
D9V4, continuous
                   vv
clus                GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  5P GAIN MUTATED                               3                   4
  5P GAIN WILD-TYPE                            14                  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                14
  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 350 161
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     32   17
  5P GAIN WILD-TYPE  350  161
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  NO               32               350
  YES              17               161
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5P GAIN MUTATED       1                         4    43
  5P GAIN WILD-TYPE    12                        35   442
D9V7, multiclass
                           clus
vv                          5P GAIN MUTATED 5P GAIN WILD-TYPE
  ASIAN                                   1                12
  BLACK OR AFRICAN AMERICAN               4                35
  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  10 420
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      2   42
  5P GAIN WILD-TYPE   10  420
                        clus
vv                       5P GAIN MUTATED 5P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                10
  NOT HISPANIC OR LATINO              42               420
[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  92 427
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               41               519 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               35               427 
$`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         7.04         3.91         5.52 
TCGA-06-0409 TCGA-06-0410 TCGA-06-0645 TCGA-06-0649 TCGA-06-1806 TCGA-06-2557 
       70.52         4.70         3.22         2.04        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         3.52         1.28        14.86        27.78 
TCGA-12-1096 TCGA-12-1098 TCGA-12-1602 TCGA-12-3646 TCGA-14-1396 TCGA-14-1823 
        9.11         3.98         6.41        43.23         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 
        9.17         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        55.86        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        10.36         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         0.23 
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         0.16 
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        16.21         2.70 
TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 
        0.26         4.04        47.31         0.10         3.58        22.72 
TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 
       32.52        10.52        18.74        14.07        23.08        22.16 
TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 
       10.75         0.20         9.21         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        16.70         9.80         7.86        19.46        11.80 
TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 
       12.79         8.65         3.19         5.46         9.44        11.80 
TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 
        2.56        56.88        10.65         5.29        19.04         3.12 
TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 
       13.02         0.23         2.20         2.73        91.00         2.01 
TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 
       53.98        19.00         2.53        40.37        73.84        26.33 
TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0197 
       28.47        14.93        10.29        18.31         4.67         2.60 
TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 
        0.39         6.48         5.49         4.96        11.84         0.20 
TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 
       12.43        22.49         0.36        18.02        10.36        11.80 
TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0402 TCGA-06-0412 TCGA-06-0413 
       20.42        14.96        10.32         0.26         8.05         0.16 
TCGA-06-0414 TCGA-06-0644 TCGA-06-0646 TCGA-06-0648 TCGA-06-0650 TCGA-06-0686 
       35.01        12.33         4.47         9.67        23.57         9.40 
TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 
       22.32        19.56         5.39         2.70         2.17         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        22.98         5.85 
TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 
        5.42        20.94         7.43         6.35         3.58        26.79 
TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-2558 TCGA-06-2559 
        8.65         7.89        13.61        33.90         0.76         4.93 
TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 
        9.27         2.83        30.64         5.95         6.81         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        11.24         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         3.95         7.79         5.39         1.48         0.49 
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-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-08-0244 TCGA-08-0245 
        4.96         1.87         3.12         2.56        22.68        34.75 
TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 
        3.91       108.82         1.74         4.34        13.78        10.39 
TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 
        7.59         3.42        53.82         1.28         6.41        15.06 
TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 
       22.52        14.70        35.64        19.53         0.95         9.17 
TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 
       10.85        15.72         3.19        10.59         0.30         0.56 
TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0520 TCGA-08-0521 
       11.77         8.52        18.44        58.19        10.75         4.80 
TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 
        6.54        15.98        17.33         5.52        14.01        14.43 
TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 
        1.64        10.39         5.95         7.17        65.92         0.10 
TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 
       38.17        25.97        24.13         6.12         2.63        18.12 
TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 
       28.41        12.43        53.10        43.10         5.49         9.11 
TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 
       14.27        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         6.25 
TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1097 
       30.54        21.63        11.97        11.38        15.85        14.53 
TCGA-12-1099 TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 TCGA-12-3644 TCGA-12-3648 
        3.42         9.44        25.28        13.61        59.41        25.78 
TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 
       11.54        10.95        11.77        34.52        11.74        13.12 
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-14-1401 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-14-1453 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         6.15        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-15-1447 TCGA-15-1449 
        3.42         9.86        50.53        19.10        53.19         5.52 
TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 
        3.91         9.93        26.07        16.31         4.31        29.03 
TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 
        0.82         9.90        13.35         3.65        18.28        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         0.43        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         3.48 
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        16.47         7.00         7.04 
TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 
        6.64        11.28         8.02        18.64         4.73         7.96 
TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A6J5 
        1.78         6.51         5.39         5.29         5.42        16.57 
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         1.22         1.58 
TCGA-26-6173 TCGA-26-6174 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 
        7.92         2.33         4.80        16.60         9.86        18.25 
TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 
       33.14        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-28-5207 TCGA-28-5208 TCGA-28-5209 
        7.30         5.26         3.91         9.04        15.58        14.53 
TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5218 TCGA-28-5219 
       11.77        31.27        14.20         7.79         4.21        22.68 
TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 
       10.49         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-32-2615 TCGA-32-2616 TCGA-32-2634 
       16.93        12.23        20.78        15.95         7.36        22.78 
TCGA-32-2638 TCGA-32-4208 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 
       21.17        21.14        12.59        19.86        10.85        10.62 
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-74-6573 TCGA-74-6575 
       11.84         0.20        11.54         7.76         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 
       17.72        26.30         5.92 

  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 
             7.04             10.36 
[1] "1.1 - 92.7 (7.0)"   "0.1 - 127.6 (10.4)"
[1] "hr=" "1.1"
D10V2, continuous
D10V3, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    21  20
  5Q GAIN WILD-TYPE 199 320
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     21   20
  5Q GAIN WILD-TYPE  199  320
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE              21               199
  MALE                20               320
[1] 2 2
[1] FALSE
D10V4, continuous
                   vv
clus                GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  5Q GAIN MUTATED                               3                   3
  5Q GAIN WILD-TYPE                            14                  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                14
  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 356 163
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     26   15
  5Q GAIN WILD-TYPE  356  163
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  NO               26               356
  YES              15               163
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5Q GAIN MUTATED       1                         4    35
  5Q GAIN WILD-TYPE    12                        35   450
D10V7, multiclass
                           clus
vv                          5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  ASIAN                                   1                12
  BLACK OR AFRICAN AMERICAN               4                35
  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  12 425
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      0   37
  5Q GAIN WILD-TYPE   12  425
                        clus
vv                       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                12
  NOT HISPANIC OR LATINO              37               425
[1] 2 2
[1] FALSE

Clustering(11) Variable = 6P GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                 0   1
  6P GAIN MUTATED     4  19
  6P GAIN WILD-TYPE  94 443
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               23               537 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               19               443 
$`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         2.01        10.36         4.70        35.01 
TCGA-08-0386 TCGA-08-0516 TCGA-12-0619 TCGA-12-0662 TCGA-12-0776 TCGA-12-1092 
       15.72        18.44        10.39        38.17         9.11        21.63 
TCGA-12-1598 TCGA-14-1454 TCGA-14-1794 TCGA-15-1447 TCGA-15-1449 TCGA-19-1388 
        9.44        30.18         0.99        53.19         5.52        12.95 
TCGA-27-1831 TCGA-28-5216 TCGA-76-4934 TCGA-76-6280 TCGA-81-5911 
       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 
        9.17         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        55.86        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        10.36        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 
        0.23        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         0.16        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        16.21         2.70 
TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 
        0.26         4.04        47.31         0.10         3.58        22.72 
TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 
       32.52        10.52        18.74        14.07        23.08        22.16 
TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 
       10.75         0.20         9.21         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        16.70         9.80         7.86        19.46        46.59 
TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 
       11.80        12.79         8.65         3.19         5.46         9.44 
TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 
       11.80         2.56        56.88        10.65         5.29        19.04 
TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 
        3.12        13.02         0.23         2.20         2.73        91.00 
TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 
       53.98        19.00         2.53        40.37        73.84        26.33 
TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 
       28.47        14.93        10.29        18.31         4.67         7.04 
TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 
        2.60         0.39         6.48         5.49         3.91         4.96 
TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 
       11.84         0.20        12.43        22.49         0.36        18.02 
TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 
       11.80        20.42        14.96        10.32         5.52         0.26 
TCGA-06-0409 TCGA-06-0412 TCGA-06-0413 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 
       70.52         8.05         0.16        12.33         3.22         4.47 
TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 
        9.67         2.04        23.57         9.40        22.32        19.56 
TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 
        5.39         2.70         2.17         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        22.98         5.85         5.42        20.94 
TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 
        7.43         6.35         3.58        26.79         8.65         7.89 
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         0.76         4.93 
TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 
        9.27         2.83        30.64         5.95         6.81         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        11.24         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         3.95         7.79         5.39 
TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 
        1.48         0.49         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-08-0244 TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 
       22.68        34.75         3.91       108.82         1.74         4.34 
TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 
       13.78        10.39         7.59         3.42        53.82         1.28 
TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 
        6.41        15.06        22.52        14.70        35.64        19.53 
TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 
        0.95         9.17        10.85         3.19        10.59         0.30 
TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 TCGA-08-0517 TCGA-08-0518 
        0.56         3.52        11.77         8.52        58.19         1.28 
TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 
       10.75         4.80         6.54        15.98        17.33         5.52 
TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 
       14.01        14.43         1.64         5.95         7.17        65.92 
TCGA-12-0657 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 
        0.10        25.97        24.13         6.12         2.63        18.12 
TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0778 
       28.41        12.43        53.10        43.10         5.49        14.86 
TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 
       14.27        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-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 
        6.25        30.54        11.97        11.38        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         3.42        25.28        13.61         6.41 
TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 
       59.41        43.23        25.78        11.54        10.95        11.77 
TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 
       34.52        11.74        13.12         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-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 
        7.10         1.15         0.92        40.96         6.15        12.43 
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         9.86        50.53 
TCGA-15-1446 TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 
       19.10         3.91         9.93        26.07        16.31         4.31 
TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 
       29.03         0.82         9.90        13.35         3.65        18.28 
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         0.43 
TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 TCGA-19-1389 
       14.27         3.39        10.75         9.07         5.95         4.64 
TCGA-19-1390 TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 
       25.38         3.48         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 
       16.47         7.00         7.04         6.64        11.28         8.02 
TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 
       18.64         4.73         7.96         1.78         6.51         5.39 
TCGA-19-5959 TCGA-19-5960 TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 
        5.29         5.42         3.98        16.57        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         1.22         1.58         7.92         2.33 
TCGA-27-1830 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 
        4.80         9.86        18.25        33.14        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         3.91         9.04        15.58        14.53        11.77 
TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 
       31.27        14.20         7.79         4.21        22.68        10.49 
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        21.17        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        10.62         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        11.54         7.76 
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 
        1.61        26.30         5.92 

  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 
            12.95              9.86 
[1] "1.0 - 53.2 (12.9)" "0.1 - 127.6 (9.9)"
[1] "hr=" "1.2"
D11V2, continuous
D11V3, binary
                   cls
clus                  0   1
  6P GAIN MUTATED     7  16
  6P GAIN WILD-TYPE 213 324
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      7   16
  6P GAIN WILD-TYPE  213  324
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE               7               213
  MALE                16               324
[1] 2 2
[1] FALSE
D11V4, continuous
                   vv
clus                GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  6P GAIN MUTATED                               0                   0
  6P GAIN WILD-TYPE                            17                  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)                 0                17
  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   4
  6P GAIN WILD-TYPE 363 174
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     19    4
  6P GAIN WILD-TYPE  363  174
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  NO               19               363
  YES               4               174
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6P GAIN MUTATED       1                         0    21
  6P GAIN WILD-TYPE    12                        39   464
D11V7, multiclass
                           clus
vv                          6P GAIN MUTATED 6P GAIN WILD-TYPE
  ASIAN                                   1                12
  BLACK OR AFRICAN AMERICAN               0                39
  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  16
  6P GAIN WILD-TYPE  12 446
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      0   16
  6P GAIN WILD-TYPE   12  446
                        clus
vv                       6P GAIN MUTATED 6P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                12
  NOT HISPANIC OR LATINO              16               446
[1] 2 2
[1] FALSE

Clustering(12) Variable = 6Q GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                 0   1
  6Q GAIN MUTATED     5  17
  6Q GAIN WILD-TYPE  93 445
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               22               538 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               17               445 
$`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         2.01        10.36         4.70        35.01 
TCGA-06-2569 TCGA-08-0386 TCGA-08-0516 TCGA-12-0619 TCGA-12-0662 TCGA-12-0776 
        0.43        15.72        18.44        10.39        38.17         9.11 
TCGA-12-1092 TCGA-12-1598 TCGA-14-1454 TCGA-14-1794 TCGA-15-1447 TCGA-15-1449 
       21.63         9.44        30.18         0.99        53.19         5.52 
TCGA-19-1388 TCGA-28-5216 TCGA-76-4934 TCGA-81-5911 
       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 
        9.17         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        55.86        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        10.36        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 
        0.23        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         0.16        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        16.21         2.70 
TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 
        0.26         4.04        47.31         0.10         3.58        22.72 
TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 
       32.52        10.52        18.74        14.07        23.08        22.16 
TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 
       10.75         0.20         9.21         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        16.70         9.80         7.86        19.46        46.59 
TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 
       11.80        12.79         8.65         3.19         5.46         9.44 
TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 
       11.80         2.56        56.88        10.65         5.29        19.04 
TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 
        3.12        13.02         0.23         2.20         2.73        91.00 
TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 
       53.98        19.00         2.53        40.37        73.84        26.33 
TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 
       28.47        14.93        10.29        18.31         4.67         7.04 
TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 
        2.60         0.39         6.48         5.49         3.91         4.96 
TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 
       11.84         0.20        12.43        22.49         0.36        18.02 
TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 
       11.80        20.42        14.96        10.32         5.52         0.26 
TCGA-06-0409 TCGA-06-0412 TCGA-06-0413 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 
       70.52         8.05         0.16        12.33         3.22         4.47 
TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 
        9.67         2.04        23.57         9.40        22.32        19.56 
TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 
        5.39         2.70         2.17         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        22.98         5.85         5.42        20.94 
TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 
        7.43         6.35         3.58        26.79         8.65         7.89 
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         0.76         4.93 
TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 
        9.27         2.83        30.64         5.95         6.81         5.98 
TCGA-06-2567 TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 
        4.37        31.50        11.24         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         3.95         7.79         5.39         1.48 
TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 
        0.49         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-08-0244 
        4.77         4.96         1.87         3.12         2.56        22.68 
TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 
       34.75         3.91       108.82         1.74         4.34        13.78 
TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 
       10.39         7.59         3.42        53.82         1.28         6.41 
TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 
       15.06        22.52        14.70        35.64        19.53         0.95 
TCGA-08-0375 TCGA-08-0380 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 
        9.17        10.85         3.19        10.59         0.30         0.56 
TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 
        3.52        11.77         8.52        58.19         1.28        10.75 
TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 
        4.80         6.54        15.98        17.33         5.52        14.01 
TCGA-12-0616 TCGA-12-0618 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 
       14.43         1.64         5.95         7.17        65.92         0.10 
TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 
       25.97        24.13         6.12         2.63        18.12        28.41 
TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0778 TCGA-12-0780 
       12.43        53.10        43.10         5.49        14.86        14.27 
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         6.25 
TCGA-12-1091 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 
       30.54        11.97        11.38        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         3.42        25.28        13.61         6.41        59.41 
TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 
       43.23        25.78        11.54        10.95        11.77        34.52 
TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 
       11.74        13.12         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-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 TCGA-14-1795 
        1.15         0.92        40.96         6.15        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         9.86        50.53        19.10 
TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 
        3.91         9.93        26.07        16.31         4.31        29.03 
TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 
        0.82         9.90        13.35         3.65        18.28        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         0.43        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 
        3.48         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        16.47 
TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 
        7.00         7.04         6.64        11.28         8.02        18.64 
TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 
        4.73         7.96         1.78         6.51         5.39         5.29 
TCGA-19-5960 TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 
        5.42         3.98        16.57        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-27-1830 
        8.88         1.22         1.58         7.92         2.33         4.80 
TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 
       16.60         9.86        18.25        33.14        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         3.91         9.04        15.58        14.53        11.77 
TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 
       31.27        14.20         7.79         4.21        22.68        10.49 
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        21.17        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        10.62         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        11.54         7.76 
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 
        7.79         1.61        26.30         5.92 

  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 
            12.77              9.90 
[1] "0.4 - 53.2 (12.8)" "0.1 - 127.6 (9.9)"
[1] "hr=" "1.2"
D12V2, continuous
D12V3, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     8  14
  6Q GAIN WILD-TYPE 212 326
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      8   14
  6Q GAIN WILD-TYPE  212  326
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE               8               212
  MALE                14               326
[1] 2 2
[1] FALSE
D12V4, continuous
                   vv
clus                GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  6Q GAIN MUTATED                               0                   0
  6Q GAIN WILD-TYPE                            17                  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)                 0                17
  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   5
  6Q GAIN WILD-TYPE 365 173
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     17    5
  6Q GAIN WILD-TYPE  365  173
     clus
vv    6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  NO               17               365
  YES               5               173
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6Q GAIN MUTATED       1                         1    19
  6Q GAIN WILD-TYPE    12                        38   466
D12V7, multiclass
                           clus
vv                          6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  ASIAN                                   1                12
  BLACK OR AFRICAN AMERICAN               1                38
  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  15
  6Q GAIN WILD-TYPE  12 447
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      0   15
  6Q GAIN WILD-TYPE   12  447
                        clus
vv                       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                12
  NOT HISPANIC OR LATINO              15               447
[1] 2 2
[1] FALSE

Clustering(13) Variable = 7P GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                 0   1
  7P GAIN MUTATED    72 382
  7P GAIN WILD-TYPE  26  80
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              454               106 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              382                80 
$`7P GAIN MUTATED`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0016 
        9.17         4.73        18.35        23.18        10.59        55.86 
TCGA-02-0021 TCGA-02-0023 TCGA-02-0025 TCGA-02-0027 TCGA-02-0033 TCGA-02-0034 
       77.65        20.12        42.74        10.36         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         0.16        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        16.21 
TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0128 
        2.70         0.26         4.04        47.31         0.10        22.72 
TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 
       10.52        18.74        14.07        23.08        22.16        10.75 
TCGA-06-0140 TCGA-06-0141 TCGA-06-0143 TCGA-06-0145 TCGA-06-0147 TCGA-06-0148 
        0.20         9.21        11.74         2.33        16.70         9.80 
TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 
        7.86        19.46        46.59        11.80        12.79         8.65 
TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0164 TCGA-06-0166 TCGA-06-0168 
        3.19         5.46         9.44        56.88         5.29        19.04 
TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 
        3.12        13.02         0.23         2.20         2.73        91.00 
TCGA-06-0177 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0188 
        2.01        19.00         2.53        40.37        73.84        28.47 
TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 
       14.93        10.29        18.31         4.67         7.04         2.60 
TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 
        0.39         6.48         5.49         3.91         4.96        11.84 
TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0237 TCGA-06-0238 TCGA-06-0241 
        0.20        12.43        22.49        10.36        11.80        14.96 
TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0412 TCGA-06-0413 
       10.32         5.52         0.26        70.52         8.05         0.16 
TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 
       35.01        12.33         3.22         4.47         9.67         2.04 
TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0749 
       23.57         9.40        22.32        19.56         5.39         2.17 
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        22.98 
TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 
        5.85         5.42        20.94         7.43         6.35         3.58 
TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1806 TCGA-06-2557 
       26.79         8.65         7.89        13.61        15.32         1.08 
TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 
        0.76         4.93         9.27         2.83        30.64         5.95 
TCGA-06-2567 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 
        4.37        11.24         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 
        3.95         5.39         1.48         7.36         8.32        12.85 
TCGA-06-6698 TCGA-06-6699 TCGA-06-A5U1 TCGA-06-A6S1 TCGA-08-0244 TCGA-08-0245 
        4.77         1.55         1.87         2.56        22.68        34.75 
TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0352 
        1.74         4.34        13.78        10.39         7.59         1.28 
TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 
        6.41        15.06        22.52        14.70        35.64        19.53 
TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 
        0.95         9.17        10.85        15.72         3.19        10.59 
TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 TCGA-08-0518 TCGA-08-0520 TCGA-08-0525 
        0.30         0.56         3.52         1.28        10.75        15.98 
TCGA-08-0529 TCGA-08-0531 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 
       17.33         5.52        14.43         1.64        10.39         5.95 
TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 
        7.17        65.92         0.10        38.17        25.97        24.13 
TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 
        6.12         2.63        18.12        28.41        12.43        53.10 
TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0819 
       43.10         5.49         9.11        14.86        14.27        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         6.25        30.54        21.63 
TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 
       11.97        11.38        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 
        3.42         9.44        25.28        13.61         6.41        59.41 
TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 
       43.23        25.78        11.54        10.95        11.77        34.52 
TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0781 
       11.74        13.12         3.22         2.04        15.12         0.95 
TCGA-14-0783 TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 TCGA-14-0813 
        6.21        23.05         2.24        11.24        13.78         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-14-1450 TCGA-14-1451 
        0.79         1.38         1.12         3.75        58.78        23.11 
TCGA-14-1452 TCGA-14-1453 TCGA-14-1454 TCGA-14-1455 TCGA-14-1458 TCGA-14-1459 
        7.10         1.15        30.18         0.92         6.15        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-15-1446 TCGA-15-1449 
       17.49         7.96         3.42         9.86        19.10         5.52 
TCGA-16-0846 TCGA-16-0848 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 
        3.91         9.93         4.31        29.03         0.82         9.90 
TCGA-16-1056 TCGA-16-1062 TCGA-16-1063 TCGA-19-0955 TCGA-19-0957 TCGA-19-0962 
       13.35        18.28        13.97        11.77        21.90         0.43 
TCGA-19-0963 TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 TCGA-19-1388 TCGA-19-1389 
       14.27        10.75         9.07         5.95        12.95         4.64 
TCGA-19-1390 TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 TCGA-19-1791 TCGA-19-2619 
       25.38         3.48         7.17        12.66         0.13         9.67 
TCGA-19-2623 TCGA-19-2624 TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 
        7.53         0.16        16.47         7.00         7.04         6.64 
TCGA-19-5950 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5958 
       11.28        18.64         4.73         7.96         1.78         5.39 
TCGA-19-5959 TCGA-19-5960 TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 
        5.29         5.42         3.98        16.57        10.03        13.87 
TCGA-26-1440 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5135 TCGA-26-5136 
        9.73         7.13         9.37         9.40         8.88         1.22 
TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 
        1.58         7.92         2.33         4.80        16.60         9.86 
TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 
       18.25        33.14        21.30        11.51        24.76        10.39 
TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-28-1746 TCGA-28-1749 
       16.08         7.59         2.86        14.40         0.20         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         3.91         9.04 
TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 
       15.58        14.53        11.77        31.27        14.20         7.79 
TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1976 
        4.21        22.68        10.49         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-32-2616 TCGA-32-2632 TCGA-32-2638 
       14.86        12.23        20.78         7.36         8.84        21.17 
TCGA-32-4210 TCGA-32-4211 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 
        3.72        12.59        10.62         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        11.54         7.76 
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-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 
       20.98         5.03         0.23         9.27         7.73         7.79 
TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R 
        1.61        17.72        26.30         5.92 

$`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         0.23        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         3.58        32.52         2.20        20.09        11.80 
TCGA-06-0162 TCGA-06-0165 TCGA-06-0178 TCGA-06-0187 TCGA-06-0219 TCGA-06-0221 
        2.56        10.65        53.98        26.33         0.36        18.02 
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         6.81         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         0.49         4.77 
TCGA-06-6701 TCGA-06-A6S0 TCGA-08-0246 TCGA-08-0344 TCGA-08-0350 TCGA-08-0351 
        4.96         3.12         3.91       108.82         3.42        53.82 
TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0521 TCGA-08-0524 
       11.77         8.52        18.44        58.19         4.80         6.54 
TCGA-12-0615 TCGA-12-0818 TCGA-14-0740 TCGA-14-0812 TCGA-14-0862 TCGA-14-0865 
       14.01        91.76        11.97         3.25         2.89        16.50 
TCGA-14-1402 TCGA-14-1456 TCGA-14-1821 TCGA-14-3477 TCGA-15-1444 TCGA-15-1447 
       32.05        40.96        17.79         3.78        50.53        53.19 
TCGA-16-0849 TCGA-16-0850 TCGA-16-1060 TCGA-16-1460 TCGA-19-0960 TCGA-19-0964 
       26.07        16.31         3.65         6.41         8.61         3.39 
TCGA-19-1789 TCGA-19-2620 TCGA-19-2621 TCGA-19-2625 TCGA-19-5951 TCGA-19-5956 
        3.25         4.87         1.08         4.08         8.02         6.51 
TCGA-26-1442 TCGA-26-5133 TCGA-26-5134 TCGA-27-1836 TCGA-27-1837 TCGA-27-2521 
       31.33        14.86         5.49        30.05        14.04        10.39 
TCGA-27-2528 TCGA-28-1747 TCGA-28-1756 TCGA-28-2514 TCGA-28-5216 TCGA-32-1973 
       15.78         2.53         2.83         5.26        13.64        21.07 
TCGA-32-1991 TCGA-32-2495 TCGA-32-2615 TCGA-32-2634 TCGA-32-4208 TCGA-32-4213 
       16.93        15.02        15.95        22.78        21.14        19.86 
TCGA-32-4719 TCGA-41-4097 TCGA-76-6193 TCGA-76-6656 
       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            108.82 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            9.670            13.015 
[1] "0.1 - 127.6 (9.7)"  "0.2 - 108.8 (13.0)"
[1] "hr=" "1.6"
D13V2, continuous
D13V3, binary
                   cls
clus                  0   1
  7P GAIN MUTATED   178 276
  7P GAIN WILD-TYPE  42  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED    178  276
  7P GAIN WILD-TYPE   42   64
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE             178                42
  MALE               276                64
[1] 2 2
[1] FALSE
D13V4, continuous
                   vv
clus                GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  7P GAIN MUTATED                              11                  11
  7P GAIN WILD-TYPE                             6                   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)                11                 6
  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   303 151
  7P GAIN WILD-TYPE  79  27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED    303  151
  7P GAIN WILD-TYPE   79   27
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  NO              303                79
  YES             151                27
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7P GAIN MUTATED       7                        33   393
  7P GAIN WILD-TYPE     6                         6    92
D13V7, multiclass
                           clus
vv                          7P GAIN MUTATED 7P GAIN WILD-TYPE
  ASIAN                                   7                 6
  BLACK OR AFRICAN AMERICAN              33                 6
  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     8 371
  7P GAIN WILD-TYPE   4  91
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      8  371
  7P GAIN WILD-TYPE    4   91
                        clus
vv                       7P GAIN MUTATED 7P GAIN WILD-TYPE
  HISPANIC OR LATINO                   8                 4
  NOT HISPANIC OR LATINO             371                91
[1] 2 2
[1] FALSE

Clustering(14) Variable = 7Q GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                 0   1
  7Q GAIN MUTATED    76 383
  7Q GAIN WILD-TYPE  22  79
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              459               101 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              383                79 
$`7Q GAIN MUTATED`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0009 TCGA-02-0016 TCGA-02-0021 
        9.17         4.73        18.35        10.59        55.86        77.65 
TCGA-02-0023 TCGA-02-0025 TCGA-02-0027 TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 
       20.12        42.74        10.36         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         0.16 
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 
       16.21         2.70         0.26         4.04        47.31         0.10 
TCGA-06-0128 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 
       22.72        10.52        18.74        14.07        23.08        22.16 
TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0143 TCGA-06-0145 TCGA-06-0147 
       10.75         0.20         9.21        11.74         2.33        16.70 
TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 
        9.80         7.86        19.46        46.59        11.80        12.79 
TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0164 TCGA-06-0166 
        8.65         3.19         5.46         9.44        56.88         5.29 
TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 
       19.04         3.12        13.02         0.23         2.20         2.73 
TCGA-06-0176 TCGA-06-0177 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 
       91.00         2.01        19.00         2.53        40.37        73.84 
TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 
       26.33        28.47        14.93        10.29        18.31         4.67 
TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 
        7.04         2.60         0.39         6.48         5.49         3.91 
TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0237 
        4.96        11.84         0.20        12.43        22.49        10.36 
TCGA-06-0238 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 
       11.80        14.96        10.32         5.52         0.26        70.52 
TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 
        8.05         0.16        35.01        12.33         3.22         4.47 
TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 
        9.67         2.04        23.57         9.40        22.32        19.56 
TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 
        5.39         2.70         2.17         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        22.98         5.85         5.42        20.94 
TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 
        7.43         6.35         3.58        26.79         8.65         7.89 
TCGA-06-1804 TCGA-06-1806 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 
       13.61        15.32         1.08         0.76         4.93         9.27 
TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2567 TCGA-06-5408 TCGA-06-5410 
        2.83        30.64         5.95         4.37        11.24         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         3.95         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-08-0244 TCGA-08-0345 TCGA-08-0346 
        1.87         3.12         2.56        22.68         1.74         4.34 
TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 
       13.78        10.39         7.59         1.28         6.41        15.06 
TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 
       14.70        35.64        19.53         0.95         9.17        10.85 
TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 
       15.72         3.19        10.59         0.30         0.56         3.52 
TCGA-08-0518 TCGA-08-0520 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0616 
        1.28        10.75        15.98        17.33         5.52        14.43 
TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 
        1.64        10.39         5.95         7.17        65.92         0.10 
TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 
       38.17        25.97        24.13         6.12         2.63        18.12 
TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 
       28.41        12.43        53.10        43.10         5.49         9.11 
TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 
       14.86        14.27        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-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 
        6.25        21.63        11.97        11.38        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         3.42         9.44        25.28        13.61 
TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 
        6.41        59.41        43.23        25.78        11.54        10.95 
TCGA-12-3651 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 
       11.77        11.74        13.12         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-14-1454 TCGA-14-1455 TCGA-14-1458 TCGA-14-1459 
       23.11         7.10        30.18         0.92         6.15        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-15-1446 TCGA-15-1449 
       17.49         7.96         3.42         9.86        19.10         5.52 
TCGA-16-0846 TCGA-16-0848 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 
        3.91         9.93         4.31        29.03         0.82         9.90 
TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 TCGA-19-0962 
       18.28        13.97         6.41        11.77        21.90         0.43 
TCGA-19-0963 TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 TCGA-19-1388 TCGA-19-1389 
       14.27        10.75         9.07         5.95        12.95         4.64 
TCGA-19-1390 TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 TCGA-19-1791 TCGA-19-2619 
       25.38         3.48         7.17        12.66         0.13         9.67 
TCGA-19-2623 TCGA-19-2624 TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 
        7.53         0.16        16.47         7.00         7.04         6.64 
TCGA-19-5950 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5958 
       11.28        18.64         4.73         7.96         1.78         5.39 
TCGA-19-5959 TCGA-19-5960 TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 
        5.29         5.42         3.98        16.57        10.03        13.87 
TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5135 
        9.73        31.33         7.13         9.37         9.40         8.88 
TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-27-1830 TCGA-27-1831 
        1.22         1.58         7.92         2.33         4.80        16.60 
TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1837 TCGA-27-1838 
        9.86        18.25        33.14        21.30        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-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-28-5204 TCGA-28-5207 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 
        7.30         3.91         9.04        14.53        11.77        31.27 
TCGA-28-5214 TCGA-28-5215 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 
       14.20         7.79         4.21        22.68        10.49         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-32-1986 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-32-2638 TCGA-32-4210 TCGA-32-4211 
       15.02         7.36         8.84        21.17         3.72        12.59 
TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 
       10.62         0.85        13.35         8.94         9.53         0.99 
TCGA-41-3393 TCGA-41-3915 TCGA-41-5651 TCGA-41-6646 TCGA-74-6573 TCGA-74-6575 
        4.44        11.84        11.54         7.76         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-76-6280 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 
        3.29        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 
       17.72        26.30         5.92 

$`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         0.23        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 
        3.58        32.52         2.20        20.09        11.80         2.56 
TCGA-06-0165 TCGA-06-0178 TCGA-06-0219 TCGA-06-0221 TCGA-06-0240 TCGA-06-0410 
       10.65        53.98         0.36        18.02        20.42         4.70 
TCGA-06-1805 TCGA-06-2565 TCGA-06-2566 TCGA-06-2569 TCGA-06-2570 TCGA-06-5416 
       33.90         6.81         5.98         0.43        31.50         6.71 
TCGA-06-6389 TCGA-06-6693 TCGA-06-6701 TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 
        7.79         0.49         4.96        34.75         3.91       108.82 
TCGA-08-0350 TCGA-08-0351 TCGA-08-0355 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 
        3.42        53.82        22.52        11.77         8.52        18.44 
TCGA-08-0517 TCGA-08-0521 TCGA-08-0524 TCGA-12-0615 TCGA-12-0827 TCGA-12-1091 
       58.19         4.80         6.54        14.01        38.76        30.54 
TCGA-12-3652 TCGA-14-0740 TCGA-14-0812 TCGA-14-0862 TCGA-14-0865 TCGA-14-1402 
       34.52        11.97         3.25         2.89        16.50        32.05 
TCGA-14-1453 TCGA-14-1456 TCGA-14-1821 TCGA-14-3477 TCGA-15-1444 TCGA-15-1447 
        1.15        40.96        17.79         3.78        50.53        53.19 
TCGA-16-0849 TCGA-16-0850 TCGA-16-1056 TCGA-16-1060 TCGA-19-0960 TCGA-19-0964 
       26.07        16.31        13.35         3.65         8.61         3.39 
TCGA-19-1789 TCGA-19-2620 TCGA-19-2621 TCGA-19-2625 TCGA-19-5951 TCGA-19-5956 
        3.25         4.87         1.08         4.08         8.02         6.51 
TCGA-26-5133 TCGA-26-5134 TCGA-27-1836 TCGA-27-2527 TCGA-27-2528 TCGA-28-1756 
       14.86         5.49        30.05        14.40        15.78         2.83 
TCGA-28-2514 TCGA-28-5208 TCGA-28-5216 TCGA-32-1973 TCGA-32-2615 TCGA-32-2634 
        5.26        15.58        13.64        21.07        15.95        22.78 
TCGA-32-4208 TCGA-32-4213 TCGA-32-4719 TCGA-41-4097 TCGA-76-6193 
       21.14        19.86        10.85         0.20         2.70 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              0.1               0.2 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           127.59            108.82 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             9.57             14.01 
[1] "0.1 - 127.6 (9.6)"  "0.2 - 108.8 (14.0)"
[1] "hr=" "1.6"
D14V2, continuous
D14V3, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED   176 283
  7Q GAIN WILD-TYPE  44  57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED    176  283
  7Q GAIN WILD-TYPE   44   57
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE             176                44
  MALE               283                57
[1] 2 2
[1] FALSE
D14V4, continuous
                   vv
clus                GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  7Q GAIN MUTATED                              12                  11
  7Q GAIN WILD-TYPE                             5                   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)                12                 5
  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   306 153
  7Q GAIN WILD-TYPE  76  25
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED    306  153
  7Q GAIN WILD-TYPE   76   25
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  NO              306                76
  YES             153                25
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7Q GAIN MUTATED       7                        34   397
  7Q GAIN WILD-TYPE     6                         5    88
D14V7, multiclass
                           clus
vv                          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  ASIAN                                   7                 6
  BLACK OR AFRICAN AMERICAN              34                 5
  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     8 378
  7Q GAIN WILD-TYPE   4  84
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      8  378
  7Q GAIN WILD-TYPE    4   84
                        clus
vv                       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   8                 4
  NOT HISPANIC OR LATINO             378                84
[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  91 417
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               52               508 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               45               417 
$`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         0.23 
TCGA-02-0325 TCGA-06-0128 TCGA-06-0146 TCGA-06-0177 TCGA-06-0188 TCGA-06-0192 
       10.62        22.72        20.09         2.01        28.47        18.31 
TCGA-06-0209 TCGA-06-0211 TCGA-06-0409 TCGA-06-0414 TCGA-06-0686 TCGA-06-2557 
        3.91        11.84        70.52        35.01         9.40         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         3.42        53.82 
TCGA-12-0616 TCGA-12-0819 TCGA-12-1099 TCGA-12-1602 TCGA-12-3646 TCGA-12-3653 
       14.43        24.79         3.42         6.41        43.23        11.74 
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         3.48         3.98        33.14        10.39         0.20 
TCGA-28-5215 TCGA-28-5218 TCGA-28-5219 TCGA-32-1970 TCGA-32-1976 TCGA-32-1978 
        7.79         4.21        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        11.54 

$`8P GAIN WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0011 
        9.17         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        55.86        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        10.36        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         0.16 
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        16.21 
TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 
        2.70         0.26         4.04        47.31         0.10         3.58 
TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 
       32.52        10.52        18.74        14.07        23.08        22.16 
TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 
       10.75         0.20         9.21         2.20        11.74         2.33 
TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 
       16.70         9.80         7.86        19.46        46.59        11.80 
TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 
       12.79         8.65         3.19         5.46         9.44        11.80 
TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 
        2.56        56.88        10.65         5.29        19.04         3.12 
TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0178 
       13.02         0.23         2.20         2.73        91.00        53.98 
TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0189 
       19.00         2.53        40.37        73.84        26.33        14.93 
TCGA-06-0190 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 
       10.29         4.67         7.04         2.60         0.39         6.48 
TCGA-06-0208 TCGA-06-0210 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 
        5.49         4.96         0.20        12.43        22.49         0.36 
TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 
       18.02        10.36        11.80        20.42        14.96        10.32 
TCGA-06-0397 TCGA-06-0402 TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0644 
        5.52         0.26         4.70         8.05         0.16        12.33 
TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0743 
        3.22         4.47         9.67         2.04        23.57        22.32 
TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 
       19.56         5.39         2.70         2.17         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        22.98         5.85         5.42 
TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 
       20.94         7.43         6.35         3.58        26.79         8.65 
TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 TCGA-06-2558 TCGA-06-2559 
        7.89        13.61        33.90        15.32         0.76         4.93 
TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 
        9.27         2.83        30.64         5.95         6.81         5.98 
TCGA-06-2567 TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 
        4.37        31.50        11.24         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         3.95         5.39         1.48         0.49         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-08-0244 TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 
        3.12         2.56        22.68        34.75         3.91       108.82 
TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0352 
        1.74         4.34        13.78        10.39         7.59         1.28 
TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 
        6.41        15.06        22.52        14.70        35.64        19.53 
TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 
        0.95         9.17        10.85        15.72         3.19        10.59 
TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 
        0.30         0.56         3.52        11.77         8.52        18.44 
TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 
       58.19         1.28        10.75         4.80         6.54        15.98 
TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 
       17.33         5.52        14.01         1.64        10.39         5.95 
TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 
        7.17        65.92         0.10        38.17        25.97        24.13 
TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 
        6.12         2.63        18.12        28.41        12.43        53.10 
TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 
       43.10         5.49         9.11        14.86        14.27        91.76 
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         6.25        30.54        21.63 
TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 
       11.97        11.38        15.85         9.11        14.53         3.98 
TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 TCGA-12-3644 TCGA-12-3648 TCGA-12-3649 
        9.44        25.28        13.61        59.41        25.78        11.54 
TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 
       10.95        11.77        34.52        13.12         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-14-0866 
       11.24        13.78         3.25         1.35         2.89        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-14-1794 TCGA-14-1795 
        0.92        40.96         6.15        12.43         0.99         1.97 
TCGA-14-1821 TCGA-14-1823 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 
       17.79        17.85         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         9.86        50.53        19.10        53.19         5.52 
TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 
        3.91         9.93        26.07        16.31         4.31        29.03 
TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 
        0.82         9.90        13.35         3.65        18.28        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         0.43        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-19-1787 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        16.47         7.00 
TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 
        7.04         6.64        11.28         8.02        18.64         4.73 
TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 
        7.96         1.78         6.51         5.39         5.29         5.42 
TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 
       16.57        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         1.22 
TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 
        1.58         7.92         2.33         4.80        16.60         9.86 
TCGA-27-1833 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 
       18.25        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         3.91         9.04        15.58        14.53 
TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5216 TCGA-28-5220 TCGA-28-6450 
       11.77        31.27        14.20        13.64        10.49         5.42 
TCGA-32-1973 TCGA-32-1977 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 
       21.07         0.10        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-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4210 TCGA-32-4211 
        7.36        22.78        21.17        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        10.62         0.85        13.35         9.53 
TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 TCGA-41-6646 TCGA-74-6573 TCGA-74-6575 
        0.99         4.44        11.84         7.76         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 
        1.61        17.72        26.30         5.92 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              0.2               0.1 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            70.52            127.59 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            9.795            10.160 
[1] "0.2 - 70.5 (9.8)"   "0.1 - 127.6 (10.2)"
[1] "hr=" "1"  
D15V2, continuous
D15V3, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    22  30
  8P GAIN WILD-TYPE 198 310
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     22   30
  8P GAIN WILD-TYPE  198  310
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE              22               198
  MALE                30               310
[1] 2 2
[1] FALSE
D15V4, continuous
                   vv
clus                GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  8P GAIN MUTATED                               1                   2
  8P GAIN WILD-TYPE                            16                  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                16
  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 348 160
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     34   18
  8P GAIN WILD-TYPE  348  160
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  NO               34               348
  YES              18               160
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8P GAIN MUTATED       0                         7    45
  8P GAIN WILD-TYPE    13                        32   440
D15V7, multiclass
                           clus
vv                          8P GAIN MUTATED 8P GAIN WILD-TYPE
  ASIAN                                   0                13
  BLACK OR AFRICAN AMERICAN               7                32
  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  11 419
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      1   43
  8P GAIN WILD-TYPE   11  419
                        clus
vv                       8P GAIN MUTATED 8P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                11
  NOT HISPANIC OR LATINO              43               419
[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  89 412
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               59               501 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               50               412 
$`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         0.23 
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         2.01 
TCGA-06-0188 TCGA-06-0192 TCGA-06-0209 TCGA-06-0211 TCGA-06-0409 TCGA-06-0414 
       28.47        18.31         3.91        11.84        70.52        35.01 
TCGA-06-0686 TCGA-06-2557 TCGA-06-2569 TCGA-06-5856 TCGA-06-6389 TCGA-06-6694 
        9.40         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 
        3.42        53.82        18.44        14.43        91.76        24.79 
TCGA-12-0827 TCGA-12-1099 TCGA-12-1602 TCGA-12-3646 TCGA-12-3653 TCGA-14-0817 
       38.76         3.42         6.41        43.23        11.74         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         3.48         3.98        33.14        10.39         0.20 
TCGA-28-5204 TCGA-28-5215 TCGA-28-5218 TCGA-28-5219 TCGA-32-1970 TCGA-32-1976 
        3.91         7.79         4.21        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        11.54 

$`8Q GAIN WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0011 
        9.17         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        55.86        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        10.36        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         0.16        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        16.21         2.70         0.26 
TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0129 TCGA-06-0130 
        4.04        47.31         0.10         3.58        32.52        10.52 
TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 
       18.74        14.07        23.08        22.16        10.75         0.20 
TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0147 TCGA-06-0148 
        9.21         2.20        11.74         2.33        16.70         9.80 
TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 
        7.86        19.46        46.59        11.80        12.79         8.65 
TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 
        3.19         5.46         9.44        11.80         2.56        56.88 
TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 
       10.65         5.29        19.04         3.12        13.02         0.23 
TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 
        2.20         2.73        91.00        53.98        19.00         2.53 
TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0189 TCGA-06-0190 TCGA-06-0194 
       40.37        73.84        26.33        14.93        10.29         4.67 
TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0210 
        7.04         2.60         0.39         6.48         5.49         4.96 
TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 
        0.20        12.43        22.49         0.36        18.02        10.36 
TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 
       11.80        20.42        14.96        10.32         5.52         0.26 
TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 
        4.70         8.05         0.16        12.33         3.22         4.47 
TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 
        9.67         2.04        23.57        22.32        19.56         5.39 
TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 
        2.70         2.17         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        22.98         5.85         5.42        20.94         7.43 
TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 
        6.35         3.58        26.79         8.65         7.89        13.61 
TCGA-06-1805 TCGA-06-1806 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 
       33.90        15.32         0.76         4.93         9.27         2.83 
TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2570 
       30.64         5.95         6.81         5.98         4.37        31.50 
TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 
       11.24         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         3.95 
TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 
        5.39         1.48         0.49         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-08-0244 TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 
       22.68        34.75         3.91       108.82         1.74         4.34 
TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 
       13.78        10.39         7.59         1.28         6.41        15.06 
TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 
       22.52        14.70        35.64        19.53         0.95         9.17 
TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 
       10.85        15.72         3.19        10.59         0.30         0.56 
TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 
        3.52        11.77         8.52        58.19         1.28        10.75 
TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 
        4.80         6.54        15.98        17.33         5.52        14.01 
TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 
        1.64        10.39         5.95         7.17        65.92         0.10 
TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 
       38.17        25.97        24.13         6.12         2.63        18.12 
TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 
       28.41        12.43        53.10        43.10         5.49         9.11 
TCGA-12-0778 TCGA-12-0780 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 TCGA-12-0826 
       14.86        14.27        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         6.25        30.54 
TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 
       21.63        11.97        11.38        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         9.44        25.28        13.61        59.41        25.78 
TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-5295 TCGA-12-5299 
       11.54        10.95        11.77        34.52        13.12         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-14-0862 
        2.24        11.24        13.78         3.25         1.35         2.89 
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-14-1458 TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 
       30.18         0.92         6.15        12.43         0.99         1.97 
TCGA-14-1821 TCGA-14-1823 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 
       17.79        17.85         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         9.86        50.53        19.10        53.19         5.52 
TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 
        3.91         9.93        26.07        16.31         4.31        29.03 
TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 
        0.82         9.90        13.35         3.65        18.28        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         0.43        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-19-1787 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        16.47         7.00 
TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 
        7.04         6.64        11.28         8.02        18.64         4.73 
TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 
        7.96         1.78         6.51         5.39         5.29         5.42 
TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 
       16.57        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         1.22 
TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 
        1.58         7.92         2.33         4.80        16.60         9.86 
TCGA-27-1833 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 
       18.25        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-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 
        7.30         5.26         9.04        15.58        14.53        11.77 
TCGA-28-5213 TCGA-28-5214 TCGA-28-5216 TCGA-28-5220 TCGA-28-6450 TCGA-32-1973 
       31.27        14.20        13.64        10.49         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        21.17        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        10.62         0.85        13.35         9.53         0.99 
TCGA-41-3393 TCGA-41-3915 TCGA-41-6646 TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 
        4.44        11.84         7.76         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 
       17.72        26.30         5.92 

  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 
            10.39              9.93 
[1] "0.2 - 91.8 (10.4)" "0.1 - 127.6 (9.9)"
[1] "hr=" "1.1"
D16V2, continuous
D16V3, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED    26  33
  8Q GAIN WILD-TYPE 194 307
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     26   33
  8Q GAIN WILD-TYPE  194  307
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE              26               194
  MALE                33               307
[1] 2 2
[1] FALSE
D16V4, continuous
                   vv
clus                GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  8Q GAIN MUTATED                               1                   1
  8Q GAIN WILD-TYPE                            16                  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                16
  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 342 159
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     40   19
  8Q GAIN WILD-TYPE  342  159
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  NO               40               342
  YES              19               159
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8Q GAIN MUTATED       1                         7    51
  8Q GAIN WILD-TYPE    12                        32   434
D16V7, multiclass
                           clus
vv                          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  ASIAN                                   1                12
  BLACK OR AFRICAN AMERICAN               7                32
  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  11 414
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      1   48
  8Q GAIN WILD-TYPE   11  414
                        clus
vv                       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                11
  NOT HISPANIC OR LATINO              48               414
[1] 2 2
[1] FALSE

Clustering(17) Variable = 9P GAIN MUTATION ANALYSIS
D17V1, survival
                   sevent
clus2                 0   1
  9P GAIN MUTATED     8  39
  9P GAIN WILD-TYPE  90 423
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               47               513 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               39               423 
$`9P GAIN MUTATED`
TCGA-02-0001 TCGA-02-0025 TCGA-02-0051 TCGA-02-0052 TCGA-02-0069 TCGA-02-0074 
        9.17        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        32.52 
TCGA-06-0195 TCGA-06-0216 TCGA-06-0410 TCGA-06-0414 TCGA-06-0644 TCGA-06-1087 
        7.04        22.49         4.70        35.01        12.33         3.58 
TCGA-06-2569 TCGA-06-5408 TCGA-06-5416 TCGA-08-0386 TCGA-12-0691 TCGA-12-0773 
        0.43        11.24         6.71        15.72         6.12        43.10 
TCGA-12-1096 TCGA-12-3646 TCGA-14-0790 TCGA-14-0812 TCGA-14-0817 TCGA-14-0867 
        9.11        43.23        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 
        5.52         0.43         3.48         7.04         1.22        33.14 
TCGA-27-1838 TCGA-28-1751 TCGA-28-2509 TCGA-28-5204 TCGA-28-5215 TCGA-28-5216 
       11.51         7.63         4.77         3.91         7.79        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        55.86        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        10.36        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         0.23        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         0.16        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        16.21         2.70         0.26         4.04        47.31 
TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 
        0.10         3.58        22.72        10.52        18.74        14.07 
TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 
       23.08        22.16        10.75         0.20         9.21         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        16.70         9.80         7.86 
TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 
       19.46        46.59        11.80        12.79         8.65         3.19 
TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 
        5.46         9.44        11.80         2.56        56.88        10.65 
TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 
        5.29        19.04         3.12        13.02         0.23         2.20 
TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 
        2.73        91.00         2.01        53.98        19.00         2.53 
TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 
       40.37        73.84        26.33        28.47        14.93        10.29 
TCGA-06-0192 TCGA-06-0194 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 
       18.31         4.67         2.60         0.39         6.48         5.49 
TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0219 
        3.91         4.96        11.84         0.20        12.43         0.36 
TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 
       18.02        10.36        11.80        20.42        14.96        10.32 
TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0412 TCGA-06-0413 TCGA-06-0645 
        5.52         0.26        70.52         8.05         0.16         3.22 
TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 
        4.47         9.67         2.04        23.57         9.40        22.32 
TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 
       19.56         5.39         2.70         2.17         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        22.98         5.85         5.42 
TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 
       20.94         7.43         6.35        26.79         8.65         7.89 
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         0.76         4.93 
TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 
        9.27         2.83        30.64         5.95         6.81         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 
        3.95         7.79         5.39         1.48         0.49         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-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-08-0244 TCGA-08-0245 TCGA-08-0246 
        1.87         3.12         2.56        22.68        34.75         3.91 
TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 
      108.82         1.74         4.34        13.78        10.39         7.59 
TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 
        3.42        53.82         1.28         6.41        15.06        22.52 
TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 
       14.70        35.64        19.53         0.95         9.17        10.85 
TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 
        3.19        10.59         0.30         0.56         3.52        11.77 
TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 
        8.52        18.44        58.19         1.28        10.75         4.80 
TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 
        6.54        15.98        17.33         5.52        14.01        14.43 
TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 
        1.64        10.39         5.95         7.17        65.92         0.10 
TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 
       38.17        25.97        24.13         2.63        18.12        28.41 
TCGA-12-0769 TCGA-12-0772 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 
       12.43        53.10         5.49         9.11        14.86        14.27 
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         6.25 
TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1097 
       30.54        21.63        11.97        11.38        15.85        14.53 
TCGA-12-1098 TCGA-12-1099 TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 
        3.98         3.42         9.44        25.28        13.61         6.41 
TCGA-12-3644 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 
       59.41        25.78        11.54        10.95        11.77        34.52 
TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 
       11.74        13.12         3.22         2.04        15.12        11.97 
TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 TCGA-14-0813 
        0.95         6.21        23.05         2.24        11.24         1.35 
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 
        6.15        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-16-0846 
        3.42         9.86        50.53        19.10        53.19         3.91 
TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 
        9.93        26.07        16.31         4.31        29.03         0.82 
TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 
        9.90        13.35         3.65        18.28        13.97         6.41 
TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 
       11.77        21.90         8.61        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-19-5947 
        7.53         0.16         4.08        16.47         7.00         6.64 
TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 
       11.28         8.02        18.64         4.73         7.96         1.78 
TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A6J4 TCGA-19-A6J5 
        6.51         5.39         5.29         5.42         3.98        16.57 
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-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1835 
        2.33         4.80        16.60         9.86        18.25        21.30 
TCGA-27-1836 TCGA-27-1837 TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 
       30.05        14.04        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-28-1752 TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 
        9.21         8.35         8.48         1.22         1.55         2.83 
TCGA-28-1757 TCGA-28-2502 TCGA-28-2506 TCGA-28-2513 TCGA-28-2514 TCGA-28-5207 
        0.13         0.66         6.74         7.30         5.26         9.04 
TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5218 
       15.58        14.53        11.77        31.27        14.20         4.21 
TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 
       22.68        10.49         5.42        15.39        21.07         0.49 
TCGA-32-1977 TCGA-32-1978 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 
        0.10        15.85         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-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 
       22.78        21.17        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        10.62         0.85        13.35         8.94         9.53 
TCGA-41-3392 TCGA-41-3393 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 TCGA-74-6573 
        0.99         4.44         0.20        11.54         7.76         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-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 
        3.29         2.70        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 
       17.72        26.30         5.92 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
             0.43              0.10 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            43.23            127.59 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            10.19             10.03 
[1] "0.4 - 43.2 (10.2)"  "0.1 - 127.6 (10.0)"
[1] "hr=" "1.1"
D17V2, continuous
D17V3, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    23  24
  9P GAIN WILD-TYPE 197 316
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     23   24
  9P GAIN WILD-TYPE  197  316
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE              23               197
  MALE                24               316
[1] 2 2
[1] FALSE
D17V4, continuous
                   vv
clus                GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  9P GAIN MUTATED                               0                   0
  9P GAIN WILD-TYPE                            17                  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                17
  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 351 162
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     31   16
  9P GAIN WILD-TYPE  351  162
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  NO               31               351
  YES              16               162
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9P GAIN MUTATED       2                         2    42
  9P GAIN WILD-TYPE    11                        37   443
D17V7, multiclass
                           clus
vv                          9P GAIN MUTATED 9P GAIN WILD-TYPE
  ASIAN                                   2                11
  BLACK OR AFRICAN AMERICAN               2                37
  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  10 426
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      2   36
  9P GAIN WILD-TYPE   10  426
                        clus
vv                       9P GAIN MUTATED 9P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                10
  NOT HISPANIC OR LATINO              36               426
[1] 2 2
[1] FALSE

Clustering(18) Variable = 9Q GAIN MUTATION ANALYSIS
D18V1, survival
                   sevent
clus2                 0   1
  9Q GAIN MUTATED    12  59
  9Q GAIN WILD-TYPE  86 403
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               71               489 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               59               403 
$`9Q GAIN MUTATED`
TCGA-02-0001 TCGA-02-0025 TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 TCGA-02-0069 
        9.17        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-06-0188 
        3.35        32.52         5.29         2.73        73.84        28.47 
TCGA-06-0195 TCGA-06-0216 TCGA-06-0410 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 
        7.04        22.49         4.70         0.16        35.01        12.33 
TCGA-06-1087 TCGA-06-2562 TCGA-06-2569 TCGA-06-5408 TCGA-08-0386 TCGA-12-0618 
        3.58         2.83         0.43        11.24        15.72         1.64 
TCGA-12-0654 TCGA-12-0691 TCGA-12-0773 TCGA-12-0776 TCGA-12-0818 TCGA-12-0827 
        7.17         6.12        43.10         9.11        91.76        38.76 
TCGA-12-1088 TCGA-12-1096 TCGA-12-1098 TCGA-12-3646 TCGA-12-5299 TCGA-14-0790 
      127.59         9.11         3.98        43.23         3.22        13.78 
TCGA-14-0812 TCGA-14-0813 TCGA-14-0817 TCGA-14-0867 TCGA-14-1821 TCGA-15-1449 
        3.25         1.35         5.39         2.04        17.79         5.52 
TCGA-19-0962 TCGA-19-1392 TCGA-19-4065 TCGA-19-A6J5 TCGA-26-5136 TCGA-26-6174 
        0.43         3.48         7.04        16.57         1.22         2.33 
TCGA-27-1834 TCGA-27-1838 TCGA-28-1751 TCGA-28-2509 TCGA-28-5204 TCGA-28-5215 
       33.14        11.51         7.63         4.77         3.91         7.79 
TCGA-28-5216 TCGA-32-1976 TCGA-32-1979 TCGA-32-1991 TCGA-32-2495 TCGA-32-2615 
       13.64         0.49        19.50        16.93        15.02        15.95 
TCGA-41-2573 TCGA-41-3915 TCGA-76-4934 TCGA-76-4935 TCGA-76-6280 
        8.94        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        55.86        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        10.36        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         0.23        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         0.16        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        16.21 
TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 
        2.70         0.26         4.04        47.31         0.10         3.58 
TCGA-06-0128 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 
       22.72        10.52        18.74        14.07        23.08        22.16 
TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 
       10.75         0.20         9.21         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        16.70         9.80         7.86        19.46        46.59 
TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 
       11.80        12.79         8.65         3.19         5.46         9.44 
TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0168 TCGA-06-0169 
       11.80         2.56        56.88        10.65        19.04         3.12 
TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 
       13.02         0.23         2.20        91.00         2.01        53.98 
TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0187 TCGA-06-0189 TCGA-06-0190 
       19.00         2.53        40.37        26.33        14.93        10.29 
TCGA-06-0192 TCGA-06-0194 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 
       18.31         4.67         2.60         0.39         6.48         5.49 
TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0219 
        3.91         4.96        11.84         0.20        12.43         0.36 
TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 
       18.02        10.36        11.80        20.42        14.96        10.32 
TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0412 TCGA-06-0645 TCGA-06-0646 
        5.52         0.26        70.52         8.05         3.22         4.47 
TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 
        9.67         2.04        23.57         9.40        22.32        19.56 
TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 
        5.39         2.70         2.17         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        22.98         5.85         5.42        20.94 
TCGA-06-1084 TCGA-06-1086 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 
        7.43         6.35        26.79         8.65         7.89        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         0.76         4.93         9.27 
TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2570 
       30.64         5.95         6.81         5.98         4.37        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         3.95 
TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 
        7.79         5.39         1.48         0.49         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-08-0244 TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 
        3.12         2.56        22.68        34.75         3.91       108.82 
TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 
        1.74         4.34        13.78        10.39         7.59         3.42 
TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 
       53.82         1.28         6.41        15.06        22.52        14.70 
TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0389 
       35.64        19.53         0.95         9.17        10.85         3.19 
TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 
       10.59         0.30         0.56         3.52        11.77         8.52 
TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 
       18.44        58.19         1.28        10.75         4.80         6.54 
TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0619 
       15.98        17.33         5.52        14.01        14.43        10.39 
TCGA-12-0620 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 
        5.95        65.92         0.10        38.17        25.97        24.13 
TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0775 
        2.63        18.12        28.41        12.43        53.10         5.49 
TCGA-12-0778 TCGA-12-0780 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 
       14.86        14.27        24.79        18.48        10.62        23.51 
TCGA-12-0826 TCGA-12-0828 TCGA-12-0829 TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 
       27.78         8.94        20.58         5.82         6.25        30.54 
TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1097 TCGA-12-1099 
       21.63        11.97        11.38        15.85        14.53         3.42 
TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 TCGA-12-3648 
        9.44        25.28        13.61         6.41        59.41        25.78 
TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 
       11.54        10.95        11.77        34.52        11.74        13.12 
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-14-0862 TCGA-14-0865 TCGA-14-0866 TCGA-14-0871 
        2.24        11.24         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         6.15        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-14-4157 TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 
        3.78         3.42         9.86        50.53        19.10        53.19 
TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 
        3.91         9.93        26.07        16.31         4.31        29.03 
TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 
        0.82         9.90        13.35         3.65        18.28        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-19-2629 TCGA-19-2631 
        1.08         7.53         0.16         4.08        16.47         7.00 
TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 
        6.64        11.28         8.02        18.64         4.73         7.96 
TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A6J4 
        1.78         6.51         5.39         5.29         5.42         3.98 
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-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1835 TCGA-27-1836 
        4.80        16.60         9.86        18.25        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         9.04        15.58 
TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5218 TCGA-28-5219 
       14.53        11.77        31.27        14.20         4.21        22.68 
TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 TCGA-32-1977 TCGA-32-1978 
       10.49         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        21.17        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        10.62         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        11.54         7.76 
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-76-6191 
        4.80         4.54         3.09         3.65         9.17        16.70 
TCGA-76-6192 TCGA-76-6193 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 
        3.29         2.70        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 
       17.72        26.30         5.92 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
             0.16              0.10 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           127.59            108.82 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
             9.17             10.29 
[1] "0.2 - 127.6 (9.2)"  "0.1 - 108.8 (10.3)"
[1] "hr=" "1"  
D18V2, continuous
D18V3, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    33  38
  9Q GAIN WILD-TYPE 187 302
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     33   38
  9Q GAIN WILD-TYPE  187  302
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE              33               187
  MALE                38               302
[1] 2 2
[1] FALSE
D18V4, continuous
                   vv
clus                GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  9Q GAIN MUTATED                               1                   1
  9Q GAIN WILD-TYPE                            16                  17
                   vv
clus                UNTREATED PRIMARY (DE NOVO) GBM
  9Q GAIN MUTATED                                69
  9Q GAIN WILD-TYPE                             456
D18V5, multiclass
                                 clus
vv                                9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                 1                16
  TREATED PRIMARY GBM                           1                17
  UNTREATED PRIMARY (DE NOVO) GBM              69               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"
D18V6, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    49  22
  9Q GAIN WILD-TYPE 333 156
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     49   22
  9Q GAIN WILD-TYPE  333  156
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  NO               49               333
  YES              22               156
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9Q GAIN MUTATED       2                         3    65
  9Q GAIN WILD-TYPE    11                        36   420
D18V7, multiclass
                           clus
vv                          9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  ASIAN                                   2                11
  BLACK OR AFRICAN AMERICAN               3                36
  WHITE                                  65               420
[1] 3 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  57
  9Q GAIN WILD-TYPE  10 405
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      2   57
  9Q GAIN WILD-TYPE   10  405
                        clus
vv                       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                10
  NOT HISPANIC OR LATINO              57               405
[1] 2 2
[1] FALSE

Clustering(19) Variable = 10P GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                  0   1
  10P GAIN MUTATED     4   8
  10P GAIN WILD-TYPE  94 454
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                12                548 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 8                454 
$`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-08-0350 TCGA-08-0351 TCGA-08-0517 TCGA-12-1099 TCGA-14-3477 TCGA-32-2632 
        3.42        53.82        58.19         3.42         3.78         8.84 

$`10P GAIN WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 
        9.17         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        55.86        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        10.36        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         0.23 
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         0.16        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        16.21         2.70         0.26         4.04        47.31 
TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 
        0.10         3.58        22.72        32.52        10.52        18.74 
TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 
       14.07        23.08        22.16        10.75         0.20         9.21 
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        16.70         9.80 
TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 
        7.86        19.46        46.59        11.80        12.79         8.65 
TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 
        3.19         5.46         9.44        11.80         2.56        56.88 
TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 
       10.65         5.29        19.04         3.12        13.02         0.23 
TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 
        2.20         2.73        91.00         2.01        53.98        19.00 
TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 
        2.53        40.37        73.84        26.33        28.47        14.93 
TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 
       10.29        18.31         4.67         7.04         2.60         0.39 
TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 
        6.48         5.49         3.91         4.96        11.84         0.20 
TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 
       12.43        22.49         0.36        18.02        10.36        11.80 
TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 
       20.42        14.96        10.32         5.52         0.26        70.52 
TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 
        4.70         8.05         0.16        35.01        12.33         3.22 
TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 
        4.47         9.67         2.04        23.57         9.40        22.32 
TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 
       19.56         5.39         2.70         2.17         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        22.98         5.85         5.42 
TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 
       20.94         7.43         6.35         3.58        26.79         8.65 
TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 TCGA-06-2557 TCGA-06-2558 
        7.89        13.61        33.90        15.32         1.08         0.76 
TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 
        4.93         9.27         2.83        30.64         5.95         6.81 
TCGA-06-2566 TCGA-06-2567 TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 
        5.98         4.37        31.50        11.24         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         3.95         7.79         5.39 
TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 
        1.48         0.49         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-08-0244 TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 
       22.68        34.75         3.91       108.82         1.74         4.34 
TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 
       13.78        10.39         7.59         1.28         6.41        15.06 
TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 
       22.52        14.70        35.64        19.53         0.95         9.17 
TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 
       10.85        15.72         3.19        10.59         0.30         0.56 
TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0518 TCGA-08-0520 
        3.52        11.77         8.52        18.44         1.28        10.75 
TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 
        4.80         6.54        15.98        17.33         5.52        14.01 
TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 
       14.43         1.64        10.39         5.95         7.17        65.92 
TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 
        0.10        38.17        25.97        24.13         6.12         2.63 
TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 
       18.12        28.41        12.43        53.10        43.10         5.49 
TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 
        9.11        14.86        14.27        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         6.25        30.54        21.63        11.97 
TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1598 
       11.38        15.85         9.11        14.53         3.98         9.44 
TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 
       25.28        13.61         6.41        59.41        43.23        25.78 
TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 
       11.54        10.95        11.77        34.52        11.74        13.12 
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-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 
        0.92        40.96         6.15        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-14-4157 TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 
        7.96         3.42         9.86        50.53        19.10        53.19 
TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 
        5.52         3.91         9.93        26.07        16.31         4.31 
TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 
       29.03         0.82         9.90        13.35         3.65        18.28 
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         0.43 
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         3.48         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        16.47         7.00         7.04         6.64        11.28 
TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 
        8.02        18.64         4.73         7.96         1.78         6.51 
TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 
        5.39         5.29         5.42         3.98        16.57        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         1.22         1.58         7.92 
TCGA-26-6174 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 
        2.33         4.80        16.60         9.86        18.25        33.14 
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         3.91         9.04        15.58 
TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 
       14.53        11.77        31.27        14.20         7.79        13.64 
TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 
        4.21        22.68        10.49         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-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4210 
       15.95         7.36        22.78        21.17        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        10.62         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-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 
       11.54         7.76         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 
       26.30         5.92 

  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 
            24.705              9.980 
[1] "0.4 - 100.0 (24.7)" "0.1 - 127.6 (10.0)"
[1] "hr=" "2.7"
D19V2, continuous
D19V3, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     8   4
  10P GAIN WILD-TYPE 212 336
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      8    4
  10P GAIN WILD-TYPE  212  336
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE                8                212
  MALE                  4                336
[1] 2 2
[1] FALSE
D19V4, continuous
                    vv
clus                 GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  10P GAIN MUTATED                               0                   1
  10P GAIN WILD-TYPE                            17                  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)                  0                 17
  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   4
  10P GAIN WILD-TYPE 374 174
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      8    4
  10P GAIN WILD-TYPE  374  174
     clus
vv    10P GAIN MUTATED 10P GAIN WILD-TYPE
  NO                 8                374
  YES                4                174
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10P GAIN MUTATED       1                         3     8
  10P GAIN WILD-TYPE    12                        36   477
D19V7, multiclass
                           clus
vv                          10P GAIN MUTATED 10P GAIN WILD-TYPE
  ASIAN                                    1                 12
  BLACK OR AFRICAN AMERICAN                3                 36
  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  11
  10P GAIN WILD-TYPE  11 451
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      1   11
  10P GAIN WILD-TYPE   11  451
                        clus
vv                       10P GAIN MUTATED 10P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 11
  NOT HISPANIC OR LATINO               11                451
[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  98 459
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 3                557 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 3                459 
$`10Q GAIN MUTATED`
TCGA-02-0011 TCGA-12-1099 TCGA-32-2632 
       20.71         3.42         8.84 

$`10Q GAIN WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 
        9.17         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        55.86        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        10.36        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         0.23        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         0.16 
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        16.21 
TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 
        2.70         0.26         4.04        47.31         0.10         3.58 
TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 
       22.72        32.52        10.52        18.74        14.07        23.08 
TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 
       22.16        10.75         0.20         9.21         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        16.70         9.80         7.86        19.46 
TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 
       46.59        11.80        12.79         8.65         3.19         5.46 
TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 
        9.44        11.80         2.56        56.88        10.65         5.29 
TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 
       19.04         3.12        13.02         0.23         2.20         2.73 
TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 
       91.00         2.01        53.98        19.00         2.53        40.37 
TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 
       73.84        26.33        28.47        14.93        10.29        18.31 
TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 
        4.67         7.04         2.60         0.39         6.48         5.49 
TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 
        3.91         4.96        11.84         0.20        12.43        22.49 
TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 
        0.36        18.02        10.36        11.80        20.42        14.96 
TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 
       10.32         5.52         0.26        70.52         4.70         8.05 
TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 
        0.16        35.01        12.33         3.22         4.47         9.67 
TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 
        2.04        23.57         9.40        22.32        19.56         5.39 
TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 
        2.70         2.17         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        22.98         5.85         5.42        20.94         7.43 
TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 
        6.35         3.58        26.79         8.65         7.89        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         0.76         4.93         9.27 
TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 
        2.83        30.64         5.95         6.81         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        11.24         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         3.95         7.79         5.39         1.48 
TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 
        0.49         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-08-0244 
        4.77         4.96         1.87         3.12         2.56        22.68 
TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 
       34.75         3.91       108.82         1.74         4.34        13.78 
TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 
       10.39         7.59         3.42        53.82         1.28         6.41 
TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 
       15.06        22.52        14.70        35.64        19.53         0.95 
TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 
        9.17        10.85        15.72         3.19        10.59         0.30 
TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 
        0.56         3.52        11.77         8.52        18.44        58.19 
TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 
        1.28        10.75         4.80         6.54        15.98        17.33 
TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 
        5.52        14.01        14.43         1.64        10.39         5.95 
TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 
        7.17        65.92         0.10        38.17        25.97        24.13 
TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 
        6.12         2.63        18.12        28.41        12.43        53.10 
TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 
       43.10         5.49         9.11        14.86        14.27        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         6.25        30.54 
TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 
       21.63        11.97        11.38        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         9.44        25.28        13.61         6.41        59.41 
TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 
       43.23        25.78        11.54        10.95        11.77        34.52 
TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 
       11.74        13.12         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         6.15        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         9.86 
TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 
       50.53        19.10        53.19         5.52         3.91         9.93 
TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 
       26.07        16.31         4.31        29.03         0.82         9.90 
TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 
       13.35         3.65        18.28        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         0.43        14.27         3.39        10.75 
TCGA-19-1386 TCGA-19-1387 TCGA-19-1388 TCGA-19-1389 TCGA-19-1390 TCGA-19-1392 
        9.07         5.95        12.95         4.64        25.38         3.48 
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        16.47         7.00 
TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 
        7.04         6.64        11.28         8.02        18.64         4.73 
TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 
        7.96         1.78         6.51         5.39         5.29         5.42 
TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 
        3.98        16.57        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-27-1830 TCGA-27-1831 
        1.22         1.58         7.92         2.33         4.80        16.60 
TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 
        9.86        18.25        33.14        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 
        3.91         9.04        15.58        14.53        11.77        31.27 
TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 
       14.20         7.79        13.64         4.21        22.68        10.49 
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-32-2634 
       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 
       21.17        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 
       10.62         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-74-6573 
        4.44        11.84         0.20        11.54         7.76         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 
        7.79         1.61        17.72        26.30         5.92 

  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
              3.42               0.10 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
             20.71             127.59 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
              8.84              10.19 
[1] "3.4 - 20.7 (8.8)"   "0.1 - 127.6 (10.2)"
[1] "hr=" "1.5"
D20V2, continuous
D20V3, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     2   1
  10Q GAIN WILD-TYPE 218 339
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      2    1
  10Q GAIN WILD-TYPE  218  339
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  FEMALE                2                218
  MALE                  1                339
[1] 2 2
[1] FALSE
D20V4, continuous
[1] "Remove cluster labels:" "10Q GAIN MUTATED"      
clus
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 2                414 
        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-A6S1         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-74-6573         TCGA-74-6575         TCGA-74-6577 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-74-6578         TCGA-74-6581         TCGA-74-6584 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-76-4925         TCGA-76-4926         TCGA-76-4928 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-76-4929         TCGA-76-4931         TCGA-76-4934 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-76-4935         TCGA-76-6191         TCGA-76-6192 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-76-6193         TCGA-76-6280         TCGA-76-6282 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-76-6285         TCGA-76-6286         TCGA-76-6656 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-76-6657         TCGA-76-6661         TCGA-76-6662 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-76-6663         TCGA-76-6664         TCGA-81-5910 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
                    vv
clus                 GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  10Q GAIN MUTATED                               0                   0
  10Q GAIN WILD-TYPE                            17                  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                 17
  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 381 176
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      1    2
  10Q GAIN WILD-TYPE  381  176
     clus
vv    10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  NO                 1                381
  YES                2                176
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10Q GAIN MUTATED       0                         0     3
  10Q GAIN WILD-TYPE    13                        39   482
D20V7, multiclass
                           clus
vv                          10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  ASIAN                                    0                 13
  BLACK OR AFRICAN AMERICAN                0                 39
  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  11 460
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      1    2
  10Q GAIN WILD-TYPE   11  460
                        clus
vv                       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 11
  NOT HISPANIC OR LATINO                2                460
[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  96 447
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                17                543 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                15                447 
$`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        10.52        28.47        22.32 
TCGA-06-1087 TCGA-08-0386 TCGA-12-0826 TCGA-12-0827 TCGA-12-1093 TCGA-12-1598 
        3.58        15.72        27.78        38.76        11.97         9.44 
TCGA-19-1388 TCGA-19-4065 TCGA-27-2521 TCGA-27-2526 TCGA-28-5207 
       12.95         7.04        10.39         2.86         9.04 

$`11P GAIN WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 
        9.17         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        55.86        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        10.36        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 
        0.23        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         0.16        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        16.21         2.70         0.26 
TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 
        4.04        47.31         0.10         3.58        22.72        32.52 
TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 
       18.74        14.07        23.08        22.16        10.75         0.20 
TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 
        9.21         2.20        11.74         2.33        20.09        16.70 
TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 
        9.80         7.86        19.46        46.59        11.80        12.79 
TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 
        8.65         3.19         5.46         9.44        11.80         2.56 
TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 
       56.88        10.65         5.29        19.04         3.12        13.02 
TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 
        0.23         2.20         2.73        91.00         2.01        53.98 
TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0189 
       19.00         2.53        40.37        73.84        26.33        14.93 
TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 
       10.29        18.31         4.67         7.04         2.60         0.39 
TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 
        6.48         5.49         3.91         4.96        11.84         0.20 
TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 
       12.43        22.49         0.36        18.02        10.36        11.80 
TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 
       20.42        14.96        10.32         5.52         0.26        70.52 
TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 
        4.70         8.05         0.16        35.01        12.33         3.22 
TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0744 
        4.47         9.67         2.04        23.57         9.40        19.56 
TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 
        5.39         2.70         2.17         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        22.98         5.85         5.42        20.94 
TCGA-06-1084 TCGA-06-1086 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 
        7.43         6.35        26.79         8.65         7.89        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         0.76         4.93         9.27 
TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 
        2.83        30.64         5.95         6.81         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        11.24         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         3.95         7.79         5.39         1.48 
TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 
        0.49         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-08-0244 
        4.77         4.96         1.87         3.12         2.56        22.68 
TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 
       34.75         3.91       108.82         1.74         4.34        13.78 
TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 
       10.39         7.59         3.42        53.82         1.28         6.41 
TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 
       15.06        22.52        14.70        35.64        19.53         0.95 
TCGA-08-0375 TCGA-08-0380 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 
        9.17        10.85         3.19        10.59         0.30         0.56 
TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 
        3.52        11.77         8.52        18.44        58.19         1.28 
TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 
       10.75         4.80         6.54        15.98        17.33         5.52 
TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 
       14.01        14.43         1.64        10.39         5.95         7.17 
TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 
       65.92         0.10        38.17        25.97        24.13         6.12 
TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 
        2.63        18.12        28.41        12.43        53.10        43.10 
TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 
        5.49         9.11        14.86        14.27        91.76        24.79 
TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 
       18.48        10.62        23.51         8.94        20.58       127.59 
TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 TCGA-12-1092 TCGA-12-1094 TCGA-12-1095 
        5.82         6.25        30.54        21.63        11.38        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         3.42        25.28        13.61 
TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 
        6.41        59.41        43.23        25.78        11.54        10.95 
TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 
       11.77        34.52        11.74        13.12         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-14-1454 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 
        6.15        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         9.86        50.53        19.10        53.19         5.52 
TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 
        3.91         9.93        26.07        16.31         4.31        29.03 
TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 
        0.82         9.90        13.35         3.65        18.28        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         0.43        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 
        3.48         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        16.47 
TCGA-19-2631 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 
        7.00         6.64        11.28         8.02        18.64         4.73 
TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 
        7.96         1.78         6.51         5.39         5.29         5.42 
TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 
        3.98        16.57        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-27-1830 TCGA-27-1831 
        1.22         1.58         7.92         2.33         4.80        16.60 
TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 
        9.86        18.25        33.14        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-28-1750 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-28-5208 
        6.74         4.77         7.30         5.26         3.91        15.58 
TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 
       14.53        11.77        31.27        14.20         7.79        13.64 
TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 
        4.21        22.68        10.49         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        21.17        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        10.62         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-74-6573 TCGA-74-6575 TCGA-74-6577 
        0.20        11.54         7.76         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 
       17.72        26.30         5.92 

  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 
             11.67               9.90 
[1] "2.9 - 82.6 (11.7)" "0.1 - 127.6 (9.9)"
[1] "hr=" "1.2"
D21V2, continuous
D21V3, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     6  11
  11P GAIN WILD-TYPE 214 329
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      6   11
  11P GAIN WILD-TYPE  214  329
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE                6                214
  MALE                 11                329
[1] 2 2
[1] FALSE
D21V4, continuous
                    vv
clus                 GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  11P GAIN MUTATED                               0                   0
  11P GAIN WILD-TYPE                            17                  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                 17
  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 369 174
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     13    4
  11P GAIN WILD-TYPE  369  174
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  NO                13                369
  YES                4                174
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11P GAIN MUTATED       0                         0    17
  11P GAIN WILD-TYPE    13                        39   468
D21V7, multiclass
                           clus
vv                          11P GAIN MUTATED 11P GAIN WILD-TYPE
  ASIAN                                    0                 13
  BLACK OR AFRICAN AMERICAN                0                 39
  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  11 447
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      1   15
  11P GAIN WILD-TYPE   11  447
                        clus
vv                       11P GAIN MUTATED 11P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 11
  NOT HISPANIC OR LATINO               15                447
[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  96 450
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                14                546 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                12                450 
$`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         2.73         6.35 
TCGA-06-1087 TCGA-08-0386 TCGA-12-0818 TCGA-12-0826 TCGA-12-0827 TCGA-19-1388 
        3.58        15.72        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 
        9.17         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        55.86        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        10.36        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         0.23        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         0.16        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        16.21         2.70         0.26 
TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0129 TCGA-06-0130 
        4.04        47.31         0.10         3.58        32.52        10.52 
TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 
       18.74        14.07        23.08        22.16        10.75         0.20 
TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 
        9.21         2.20        11.74         2.33        20.09        16.70 
TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 
        9.80         7.86        19.46        46.59        11.80        12.79 
TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 
        8.65         3.19         5.46         9.44        11.80         2.56 
TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 
       56.88        10.65         5.29        19.04         3.12        13.02 
TCGA-06-0173 TCGA-06-0174 TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 
        0.23         2.20        91.00         2.01        53.98        19.00 
TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 
        2.53        40.37        73.84        26.33        28.47        14.93 
TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 
       10.29        18.31         4.67         7.04         2.60         0.39 
TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 
        6.48         5.49         3.91         4.96        11.84         0.20 
TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 
       12.43        22.49         0.36        18.02        10.36        11.80 
TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 
       20.42        14.96        10.32         5.52         0.26        70.52 
TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 
        4.70         8.05         0.16        35.01        12.33         3.22 
TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 
        4.47         9.67         2.04        23.57         9.40        22.32 
TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 
       19.56         5.39         2.70         2.17         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        22.98         5.85         5.42 
TCGA-06-0939 TCGA-06-1084 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 
       20.94         7.43        26.79         8.65         7.89        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         0.76         4.93         9.27 
TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 
        2.83        30.64         5.95         6.81         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        11.24         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         3.95         7.79         5.39         1.48 
TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 
        0.49         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-08-0244 
        4.77         4.96         1.87         3.12         2.56        22.68 
TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 
       34.75         3.91       108.82         1.74         4.34        13.78 
TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 
       10.39         7.59         3.42        53.82         1.28         6.41 
TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 
       15.06        22.52        14.70        35.64        19.53         0.95 
TCGA-08-0375 TCGA-08-0380 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 
        9.17        10.85         3.19        10.59         0.30         0.56 
TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 
        3.52        11.77         8.52        18.44        58.19         1.28 
TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 
       10.75         4.80         6.54        15.98        17.33         5.52 
TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 
       14.01        14.43         1.64        10.39         5.95         7.17 
TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 
       65.92         0.10        38.17        25.97        24.13         6.12 
TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 
        2.63        18.12        28.41        12.43        53.10        43.10 
TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0819 TCGA-12-0820 
        5.49         9.11        14.86        14.27        24.79        18.48 
TCGA-12-0821 TCGA-12-0822 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 
       10.62        23.51         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 
        6.25        30.54        21.63        11.97        11.38        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         3.42         9.44        25.28 
TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 
       13.61         6.41        59.41        43.23        25.78        11.54 
TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 
       10.95        11.77        34.52        11.74        13.12         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         6.15        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         9.86        50.53        19.10        53.19 
TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 
        5.52         3.91         9.93        26.07        16.31         4.31 
TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 
       29.03         0.82         9.90        13.35         3.65        18.28 
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         0.43 
TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 TCGA-19-1389 
       14.27         3.39        10.75         9.07         5.95         4.64 
TCGA-19-1390 TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 
       25.38         3.48         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 
       16.47         7.00         6.64        11.28         8.02        18.64 
TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 
        4.73         7.96         1.78         6.51         5.39         5.29 
TCGA-19-5960 TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 
        5.42         3.98        16.57        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-27-1830 
        8.88         1.22         1.58         7.92         2.33         4.80 
TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 
       16.60         9.86        18.25        33.14        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-28-1755 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 
        3.91         9.04        15.58        14.53        11.77        31.27 
TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 
       14.20         7.79        13.64         4.21        22.68        10.49 
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        21.17        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        10.62         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        11.54         7.76 
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 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              2.73               0.10 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             91.76             127.59 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            14.335              9.900 
[1] "2.7 - 91.8 (14.3)" "0.1 - 127.6 (9.9)"
[1] "hr=" "1.5"
D22V2, continuous
D22V3, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     3  11
  11Q GAIN WILD-TYPE 217 329
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      3   11
  11Q GAIN WILD-TYPE  217  329
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE                3                217
  MALE                 11                329
[1] 2 2
[1] FALSE
D22V4, continuous
                    vv
clus                 GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  11Q GAIN MUTATED                               0                   1
  11Q GAIN WILD-TYPE                            17                  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                 17
  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 370 176
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     12    2
  11Q GAIN WILD-TYPE  370  176
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  NO                12                370
  YES                2                176
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11Q GAIN MUTATED       0                         1    13
  11Q GAIN WILD-TYPE    13                        38   472
D22V7, multiclass
                           clus
vv                          11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  ASIAN                                    0                 13
  BLACK OR AFRICAN AMERICAN                1                 38
  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  11 449
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      1   13
  11Q GAIN WILD-TYPE   11  449
                        clus
vv                       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 11
  NOT HISPANIC OR LATINO               13                449
[1] 2 2
[1] FALSE

Clustering(23) Variable = 12P GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                  0   1
  12P GAIN MUTATED     9  49
  12P GAIN WILD-TYPE  89 413
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                58                502 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                49                413 
$`12P GAIN MUTATED`
TCGA-02-0001 TCGA-02-0024 TCGA-02-0051 TCGA-02-0054 TCGA-02-0070 TCGA-02-0074 
        9.17        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 
        2.56        56.88        40.37        26.33        28.47        18.31 
TCGA-06-0216 TCGA-06-0409 TCGA-06-0649 TCGA-06-0743 TCGA-06-0877 TCGA-06-1086 
       22.49        70.52         2.04        22.32         5.65         6.35 
TCGA-06-1087 TCGA-06-2561 TCGA-06-5415 TCGA-06-6389 TCGA-06-6694 TCGA-08-0246 
        3.58         9.27         8.55         7.79         7.36         3.91 
TCGA-08-0516 TCGA-12-0691 TCGA-12-0776 TCGA-12-0778 TCGA-12-1090 TCGA-12-1098 
       18.44         6.12         9.11        14.86         6.25         3.98 
TCGA-12-1598 TCGA-12-3653 TCGA-14-0740 TCGA-14-0790 TCGA-14-1396 TCGA-14-1453 
        9.44        11.74        11.97        13.78         1.12         1.15 
TCGA-14-1821 TCGA-14-1823 TCGA-14-2554 TCGA-15-1449 TCGA-16-1460 TCGA-19-1787 
       17.79        17.85        17.49         5.52         6.41        12.66 
TCGA-27-1838 TCGA-28-1756 TCGA-28-2506 TCGA-28-5207 TCGA-28-5218 TCGA-32-1979 
       11.51         2.83         6.74         9.04         4.21        19.50 
TCGA-32-2615 TCGA-32-4208 TCGA-32-5222 TCGA-74-6577 
       15.95        21.14        10.62         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        55.86        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        10.36        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         0.23        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         0.16        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        16.21         2.70         0.26         4.04 
TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 
       47.31         0.10         3.58        22.72        32.52        10.52 
TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 
       18.74        14.07        23.08        22.16        10.75         0.20 
TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0147 TCGA-06-0148 
        9.21         2.20        11.74         2.33        16.70         9.80 
TCGA-06-0149 TCGA-06-0150 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 
        7.86        19.46        11.80        12.79         8.65         3.19 
TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 
        5.46         9.44        11.80        10.65         5.29        19.04 
TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 
        3.12        13.02         0.23         2.20         2.73        91.00 
TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0185 TCGA-06-0189 
        2.01        53.98        19.00         2.53        73.84        14.93 
TCGA-06-0190 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 
       10.29         4.67         7.04         2.60         0.39         6.48 
TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 
        5.49         3.91         4.96        11.84         0.20        12.43 
TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 
        0.36        18.02        10.36        11.80        20.42        14.96 
TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 
       10.32         5.52         0.26         4.70         8.05         0.16 
TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0650 
       35.01        12.33         3.22         4.47         9.67        23.57 
TCGA-06-0686 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 
        9.40        19.56         5.39         2.70         2.17         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        22.98         5.85         5.42 
TCGA-06-0939 TCGA-06-1084 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 
       20.94         7.43        26.79         8.65         7.89        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         0.76         4.93         2.83 
TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 
       30.64         5.95         6.81         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        11.24         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 
        3.95         5.39         1.48         0.49         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-08-0244 TCGA-08-0245 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 
        2.56        22.68        34.75       108.82         1.74         4.34 
TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 
       13.78        10.39         7.59         3.42        53.82         1.28 
TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 
        6.41        15.06        22.52        14.70        35.64        19.53 
TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 
        0.95         9.17        10.85        15.72         3.19        10.59 
TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 TCGA-08-0517 
        0.30         0.56         3.52        11.77         8.52        58.19 
TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 
        1.28        10.75         4.80         6.54        15.98        17.33 
TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 
        5.52        14.01        14.43         1.64        10.39         5.95 
TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 
        7.17        65.92         0.10        38.17        25.97        24.13 
TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 
        2.63        18.12        28.41        12.43        53.10        43.10 
TCGA-12-0775 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 
        5.49        14.27        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-12-1091 TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 
        5.82        30.54        21.63        11.97        11.38        15.85 
TCGA-12-1096 TCGA-12-1097 TCGA-12-1099 TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 
        9.11        14.53         3.42        25.28        13.61         6.41 
TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 
       59.41        43.23        25.78        11.54        10.95        11.77 
TCGA-12-3652 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0781 
       34.52        13.12         3.22         2.04        15.12         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 
        6.15        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         9.86        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         9.93        26.07        16.31 
TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 
        4.31        29.03         0.82         9.90        13.35         3.65 
TCGA-16-1062 TCGA-16-1063 TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 TCGA-19-0962 
       18.28        13.97        11.77        21.90         8.61         0.43 
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-19-1789 TCGA-19-1791 
        4.64        25.38         3.48         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 
       16.47         7.00         7.04         6.64        11.28         8.02 
TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 
       18.64         4.73         7.96         1.78         6.51         5.39 
TCGA-19-5959 TCGA-19-5960 TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 
        5.29         5.42         3.98        16.57        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         1.22         1.58         7.92         2.33 
TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 
        4.80        16.60         9.86        18.25        33.14        21.30 
TCGA-27-1836 TCGA-27-1837 TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 
       30.05        14.04        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-28-1757 TCGA-28-2502 TCGA-28-2509 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 
        0.13         0.66         4.77         7.30         5.26         3.91 
TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 
       15.58        14.53        11.77        31.27        14.20         7.79 
TCGA-28-5216 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 
       13.64        22.68        10.49         5.42        15.39        21.07 
TCGA-32-1976 TCGA-32-1977 TCGA-32-1978 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 
        0.49         0.10        15.85         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-32-4210 TCGA-32-4211 TCGA-32-4213 
        8.84        22.78        21.17         3.72        12.59        19.86 
TCGA-32-4719 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 
       10.85         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-74-6573 
        4.44        11.84         0.20        11.54         7.76         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 
        1.61        17.72        26.30         5.92 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              1.12               0.10 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             70.52             127.59 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            11.065              9.915 
[1] "1.1 - 70.5 (11.1)" "0.1 - 127.6 (9.9)"
[1] "hr=" "1.1"
D23V2, continuous
D23V3, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    25  33
  12P GAIN WILD-TYPE 195 307
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     25   33
  12P GAIN WILD-TYPE  195  307
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE               25                195
  MALE                 33                307
[1] 2 2
[1] FALSE
D23V4, continuous
                    vv
clus                 GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  12P GAIN MUTATED                               1                   1
  12P GAIN WILD-TYPE                            16                  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)                  1                 16
  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  16
  12P GAIN WILD-TYPE 340 162
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     42   16
  12P GAIN WILD-TYPE  340  162
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  NO                42                340
  YES               16                162
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12P GAIN MUTATED       1                         3    50
  12P GAIN WILD-TYPE    12                        36   435
D23V7, multiclass
                           clus
vv                          12P GAIN MUTATED 12P GAIN WILD-TYPE
  ASIAN                                    1                 12
  BLACK OR AFRICAN AMERICAN                3                 36
  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  45
  12P GAIN WILD-TYPE  11 417
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      1   45
  12P GAIN WILD-TYPE   11  417
                        clus
vv                       12P GAIN MUTATED 12P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 11
  NOT HISPANIC OR LATINO               45                417
[1] 2 2
[1] FALSE

Clustering(24) Variable = 12Q GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                  0   1
  12Q GAIN MUTATED     7  40
  12Q GAIN WILD-TYPE  91 422
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                47                513 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                40                422 
$`12Q GAIN MUTATED`
TCGA-02-0001 TCGA-02-0051 TCGA-02-0054 TCGA-02-0060 TCGA-02-0070 TCGA-02-0074 
        9.17        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        56.88        28.47 
TCGA-06-0192 TCGA-06-0216 TCGA-06-0409 TCGA-06-0743 TCGA-06-0877 TCGA-06-1086 
       18.31        22.49        70.52        22.32         5.65         6.35 
TCGA-06-1087 TCGA-06-2561 TCGA-06-5415 TCGA-06-6391 TCGA-06-6694 TCGA-08-0246 
        3.58         9.27         8.55         1.48         7.36         3.91 
TCGA-12-0691 TCGA-12-0778 TCGA-12-1090 TCGA-12-1098 TCGA-12-3653 TCGA-14-0790 
        6.12        14.86         6.25         3.98        11.74        13.78 
TCGA-14-1396 TCGA-14-1453 TCGA-14-1821 TCGA-14-1823 TCGA-14-2554 TCGA-15-1449 
        1.12         1.15        17.79        17.85        17.49         5.52 
TCGA-19-1786 TCGA-19-1787 TCGA-27-1838 TCGA-28-2506 TCGA-28-5207 TCGA-28-5218 
        7.17        12.66        11.51         6.74         9.04         4.21 
TCGA-32-1979 TCGA-32-2615 TCGA-32-4208 TCGA-32-5222 TCGA-74-6577 
       19.50        15.95        21.14        10.62         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        55.86        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        10.36        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         0.23        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         0.16        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        16.21         2.70         0.26 
TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 
        4.04        47.31         0.10         3.58        22.72        32.52 
TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 
       10.52        18.74        14.07        23.08        22.16        10.75 
TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 
        0.20         9.21         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 
       16.70         9.80         7.86        19.46        11.80        12.79 
TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 
        8.65         3.19         5.46         9.44        11.80         2.56 
TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 
       10.65         5.29        19.04         3.12        13.02         0.23 
TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 
        2.20         2.73        91.00         2.01        53.98        19.00 
TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0189 TCGA-06-0190 
        2.53        40.37        73.84        26.33        14.93        10.29 
TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 
        4.67         7.04         2.60         0.39         6.48         5.49 
TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0219 
        3.91         4.96        11.84         0.20        12.43         0.36 
TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 
       18.02        10.36        11.80        20.42        14.96        10.32 
TCGA-06-0397 TCGA-06-0402 TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 
        5.52         0.26         4.70         8.05         0.16        35.01 
TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 
       12.33         3.22         4.47         9.67         2.04        23.57 
TCGA-06-0686 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 
        9.40        19.56         5.39         2.70         2.17         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        22.98         5.85         5.42 
TCGA-06-0939 TCGA-06-1084 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 
       20.94         7.43        26.79         8.65         7.89        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         0.76         4.93         2.83 
TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 
       30.64         5.95         6.81         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        11.24         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 
        3.95         7.79         5.39         0.49         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-08-0244 TCGA-08-0245 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 
        2.56        22.68        34.75       108.82         1.74         4.34 
TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 
       13.78        10.39         7.59         3.42        53.82         1.28 
TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 
        6.41        15.06        22.52        14.70        35.64        19.53 
TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 
        0.95         9.17        10.85        15.72         3.19        10.59 
TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 
        0.30         0.56         3.52        11.77         8.52        18.44 
TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 
       58.19         1.28        10.75         4.80         6.54        15.98 
TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 
       17.33         5.52        14.01        14.43         1.64        10.39 
TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 
        5.95         7.17        65.92         0.10        38.17        25.97 
TCGA-12-0688 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 
       24.13         2.63        18.12        28.41        12.43        53.10 
TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 
       43.10         5.49         9.11        14.27        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        30.54        21.63        11.97 
TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1099 TCGA-12-1598 
       11.38        15.85         9.11        14.53         3.42         9.44 
TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 
       25.28        13.61         6.41        59.41        43.23        25.78 
TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-5295 TCGA-12-5299 
       11.54        10.95        11.77        34.52        13.12         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-14-0812 TCGA-14-0813 TCGA-14-0817 TCGA-14-0862 
        2.24        11.24         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-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 
        7.10        30.18         0.92        40.96         6.15        12.43 
TCGA-14-1794 TCGA-14-1795 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2555 
        0.99         1.97         7.63         5.88         7.17         7.96 
TCGA-14-3477 TCGA-14-4157 TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 
        3.78         3.42         9.86        50.53        19.10        53.19 
TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 
        3.91         9.93        26.07        16.31         4.31        29.03 
TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 
        0.82         9.90        13.35         3.65        18.28        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         0.43        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         3.48         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        16.47         7.00 
TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 
        7.04         6.64        11.28         8.02        18.64         4.73 
TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 
        7.96         1.78         6.51         5.39         5.29         5.42 
TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 
        3.98        16.57        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-27-1830 TCGA-27-1831 
        1.22         1.58         7.92         2.33         4.80        16.60 
TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 
        9.86        18.25        33.14        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-28-1756 TCGA-28-1757 
        7.63         8.48         1.22         1.55         2.83         0.13 
TCGA-28-2502 TCGA-28-2509 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5208 
        0.66         4.77         7.30         5.26         3.91        15.58 
TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 
       14.53        11.77        31.27        14.20         7.79        13.64 
TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 
       22.68        10.49         5.42        15.39        21.07         0.49 
TCGA-32-1977 TCGA-32-1978 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 
        0.10        15.85         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-32-2634 TCGA-32-2638 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 
       22.78        21.17         3.72        12.59        19.86        10.85 
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-74-6573 TCGA-74-6575 
       11.84         0.20        11.54         7.76         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 
       17.72        26.30         5.92 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              1.12               0.10 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             70.52             127.59 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             10.19              10.03 
[1] "1.1 - 70.5 (10.2)"  "0.1 - 127.6 (10.0)"
[1] "hr=" "1"  
D24V2, continuous
D24V3, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    22  25
  12Q GAIN WILD-TYPE 198 315
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     22   25
  12Q GAIN WILD-TYPE  198  315
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE               22                198
  MALE                 25                315
[1] 2 2
[1] FALSE
D24V4, continuous
                    vv
clus                 GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  12Q GAIN MUTATED                               1                   0
  12Q GAIN WILD-TYPE                            16                  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)                  1                 16
  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  13
  12Q GAIN WILD-TYPE 348 165
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     34   13
  12Q GAIN WILD-TYPE  348  165
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  NO                34                348
  YES               13                165
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12Q GAIN MUTATED       3                         2    39
  12Q GAIN WILD-TYPE    10                        37   446
D24V7, multiclass
                           clus
vv                          12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  ASIAN                                    3                 10
  BLACK OR AFRICAN AMERICAN                2                 37
  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  36
  12Q GAIN WILD-TYPE  12 426
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      0   36
  12Q GAIN WILD-TYPE   12  426
                        clus
vv                       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 12
  NOT HISPANIC OR LATINO               36                426
[1] 2 2
[1] FALSE

Clustering(25) Variable = 13Q GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                  0   1
  13Q GAIN MUTATED     1   9
  13Q GAIN WILD-TYPE  97 453
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                10                550 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 9                453 
$`13Q GAIN MUTATED`
TCGA-02-0001 TCGA-02-0281 TCGA-08-0386 TCGA-14-0817 TCGA-14-0871 TCGA-19-1390 
        9.17         3.98        15.72         5.39        28.93        25.38 
TCGA-19-A6J4 TCGA-26-5136 TCGA-28-5207 TCGA-32-2615 
        3.98         1.22         9.04        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        55.86        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        10.36        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         0.23        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         0.16        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        16.21         2.70 
TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 
        0.26         4.04        47.31         0.10         3.58        22.72 
TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 
       32.52        10.52        18.74        14.07        23.08        22.16 
TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 
       10.75         0.20         9.21         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        16.70         9.80         7.86        19.46        46.59 
TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 
       11.80        12.79         8.65         3.19         5.46         9.44 
TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 
       11.80         2.56        56.88        10.65         5.29        19.04 
TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 
        3.12        13.02         0.23         2.20         2.73        91.00 
TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 
        2.01        53.98        19.00         2.53        40.37        73.84 
TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 
       26.33        28.47        14.93        10.29        18.31         4.67 
TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 
        7.04         2.60         0.39         6.48         5.49         3.91 
TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 
        4.96        11.84         0.20        12.43        22.49         0.36 
TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 
       18.02        10.36        11.80        20.42        14.96        10.32 
TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 
        5.52         0.26        70.52         4.70         8.05         0.16 
TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 
       35.01        12.33         3.22         4.47         9.67         2.04 
TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 
       23.57         9.40        22.32        19.56         5.39         2.70 
TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 
        2.17         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 
       22.98         5.85         5.42        20.94         7.43         6.35 
TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 
        3.58        26.79         8.65         7.89        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         0.76         4.93         9.27         2.83 
TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 
       30.64         5.95         6.81         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        11.24         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         3.95         7.79         5.39         1.48         0.49 
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-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-08-0244 TCGA-08-0245 
        4.96         1.87         3.12         2.56        22.68        34.75 
TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 
        3.91       108.82         1.74         4.34        13.78        10.39 
TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 
        7.59         3.42        53.82         1.28         6.41        15.06 
TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 
       22.52        14.70        35.64        19.53         0.95         9.17 
TCGA-08-0380 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 
       10.85         3.19        10.59         0.30         0.56         3.52 
TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 
       11.77         8.52        18.44        58.19         1.28        10.75 
TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 
        4.80         6.54        15.98        17.33         5.52        14.01 
TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 
       14.43         1.64        10.39         5.95         7.17        65.92 
TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 
        0.10        38.17        25.97        24.13         6.12         2.63 
TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 
       18.12        28.41        12.43        53.10        43.10         5.49 
TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 
        9.11        14.86        14.27        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         6.25        30.54        21.63        11.97 
TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 
       11.38        15.85         9.11        14.53         3.98         3.42 
TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 
        9.44        25.28        13.61         6.41        59.41        43.23 
TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 
       25.78        11.54        10.95        11.77        34.52        11.74 
TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 
       13.12         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-14-0865 TCGA-14-0866 TCGA-14-0867 TCGA-14-1034 
        1.35         2.89        16.50        26.33         2.04        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         6.15        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         9.86        50.53        19.10        53.19 
TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 
        5.52         3.91         9.93        26.07        16.31         4.31 
TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 
       29.03         0.82         9.90        13.35         3.65        18.28 
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         0.43 
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-19-1392 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 
        4.64         3.48         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 
       16.47         7.00         7.04         6.64        11.28         8.02 
TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 
       18.64         4.73         7.96         1.78         6.51         5.39 
TCGA-19-5959 TCGA-19-5960 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 
        5.29         5.42        16.57        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-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-27-1830 TCGA-27-1831 
        8.88         1.58         7.92         2.33         4.80        16.60 
TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 
        9.86        18.25        33.14        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-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 
        3.91        15.58        14.53        11.77        31.27        14.20 
TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 
        7.79        13.64         4.21        22.68        10.49         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        21.17 
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        10.62 
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-74-6573 TCGA-74-6575 
       11.84         0.20        11.54         7.76         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 
        1.61        17.72        26.30         5.92 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              1.22               0.10 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             28.93             127.59 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             9.105             10.240 
[1] "1.2 - 28.9 (9.1)"   "0.1 - 127.6 (10.2)"
[1] "hr=" "1.2"
D25V2, continuous
D25V3, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     6   4
  13Q GAIN WILD-TYPE 214 336
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      6    4
  13Q GAIN WILD-TYPE  214  336
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE                6                214
  MALE                  4                336
[1] 2 2
[1] FALSE
D25V4, continuous
                    vv
clus                 GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  13Q GAIN MUTATED                               1                   0
  13Q GAIN WILD-TYPE                            16                  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                 16
  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 378 172
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      4    6
  13Q GAIN WILD-TYPE  378  172
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  NO                 4                378
  YES                6                172
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  13Q GAIN MUTATED       0                         1     9
  13Q GAIN WILD-TYPE    13                        38   476
D25V7, multiclass
                           clus
vv                          13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  ASIAN                                    0                 13
  BLACK OR AFRICAN AMERICAN                1                 38
  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  12 455
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      0    7
  13Q GAIN WILD-TYPE   12  455
                        clus
vv                       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 12
  NOT HISPANIC OR LATINO                7                455
[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  97 441
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                22                538 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                21                441 
$`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         2.01 
TCGA-06-0195 TCGA-06-0414 TCGA-06-1087 TCGA-06-2569 TCGA-08-0246 TCGA-08-0386 
        7.04        35.01         3.58         0.43         3.91        15.72 
TCGA-08-0510 TCGA-08-0514 TCGA-12-0619 TCGA-12-0776 TCGA-12-3646 TCGA-14-0867 
        3.52         8.52        10.39         9.11        43.23         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 
        9.17         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        55.86        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        10.36        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 
        0.23        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         0.16        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        16.21         2.70         0.26 
TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 
        4.04        47.31         0.10         3.58        22.72        32.52 
TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 
       10.52        18.74        14.07        23.08        22.16        10.75 
TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 
        0.20         9.21         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 
       16.70         9.80         7.86        19.46        11.80        12.79 
TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 
        8.65         3.19         5.46        11.80         2.56        56.88 
TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 
       10.65         5.29        19.04         3.12        13.02         0.23 
TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 
        2.20         2.73        91.00        53.98        19.00         2.53 
TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 
       40.37        73.84        26.33        28.47        14.93        10.29 
TCGA-06-0192 TCGA-06-0194 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 
       18.31         4.67         2.60         0.39         6.48         5.49 
TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 
        3.91         4.96        11.84         0.20        12.43        22.49 
TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 
        0.36        18.02        10.36        11.80        20.42        14.96 
TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 
       10.32         5.52         0.26        70.52         4.70         8.05 
TCGA-06-0413 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 
        0.16        12.33         3.22         4.47         9.67         2.04 
TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 
       23.57         9.40        22.32        19.56         5.39         2.70 
TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 
        2.17         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 
       22.98         5.85         5.42        20.94         7.43         6.35 
TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 
       26.79         8.65         7.89        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         0.76         4.93         9.27         2.83        30.64 
TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2570 TCGA-06-5408 
        5.95         6.81         5.98         4.37        31.50        11.24 
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         3.95 
TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 
        7.79         5.39         1.48         0.49         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-08-0244 TCGA-08-0245 TCGA-08-0344 TCGA-08-0345 
        3.12         2.56        22.68        34.75       108.82         1.74 
TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 
        4.34        13.78        10.39         7.59         3.42        53.82 
TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 
        1.28         6.41        15.06        22.52        14.70        35.64 
TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0389 TCGA-08-0390 
       19.53         0.95         9.17        10.85         3.19        10.59 
TCGA-08-0392 TCGA-08-0509 TCGA-08-0512 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 
        0.30         0.56        11.77        18.44        58.19         1.28 
TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 
       10.75         4.80         6.54        15.98        17.33         5.52 
TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 
       14.01        14.43         1.64         5.95         7.17        65.92 
TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 
        0.10        38.17        25.97        24.13         6.12         2.63 
TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 
       18.12        28.41        12.43        53.10        43.10         5.49 
TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 
       14.86        14.27        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         6.25        30.54        21.63        11.97        11.38 
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         3.42         9.44 
TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 TCGA-12-3648 TCGA-12-3649 
       25.28        13.61         6.41        59.41        25.78        11.54 
TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 
       10.95        11.77        34.52        11.74        13.12         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 
        6.15        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         9.86        50.53        19.10        53.19         5.52 
TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 
        9.93        26.07        16.31         4.31        29.03         0.82 
TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 
        9.90        13.35         3.65        18.28        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         0.43        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 
        3.48         7.17        12.66         3.25         0.13         9.67 
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        16.47         7.00 
TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 
        7.04         6.64        11.28         8.02        18.64         4.73 
TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 
        7.96         1.78         6.51         5.39         5.29         5.42 
TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 
        3.98        16.57        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-27-1830 TCGA-27-1831 
        1.22         1.58         7.92         2.33         4.80        16.60 
TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 
        9.86        18.25        33.14        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 
        3.91         9.04        15.58        14.53        11.77        31.27 
TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 
       14.20         7.79        13.64         4.21        22.68        10.49 
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        21.17 
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        10.62 
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-74-6573 TCGA-74-6575 
       11.84         0.20        11.54         7.76         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 
        1.61        17.72        26.30         5.92 

  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 
             8.975             10.340 
[1] "0.4 - 46.6 (9.0)"   "0.1 - 127.6 (10.3)"
[1] "hr=" "1.3"
D26V2, continuous
D26V3, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     7  15
  14Q GAIN WILD-TYPE 213 325
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      7   15
  14Q GAIN WILD-TYPE  213  325
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE                7                213
  MALE                 15                325
[1] 2 2
[1] FALSE
D26V4, continuous
                    vv
clus                 GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  14Q GAIN MUTATED                               2                   2
  14Q GAIN WILD-TYPE                            15                  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                 15
  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 368 170
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     14    8
  14Q GAIN WILD-TYPE  368  170
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  NO                14                368
  YES                8                170
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  14Q GAIN MUTATED       0                         1    21
  14Q GAIN WILD-TYPE    13                        38   464
D26V7, multiclass
                           clus
vv                          14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  ASIAN                                    0                 13
  BLACK OR AFRICAN AMERICAN                1                 38
  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  12 441
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      0   21
  14Q GAIN WILD-TYPE   12  441
                        clus
vv                       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 12
  NOT HISPANIC OR LATINO               21                441
[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  96 440
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                24                536 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                22                440 
$`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        10.52 
TCGA-06-0151 TCGA-06-0166 TCGA-06-0177 TCGA-06-0414 TCGA-06-1087 TCGA-08-0392 
       46.59         5.29         2.01        35.01         3.58         0.30 
TCGA-12-0818 TCGA-12-0826 TCGA-12-3653 TCGA-14-0812 TCGA-14-1823 TCGA-14-3477 
       91.76        27.78        11.74         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         4.21        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 
        9.17         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        55.86        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        10.36        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 
        0.23        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         0.16        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        16.21         2.70         0.26         4.04        47.31 
TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0132 TCGA-06-0133 
        0.10         3.58        22.72        32.52        18.74        14.07 
TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 
       23.08        22.16        10.75         0.20         9.21         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        16.70         9.80         7.86 
TCGA-06-0150 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 
       19.46        11.80        12.79         8.65         3.19         5.46 
TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0168 
        9.44        11.80         2.56        56.88        10.65        19.04 
TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 
        3.12        13.02         0.23         2.20         2.73        91.00 
TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 
       53.98        19.00         2.53        40.37        73.84        26.33 
TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 
       28.47        14.93        10.29        18.31         4.67         7.04 
TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 
        2.60         0.39         6.48         5.49         3.91         4.96 
TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 
       11.84         0.20        12.43        22.49         0.36        18.02 
TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 
       10.36        11.80        20.42        14.96        10.32         5.52 
TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0644 
        0.26        70.52         4.70         8.05         0.16        12.33 
TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 
        3.22         4.47         9.67         2.04        23.57         9.40 
TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 
       22.32        19.56         5.39         2.70         2.17         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        22.98         5.85 
TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1800 TCGA-06-1801 
        5.42        20.94         7.43         6.35        26.79         8.65 
TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 TCGA-06-2557 TCGA-06-2558 
        7.89        13.61        33.90        15.32         1.08         0.76 
TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 
        4.93         9.27         2.83        30.64         5.95         6.81 
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        11.24         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         3.95         7.79 
TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 
        5.39         1.48         0.49         7.36         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-08-0244 TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 
        2.56        22.68        34.75         3.91       108.82         1.74 
TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 
        4.34        13.78        10.39         7.59         3.42        53.82 
TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 
        1.28         6.41        15.06        22.52        14.70        35.64 
TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 
       19.53         0.95         9.17        10.85        15.72         3.19 
TCGA-08-0390 TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 
       10.59         0.56         3.52        11.77         8.52        18.44 
TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 
       58.19         1.28        10.75         4.80         6.54        15.98 
TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 
       17.33         5.52        14.01        14.43         1.64        10.39 
TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 
        5.95         7.17        65.92         0.10        38.17        25.97 
TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 
       24.13         6.12         2.63        18.12        28.41        12.43 
TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 
       53.10        43.10         5.49         9.11        14.86        14.27 
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         6.25        30.54        21.63 
TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 
       11.97        11.38        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 
        3.42         9.44        25.28        13.61         6.41        59.41 
TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 
       43.23        25.78        11.54        10.95        11.77        34.52 
TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 
       13.12         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-14-0813 
        6.21        23.05         2.24        11.24        13.78         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-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 
        0.92        40.96         6.15        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-14-4157 TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 
        3.42         9.86        50.53        19.10        53.19         5.52 
TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 
        3.91         9.93        26.07        16.31         4.31        29.03 
TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 
        0.82         9.90        13.35         3.65        18.28        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         0.43        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         3.48         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 
       16.47         7.00         7.04         6.64        11.28         8.02 
TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 
       18.64         4.73         7.96         1.78         6.51         5.39 
TCGA-19-5959 TCGA-19-5960 TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 
        5.29         5.42         3.98        16.57        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         1.22         1.58         7.92         2.33 
TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 
        4.80        16.60         9.86        18.25        33.14        21.30 
TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 
       30.05        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-28-2513 
        1.55         2.83         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         3.91         9.04        15.58        14.53        11.77 
TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5219 TCGA-28-5220 
       31.27        14.20         7.79        13.64        22.68        10.49 
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-32-4210 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 
       21.17        21.14         3.72        12.59        19.86        10.85 
TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-3392 TCGA-41-3393 
       10.62         0.85        13.35         8.94         0.99         4.44 
TCGA-41-3915 TCGA-41-5651 TCGA-41-6646 TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 
       11.84        11.54         7.76         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 
       26.30         5.92 

  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 
              7.41              10.24 
[1] "0.2 - 91.8 (7.4)"   "0.1 - 127.6 (10.2)"
[1] "hr=" "1.2"
D27V2, continuous
D27V3, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    11  13
  15Q GAIN WILD-TYPE 209 327
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     11   13
  15Q GAIN WILD-TYPE  209  327
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE               11                209
  MALE                 13                327
[1] 2 2
[1] FALSE
D27V4, continuous
                    vv
clus                 GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  15Q GAIN MUTATED                               1                   1
  15Q GAIN WILD-TYPE                            16                  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                 16
  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 369 167
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     13   11
  15Q GAIN WILD-TYPE  369  167
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  NO                13                369
  YES               11                167
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  15Q GAIN MUTATED       0                         1    23
  15Q GAIN WILD-TYPE    13                        38   462
D27V7, multiclass
                           clus
vv                          15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  ASIAN                                    0                 13
  BLACK OR AFRICAN AMERICAN                1                 38
  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  12 442
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      0   20
  15Q GAIN WILD-TYPE   12  442
                        clus
vv                       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 12
  NOT HISPANIC OR LATINO               20                442
[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  91 431
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                38                522 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                31                431 
$`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         5.29        28.47         2.60        10.36        70.52 
TCGA-06-1086 TCGA-06-2558 TCGA-06-2567 TCGA-08-0245 TCGA-08-0386 TCGA-08-0510 
        6.35         0.76         4.37        34.75        15.72         3.52 
TCGA-08-0516 TCGA-12-0692 TCGA-12-0821 TCGA-12-0827 TCGA-12-1088 TCGA-12-1598 
       18.44         2.63        10.62        38.76       127.59         9.44 
TCGA-12-1602 TCGA-12-3646 TCGA-14-1454 TCGA-14-3477 TCGA-15-1447 TCGA-15-1449 
        6.41        43.23        30.18         3.78        53.19         5.52 
TCGA-16-0850 TCGA-19-1388 TCGA-19-A6J4 TCGA-27-1832 TCGA-28-2506 TCGA-28-2509 
       16.31        12.95         3.98         9.86         6.74         4.77 
TCGA-28-5207 TCGA-41-2573 
        9.04         8.94 

$`16P GAIN WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 
        9.17         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        55.86        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        10.36        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         0.23        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 
        0.16        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 
       16.21         2.70         0.26         4.04        47.31         0.10 
TCGA-06-0127 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 
        3.58        32.52        10.52        18.74        14.07        23.08 
TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 
       22.16        10.75         0.20         9.21         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        16.70         9.80         7.86        19.46 
TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 
       46.59        11.80        12.79         8.65         3.19         5.46 
TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0168 
        9.44        11.80         2.56        56.88        10.65        19.04 
TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 
        3.12        13.02         0.23         2.20         2.73        91.00 
TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 
        2.01        53.98        19.00         2.53        40.37        73.84 
TCGA-06-0187 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 
       26.33        14.93        10.29        18.31         4.67         7.04 
TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 
        0.39         6.48         5.49         3.91         4.96        11.84 
TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0238 
        0.20        12.43        22.49         0.36        18.02        11.80 
TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0410 
       20.42        14.96        10.32         5.52         0.26         4.70 
TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 
        8.05         0.16        35.01        12.33         3.22         4.47 
TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 
        9.67         2.04        23.57         9.40        22.32        19.56 
TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 
        5.39         2.70         2.17         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        22.98         5.85         5.42        20.94 
TCGA-06-1084 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 
        7.43         3.58        26.79         8.65         7.89        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         9.27         2.83 
TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2569 TCGA-06-2570 
       30.64         5.95         6.81         5.98         0.43        31.50 
TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 
       11.24         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 
        3.95         7.79         5.39         1.48         0.49         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-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-08-0244 TCGA-08-0246 TCGA-08-0344 
        1.87         3.12         2.56        22.68         3.91       108.82 
TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 
        1.74         4.34        13.78        10.39         7.59         3.42 
TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 
       53.82         1.28         6.41        15.06        22.52        14.70 
TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0389 
       35.64        19.53         0.95         9.17        10.85         3.19 
TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0512 TCGA-08-0514 TCGA-08-0517 
       10.59         0.30         0.56        11.77         8.52        58.19 
TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 
        1.28        10.75         4.80         6.54        15.98        17.33 
TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 
        5.52        14.01        14.43         1.64        10.39         5.95 
TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 
        7.17        65.92         0.10        38.17        25.97        24.13 
TCGA-12-0691 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 
        6.12        18.12        28.41        12.43        53.10        43.10 
TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 
        5.49         9.11        14.86        14.27        91.76        24.79 
TCGA-12-0820 TCGA-12-0822 TCGA-12-0826 TCGA-12-0828 TCGA-12-0829 TCGA-12-1089 
       18.48        23.51        27.78         8.94        20.58         5.82 
TCGA-12-1090 TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 
        6.25        30.54        21.63        11.97        11.38        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         3.42        25.28        13.61 
TCGA-12-3644 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 
       59.41        25.78        11.54        10.95        11.77        34.52 
TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 
       11.74        13.12         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-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 TCGA-14-1794 
        1.15         0.92        40.96         6.15        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         9.86        50.53        19.10 
TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 
        3.91         9.93        26.07         4.31        29.03         0.82 
TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 
        9.90        13.35         3.65        18.28        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         0.43        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         3.48 
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        16.47         7.00 
TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 
        7.04         6.64        11.28         8.02        18.64         4.73 
TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 
        7.96         1.78         6.51         5.39         5.29         5.42 
TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 
       16.57        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         1.22 
TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-27-1830 TCGA-27-1831 TCGA-27-1833 
        1.58         7.92         2.33         4.80        16.60        18.25 
TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 
       33.14        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         3.91        15.58        14.53        11.77 
TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 
       31.27        14.20         7.79        13.64         4.21        22.68 
TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 
       10.49         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        21.17        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        10.62         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        11.54         7.76 
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 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              0.76               0.10 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
            127.59             108.82 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
            11.145              9.915 
[1] "0.8 - 127.6 (11.1)" "0.1 - 108.8 (9.9)" 
[1] "hr=" "1.5"
D28V2, continuous
D28V3, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    18  20
  16P GAIN WILD-TYPE 202 320
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     18   20
  16P GAIN WILD-TYPE  202  320
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE               18                202
  MALE                 20                320
[1] 2 2
[1] FALSE
D28V4, continuous
                    vv
clus                 GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  16P GAIN MUTATED                               1                   1
  16P GAIN WILD-TYPE                            16                  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                 16
  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 351 171
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     31    7
  16P GAIN WILD-TYPE  351  171
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  NO                31                351
  YES                7                171
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16P GAIN MUTATED       1                         5    32
  16P GAIN WILD-TYPE    12                        34   453
D28V7, multiclass
                           clus
vv                          16P GAIN MUTATED 16P GAIN WILD-TYPE
  ASIAN                                    1                 12
  BLACK OR AFRICAN AMERICAN                5                 34
  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  12 428
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      0   34
  16P GAIN WILD-TYPE   12  428
                        clus
vv                       16P GAIN MUTATED 16P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 12
  NOT HISPANIC OR LATINO               34                428
[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  91 432
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                37                523 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                30                432 
$`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         5.29        28.47         2.60        10.36        70.52 
TCGA-06-0410 TCGA-06-1086 TCGA-06-2558 TCGA-06-2567 TCGA-08-0245 TCGA-08-0386 
        4.70         6.35         0.76         4.37        34.75        15.72 
TCGA-08-0510 TCGA-08-0516 TCGA-12-0821 TCGA-12-0827 TCGA-12-1598 TCGA-12-3646 
        3.52        18.44        10.62        38.76         9.44        43.23 
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         5.52        16.31 
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         9.04 
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 
        9.17         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        55.86        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        10.36        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         0.23        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 
        0.16        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 
       16.21         2.70         0.26         4.04        47.31         0.10 
TCGA-06-0127 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 
        3.58        32.52        10.52        18.74        14.07        23.08 
TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 
       22.16        10.75         0.20         9.21         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        16.70         9.80         7.86        19.46 
TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 
       46.59        11.80        12.79         8.65         3.19         5.46 
TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0168 
        9.44        11.80         2.56        56.88        10.65        19.04 
TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 
        3.12        13.02         0.23         2.20         2.73        91.00 
TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 
        2.01        53.98        19.00         2.53        40.37        73.84 
TCGA-06-0187 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 
       26.33        14.93        10.29        18.31         4.67         7.04 
TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 
        0.39         6.48         5.49         3.91         4.96        11.84 
TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0238 
        0.20        12.43        22.49         0.36        18.02        11.80 
TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0412 
       20.42        14.96        10.32         5.52         0.26         8.05 
TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 
        0.16        35.01        12.33         3.22         4.47         9.67 
TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 
        2.04        23.57         9.40        22.32        19.56         5.39 
TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 
        2.70         2.17         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        22.98         5.85         5.42        20.94         7.43 
TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 
        3.58        26.79         8.65         7.89        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         9.27         2.83        30.64 
TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2569 TCGA-06-2570 TCGA-06-5408 
        5.95         6.81         5.98         0.43        31.50        11.24 
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         3.95 
TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 
        7.79         5.39         1.48         0.49         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-08-0244 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 
        3.12         2.56        22.68         3.91       108.82         1.74 
TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 
        4.34        13.78        10.39         7.59         3.42        53.82 
TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 
        1.28         6.41        15.06        22.52        14.70        35.64 
TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0389 TCGA-08-0390 
       19.53         0.95         9.17        10.85         3.19        10.59 
TCGA-08-0392 TCGA-08-0509 TCGA-08-0512 TCGA-08-0514 TCGA-08-0517 TCGA-08-0518 
        0.30         0.56        11.77         8.52        58.19         1.28 
TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 
       10.75         4.80         6.54        15.98        17.33         5.52 
TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 
       14.01        14.43         1.64        10.39         5.95         7.17 
TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 
       65.92         0.10        38.17        25.97        24.13         6.12 
TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 
        2.63        18.12        28.41        12.43        53.10        43.10 
TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 
        5.49         9.11        14.86        14.27        91.76        24.79 
TCGA-12-0820 TCGA-12-0822 TCGA-12-0826 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 
       18.48        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         6.25        30.54        21.63        11.97        11.38 
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         3.42        25.28 
TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 
       13.61         6.41        59.41        25.78        11.54        10.95 
TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 
       11.77        34.52        11.74        13.12         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         6.15 
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         9.86        50.53 
TCGA-15-1446 TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 TCGA-16-0861 TCGA-16-1045 
       19.10         3.91         9.93        26.07         4.31        29.03 
TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 
        0.82         9.90        13.35         3.65        18.28        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         0.43        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 
        3.48         7.17        12.66         3.25         0.13         9.67 
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        16.47         7.00 
TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 
        7.04         6.64        11.28         8.02        18.64         4.73 
TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 
        7.96         1.78         6.51         5.39         5.29         5.42 
TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 
       16.57        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         1.22 
TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 
        1.58         7.92         2.33         4.80        16.60         9.86 
TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 
       18.25        33.14        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-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5208 TCGA-28-5209 
        0.66         7.30         5.26         3.91        15.58        14.53 
TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 
       11.77        31.27        14.20         7.79        13.64         4.21 
TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 
       22.68        10.49         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        21.17        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        10.62         0.85        13.35 
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        11.54 
TCGA-41-6646 TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 
        7.76         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 
        5.92 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              0.76               0.10 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             92.65             127.59 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             11.67               9.90 
[1] "0.8 - 92.7 (11.7)" "0.1 - 127.6 (9.9)"
[1] "hr=" "1.3"
D29V2, continuous
D29V3, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    16  21
  16Q GAIN WILD-TYPE 204 319
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     16   21
  16Q GAIN WILD-TYPE  204  319
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE               16                204
  MALE                 21                319
[1] 2 2
[1] FALSE
D29V4, continuous
                    vv
clus                 GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  16Q GAIN MUTATED                               1                   1
  16Q GAIN WILD-TYPE                            16                  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                 16
  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 352 171
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     30    7
  16Q GAIN WILD-TYPE  352  171
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  NO                30                352
  YES                7                171
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16Q GAIN MUTATED       1                         5    31
  16Q GAIN WILD-TYPE    12                        34   454
D29V7, multiclass
                           clus
vv                          16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  ASIAN                                    1                 12
  BLACK OR AFRICAN AMERICAN                5                 34
  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  12 430
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      0   32
  16Q GAIN WILD-TYPE   12  430
                        clus
vv                       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 12
  NOT HISPANIC OR LATINO               32                430
[1] 2 2
[1] FALSE

Clustering(30) Variable = 17P GAIN MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                  0   1
  17P GAIN MUTATED     5  42
  17P GAIN WILD-TYPE  93 420
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                47                513 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                42                420 
$`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         5.29         0.23        28.47         7.04        22.49 
TCGA-06-0409 TCGA-06-0414 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-1087 
       70.52        35.01         9.40        22.32        19.56         3.58 
TCGA-06-1801 TCGA-06-2557 TCGA-06-6694 TCGA-06-A5U1 TCGA-08-0510 TCGA-12-0821 
        8.65         1.08         7.36         1.87         3.52        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        13.61         6.41         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         9.04 
TCGA-28-5218 TCGA-32-2615 TCGA-32-4210 TCGA-41-2575 TCGA-41-4097 
        4.21        15.95         3.72         9.53         0.20 

$`17P GAIN WILD-TYPE`
TCGA-02-0001 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 TCGA-02-0011 
        9.17        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        55.86        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        10.36        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         0.23        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         0.16        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 
       16.21         2.70         0.26         4.04        47.31         0.10 
TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 
        3.58        22.72        32.52        10.52        18.74        14.07 
TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 
       23.08        22.16        10.75         0.20         9.21         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        16.70         9.80         7.86 
TCGA-06-0150 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 
       19.46        11.80        12.79         8.65         3.19         5.46 
TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0168 
        9.44        11.80         2.56        56.88        10.65        19.04 
TCGA-06-0169 TCGA-06-0171 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 
        3.12        13.02         2.20         2.73        91.00         2.01 
TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 
       53.98        19.00         2.53        40.37        73.84        26.33 
TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0197 TCGA-06-0201 
       14.93        10.29        18.31         4.67         2.60         0.39 
TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 
        6.48         5.49         3.91         4.96        11.84         0.20 
TCGA-06-0214 TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 
       12.43         0.36        18.02        10.36        11.80        20.42 
TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0410 TCGA-06-0412 
       14.96        10.32         5.52         0.26         4.70         8.05 
TCGA-06-0413 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 
        0.16        12.33         3.22         4.47         9.67         2.04 
TCGA-06-0650 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 
       23.57         5.39         2.70         2.17         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        22.98         5.85         5.42 
TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1800 TCGA-06-1802 TCGA-06-1804 
       20.94         7.43         6.35        26.79         7.89        13.61 
TCGA-06-1805 TCGA-06-1806 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 
       33.90        15.32         0.76         4.93         9.27         2.83 
TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 
       30.64         5.95         6.81         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        11.24         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         3.95         7.79         5.39         1.48         0.49 
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-A6S0 TCGA-06-A6S1 TCGA-08-0244 TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 
        3.12         2.56        22.68        34.75         3.91       108.82 
TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 
        1.74         4.34        13.78        10.39         7.59         3.42 
TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 
       53.82         1.28         6.41        15.06        22.52        14.70 
TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 
       35.64        19.53         0.95         9.17        10.85        15.72 
TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0512 TCGA-08-0514 
        3.19        10.59         0.30         0.56        11.77         8.52 
TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 
       18.44        58.19         1.28        10.75         4.80         6.54 
TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 
       15.98        17.33         5.52        14.01        14.43         1.64 
TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 
       10.39         5.95         7.17        65.92         0.10        38.17 
TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 
       25.97        24.13         6.12         2.63        18.12        28.41 
TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 
       12.43        53.10        43.10         5.49         9.11        14.86 
TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0826 TCGA-12-0828 
       14.27        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-12-1092 
       20.58       127.59         5.82         6.25        30.54        21.63 
TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 
       11.97        11.38        15.85        14.53         3.98         3.42 
TCGA-12-1598 TCGA-12-1599 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 
        9.44        25.28        59.41        43.23        25.78        11.54 
TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 
       10.95        11.77        34.52        11.74        13.12         3.22 
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-14-0817 TCGA-14-0862 TCGA-14-0866 
       11.24        13.78         3.25         5.39         2.89        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         6.15        12.43 
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         9.86        50.53        19.10 
TCGA-15-1447 TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 TCGA-16-0850 TCGA-16-0861 
       53.19         5.52         3.91         9.93        16.31         4.31 
TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 
       29.03         0.82         9.90        13.35         3.65        18.28 
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         0.43 
TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 TCGA-19-1389 
       14.27         3.39        10.75         9.07         5.95         4.64 
TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 
        3.48         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        16.47 
TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 
        7.00         7.04         6.64        11.28         8.02        18.64 
TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 
        4.73         7.96         1.78         6.51         5.39         5.29 
TCGA-19-5960 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 
        5.42        16.57        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-27-1830 TCGA-27-1831 
        1.22         1.58         7.92         2.33         4.80        16.60 
TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 
        9.86        18.25        33.14        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-28-1747 TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 
       14.40        15.78         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-28-2509 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5208 TCGA-28-5209 
        4.77         7.30         5.26         3.91        15.58        14.53 
TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5219 
       11.77        31.27        14.20         7.79        13.64        22.68 
TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 
       10.49         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-32-2616 TCGA-32-2632 
       16.93        12.23        20.78        15.02         7.36         8.84 
TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 
       22.78        21.17        21.14        12.59        19.86        10.85 
TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-3392 TCGA-41-3393 
       10.62         0.85        13.35         8.94         0.99         4.44 
TCGA-41-3915 TCGA-41-5651 TCGA-41-6646 TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 
       11.84        11.54         7.76         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 
       17.72        26.30         5.92 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
               0.2                0.1 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             70.52             127.59 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              9.04              10.36 
[1] "0.2 - 70.5 (9.0)"   "0.1 - 127.6 (10.4)"
[1] "hr=" "1.2"
D30V2, continuous
D30V3, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    14  33
  17P GAIN WILD-TYPE 206 307
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     14   33
  17P GAIN WILD-TYPE  206  307
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE               14                206
  MALE                 33                307
[1] 2 2
[1] FALSE
D30V4, continuous
                    vv
clus                 GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  17P GAIN MUTATED                               3                   1
  17P GAIN WILD-TYPE                            14                  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)                  3                 14
  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  18
  17P GAIN WILD-TYPE 353 160
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     29   18
  17P GAIN WILD-TYPE  353  160
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  NO                29                353
  YES               18                160
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17P GAIN MUTATED       0                         5    40
  17P GAIN WILD-TYPE    13                        34   445
D30V7, multiclass
                           clus
vv                          17P GAIN MUTATED 17P GAIN WILD-TYPE
  ASIAN                                    0                 13
  BLACK OR AFRICAN AMERICAN                5                 34
  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  41
  17P GAIN WILD-TYPE  11 421
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      1   41
  17P GAIN WILD-TYPE   11  421
                        clus
vv                       17P GAIN MUTATED 17P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 11
  NOT HISPANIC OR LATINO               41                421
[1] 2 2
[1] FALSE

Clustering(31) Variable = 17Q GAIN MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                  0   1
  17Q GAIN MUTATED     4  54
  17Q GAIN WILD-TYPE  94 408
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                58                502 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                54                408 
$`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         5.29         0.23        28.47         7.04        22.49 
TCGA-06-0237 TCGA-06-0409 TCGA-06-0410 TCGA-06-0414 TCGA-06-0686 TCGA-06-0743 
       10.36        70.52         4.70        35.01         9.40        22.32 
TCGA-06-0744 TCGA-06-1087 TCGA-06-1801 TCGA-06-2557 TCGA-06-6694 TCGA-06-A5U1 
       19.56         3.58         8.65         1.08         7.36         1.87 
TCGA-08-0510 TCGA-12-0619 TCGA-12-0821 TCGA-12-0822 TCGA-12-0827 TCGA-12-1092 
        3.52        10.39        10.62        23.51        38.76        21.63 
TCGA-12-1096 TCGA-12-1600 TCGA-12-1602 TCGA-12-5301 TCGA-14-0813 TCGA-14-0865 
        9.11        13.61         6.41         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         5.52         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         9.04 
TCGA-28-5215 TCGA-28-5218 TCGA-32-2495 TCGA-32-2615 TCGA-32-2616 TCGA-32-4210 
        7.79         4.21        15.02        15.95         7.36         3.72 
TCGA-41-2575 TCGA-41-3915 TCGA-41-4097 TCGA-76-6280 
        9.53        11.84         0.20        11.38 

$`17Q GAIN WILD-TYPE`
TCGA-02-0001 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 TCGA-02-0011 
        9.17        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        55.86        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        10.36        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         0.23        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         0.16        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 
       16.21         2.70         0.26         4.04        47.31         0.10 
TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 
        3.58        22.72        32.52        10.52        18.74        14.07 
TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 
       23.08        22.16        10.75         0.20         9.21         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        16.70         9.80         7.86 
TCGA-06-0150 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 
       19.46        11.80        12.79         8.65         3.19         5.46 
TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0168 
        9.44        11.80         2.56        56.88        10.65        19.04 
TCGA-06-0169 TCGA-06-0171 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 
        3.12        13.02         2.20         2.73        91.00         2.01 
TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 
       53.98        19.00         2.53        40.37        73.84        26.33 
TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0197 TCGA-06-0201 
       14.93        10.29        18.31         4.67         2.60         0.39 
TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 
        6.48         5.49         3.91         4.96        11.84         0.20 
TCGA-06-0214 TCGA-06-0219 TCGA-06-0221 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 
       12.43         0.36        18.02        11.80        20.42        14.96 
TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0412 TCGA-06-0413 TCGA-06-0644 
       10.32         5.52         0.26         8.05         0.16        12.33 
TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0745 
        3.22         4.47         9.67         2.04        23.57         5.39 
TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 
        2.70         2.17         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        22.98         5.85         5.42        20.94         7.43 
TCGA-06-1086 TCGA-06-1800 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 
        6.35        26.79         7.89        13.61        33.90        15.32 
TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 
        0.76         4.93         9.27         2.83        30.64         5.95 
TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-5408 
        6.81         5.98         4.37         0.43        31.50        11.24 
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         3.95 
TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6695 TCGA-06-6697 
        7.79         5.39         1.48         0.49         8.32        12.85 
TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-06-A6S0 TCGA-06-A6S1 
        4.77         1.55         4.77         4.96         3.12         2.56 
TCGA-08-0244 TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 
       22.68        34.75         3.91       108.82         1.74         4.34 
TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 
       13.78        10.39         7.59         3.42        53.82         1.28 
TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 
        6.41        15.06        22.52        14.70        35.64        19.53 
TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 
        0.95         9.17        10.85        15.72         3.19        10.59 
TCGA-08-0392 TCGA-08-0509 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 
        0.30         0.56        11.77         8.52        18.44        58.19 
TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 
        1.28        10.75         4.80         6.54        15.98        17.33 
TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0620 TCGA-12-0654 
        5.52        14.01        14.43         1.64         5.95         7.17 
TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 
       65.92         0.10        38.17        25.97        24.13         6.12 
TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 
        2.63        18.12        28.41        12.43        53.10        43.10 
TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 
        5.49         9.11        14.86        14.27        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-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1097 
        6.25        30.54        11.97        11.38        15.85        14.53 
TCGA-12-1098 TCGA-12-1099 TCGA-12-1598 TCGA-12-1599 TCGA-12-3644 TCGA-12-3646 
        3.98         3.42         9.44        25.28        59.41        43.23 
TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 
       25.78        11.54        10.95        11.77        34.52        11.74 
TCGA-12-5295 TCGA-12-5299 TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 TCGA-14-0783 
       13.12         3.22        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-14-0866 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-14-1458 TCGA-14-1459 TCGA-14-1795 TCGA-14-1821 TCGA-14-1823 TCGA-14-1825 
        6.15        12.43         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         9.86 
TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 
       50.53        19.10        53.19         9.93        26.07        16.31 
TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 
        4.31        29.03         0.82         9.90        13.35         3.65 
TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 
       18.28        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 
        0.43        14.27         3.39        10.75         9.07         5.95 
TCGA-19-1389 TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 
        4.64         3.48         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 
       16.47         7.00         7.04         6.64        11.28         8.02 
TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 
       18.64         4.73         7.96         1.78         6.51         5.39 
TCGA-19-5959 TCGA-19-5960 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 
        5.29         5.42        16.57        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-27-1830 
        8.88         1.22         1.58         7.92         2.33         4.80 
TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1836 TCGA-27-1837 
       16.60         9.86        18.25        33.14        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-28-1747 TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 
       14.40        15.78         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-28-2509 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5208 TCGA-28-5209 
        4.77         7.30         5.26         3.91        15.58        14.53 
TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5216 TCGA-28-5219 TCGA-28-5220 
       11.77        31.27        14.20        13.64        22.68        10.49 
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-32-2632 TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 
       12.23        20.78         8.84        22.78        21.17        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        10.62         0.85        13.35 
TCGA-41-2573 TCGA-41-3392 TCGA-41-3393 TCGA-41-5651 TCGA-41-6646 TCGA-74-6573 
        8.94         0.99         4.44        11.54         7.76         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-76-6282 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 
        1.61        17.72        26.30         5.92 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               0.2                0.1 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             70.52             127.59 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             9.075             10.340 
[1] "0.2 - 70.5 (9.1)"   "0.1 - 127.6 (10.3)"
[1] "hr=" "1.3"
D31V2, continuous
D31V3, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    20  38
  17Q GAIN WILD-TYPE 200 302
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     20   38
  17Q GAIN WILD-TYPE  200  302
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE               20                200
  MALE                 38                302
[1] 2 2
[1] FALSE
D31V4, continuous
                    vv
clus                 GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  17Q GAIN MUTATED                               3                   2
  17Q GAIN WILD-TYPE                            14                  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)                  3                 14
  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  22
  17Q GAIN WILD-TYPE 346 156
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     36   22
  17Q GAIN WILD-TYPE  346  156
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  NO                36                346
  YES               22                156
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17Q GAIN MUTATED       0                         5    51
  17Q GAIN WILD-TYPE    13                        34   434
D31V7, multiclass
                           clus
vv                          17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  ASIAN                                    0                 13
  BLACK OR AFRICAN AMERICAN                5                 34
  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  49
  17Q GAIN WILD-TYPE  10 413
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      2   49
  17Q GAIN WILD-TYPE   10  413
                        clus
vv                       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                 10
  NOT HISPANIC OR LATINO               49                413
[1] 2 2
[1] FALSE

Clustering(32) Variable = 18P GAIN MUTATION ANALYSIS
D32V1, survival
                    sevent
clus2                  0   1
  18P GAIN MUTATED    12  45
  18P GAIN WILD-TYPE  86 417
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                57                503 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                45                417 
$`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        10.52        16.70        28.47         2.60 
TCGA-06-0209 TCGA-06-0238 TCGA-06-0402 TCGA-06-0410 TCGA-06-0414 TCGA-06-0686 
        3.91        11.80         0.26         4.70        35.01         9.40 
TCGA-06-1087 TCGA-06-1805 TCGA-06-2557 TCGA-06-2559 TCGA-06-5858 TCGA-06-6389 
        3.58        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         6.41         0.10        38.76         6.25        21.63 
TCGA-12-1598 TCGA-12-1602 TCGA-12-3651 TCGA-12-3653 TCGA-12-5295 TCGA-14-0867 
        9.44         6.41        11.77        11.74        13.12         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         5.52 
TCGA-19-0960 TCGA-19-1392 TCGA-19-1787 TCGA-19-2629 TCGA-26-5136 TCGA-27-2521 
        8.61         3.48        12.66        16.47         1.22        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        10.62 
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 
        9.17         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        55.86        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        10.36        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 
        0.23        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         0.16 
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        16.21 
TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 
        2.70         0.26         4.04        47.31         0.10         3.58 
TCGA-06-0129 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 
       32.52        18.74        14.07        23.08        22.16        10.75 
TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 
        0.20         9.21         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 
        9.80         7.86        19.46        46.59        11.80        12.79 
TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 
        8.65         3.19         5.46         9.44        11.80         2.56 
TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 
       56.88        10.65         5.29        19.04         3.12        13.02 
TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 
        0.23         2.20         2.73        91.00         2.01        53.98 
TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0189 
       19.00         2.53        40.37        73.84        26.33        14.93 
TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0201 TCGA-06-0206 
       10.29        18.31         4.67         7.04         0.39         6.48 
TCGA-06-0208 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 
        5.49         4.96        11.84         0.20        12.43        22.49 
TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 
        0.36        18.02        10.36        20.42        14.96        10.32 
TCGA-06-0397 TCGA-06-0409 TCGA-06-0412 TCGA-06-0413 TCGA-06-0644 TCGA-06-0645 
        5.52        70.52         8.05         0.16        12.33         3.22 
TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0743 TCGA-06-0744 
        4.47         9.67         2.04        23.57        22.32        19.56 
TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 
        5.39         2.70         2.17         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        22.98         5.85         5.42        20.94 
TCGA-06-1084 TCGA-06-1086 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 
        7.43         6.35        26.79         8.65         7.89        13.61 
TCGA-06-1806 TCGA-06-2558 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 
       15.32         0.76         9.27         2.83        30.64         5.95 
TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-5408 
        6.81         5.98         4.37         0.43        31.50        11.24 
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         3.95         5.39 
TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 TCGA-06-6699 
        1.48         0.49         7.36         8.32        12.85         1.55 
TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-08-0244 
        4.77         4.96         1.87         3.12         2.56        22.68 
TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 
       34.75         3.91       108.82         1.74         4.34        13.78 
TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0354 
       10.39         7.59         3.42        53.82         1.28        15.06 
TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 
       22.52        14.70        35.64        19.53         0.95         9.17 
TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 
       10.85        15.72         3.19        10.59         0.30         0.56 
TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 
        3.52        11.77         8.52        18.44        58.19         1.28 
TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 
       10.75         4.80         6.54        15.98        17.33         5.52 
TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 
       14.01        14.43         1.64        10.39         5.95         7.17 
TCGA-12-0656 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 
       65.92        38.17        25.97        24.13         6.12         2.63 
TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 
       18.12        28.41        12.43        53.10        43.10         5.49 
TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 
        9.11        14.86        14.27        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-12-1091 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 
        5.82        30.54        11.97        11.38        15.85         9.11 
TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 TCGA-12-1599 TCGA-12-1600 TCGA-12-3644 
       14.53         3.98         3.42        25.28        13.61        59.41 
TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3652 TCGA-12-5299 
       43.23        25.78        11.54        10.95        34.52         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-14-1034 TCGA-14-1037 TCGA-14-1043 
        2.89        16.50        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         6.15 
TCGA-14-1459 TCGA-14-1795 TCGA-14-1821 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 
       12.43         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         9.86        50.53        19.10 
TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 
        3.91         9.93        26.07        16.31         4.31        29.03 
TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 
        0.82         9.90        13.35         3.65        18.28        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         0.43        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-19-1789 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-19-2631 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 
       11.28         8.02        18.64         4.73         7.96         1.78 
TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A6J4 TCGA-19-A6J5 
        6.51         5.39         5.29         5.42         3.98        16.57 
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-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 
        2.33         4.80        16.60         9.86        18.25        33.14 
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-28-1746 
       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-28-2513 TCGA-28-2514 
        1.55         2.83         0.13         0.66         7.30         5.26 
TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 
        3.91         9.04        15.58        14.53        11.77        31.27 
TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 
       14.20         7.79        13.64         4.21        22.68        10.49 
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-32-1987 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        21.17        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-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 
        9.53         0.99         4.44         0.20        11.54         7.76 
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-81-5911 TCGA-87-5896 TCGA-OX-A56R 
        7.79         1.61        17.72        26.30         5.92 

  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 
              9.44              10.29 
[1] "0.1 - 65.0 (9.4)"   "0.1 - 127.6 (10.3)"
[1] "hr=" "1"  
D32V2, continuous
D32V3, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    24  33
  18P GAIN WILD-TYPE 196 307
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     24   33
  18P GAIN WILD-TYPE  196  307
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE               24                196
  MALE                 33                307
[1] 2 2
[1] FALSE
D32V4, continuous
                    vv
clus                 GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  18P GAIN MUTATED                               0                   0
  18P GAIN WILD-TYPE                            17                  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                 17
  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 342 161
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     40   17
  18P GAIN WILD-TYPE  342  161
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  NO                40                342
  YES               17                161
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18P GAIN MUTATED       0                         2    52
  18P GAIN WILD-TYPE    13                        37   433
D32V7, multiclass
                           clus
vv                          18P GAIN MUTATED 18P GAIN WILD-TYPE
  ASIAN                                    0                 13
  BLACK OR AFRICAN AMERICAN                2                 37
  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  10 415
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      2   47
  18P GAIN WILD-TYPE   10  415
                        clus
vv                       18P GAIN MUTATED 18P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                 10
  NOT HISPANIC OR LATINO               47                415
[1] 2 2
[1] FALSE

Clustering(33) Variable = 18Q GAIN MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                  0   1
  18Q GAIN MUTATED    13  44
  18Q GAIN WILD-TYPE  85 418
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                57                503 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                44                418 
$`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        10.52        16.70        28.47         2.60         3.91 
TCGA-06-0238 TCGA-06-0402 TCGA-06-0410 TCGA-06-0414 TCGA-06-0686 TCGA-06-0876 
       11.80         0.26         4.70        35.01         9.40        46.19 
TCGA-06-1087 TCGA-06-1805 TCGA-06-2557 TCGA-06-5408 TCGA-06-5858 TCGA-06-6389 
        3.58        33.90         1.08        11.24         6.15         7.79 
TCGA-06-6698 TCGA-08-0353 TCGA-12-0657 TCGA-12-0827 TCGA-12-1092 TCGA-12-1598 
        4.77         6.41         0.10        38.76        21.63         9.44 
TCGA-12-1602 TCGA-12-3651 TCGA-12-3653 TCGA-12-5295 TCGA-14-0867 TCGA-14-0871 
        6.41        11.77        11.74        13.12         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         5.52        16.31 
TCGA-19-0960 TCGA-19-1392 TCGA-19-1787 TCGA-19-2629 TCGA-26-5136 TCGA-27-2521 
        8.61         3.48        12.66        16.47         1.22        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        10.62         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 
        9.17         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        55.86        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        10.36        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         0.23        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 
        0.16        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 
       16.21         2.70         0.26         4.04        47.31         0.10 
TCGA-06-0127 TCGA-06-0129 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 
        3.58        32.52        18.74        14.07        23.08        22.16 
TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 
       10.75         0.20         9.21         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         9.80         7.86        19.46        46.59        11.80 
TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 
       12.79         8.65         3.19         5.46         9.44        11.80 
TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 
        2.56        56.88        10.65         5.29        19.04         3.12 
TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 
       13.02         0.23         2.20         2.73        91.00         2.01 
TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 
       53.98        19.00         2.53        40.37        73.84        26.33 
TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0201 
       14.93        10.29        18.31         4.67         7.04         0.39 
TCGA-06-0206 TCGA-06-0208 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 
        6.48         5.49         4.96        11.84         0.20        12.43 
TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0240 TCGA-06-0241 
       22.49         0.36        18.02        10.36        20.42        14.96 
TCGA-06-0394 TCGA-06-0397 TCGA-06-0409 TCGA-06-0412 TCGA-06-0413 TCGA-06-0644 
       10.32         5.52        70.52         8.05         0.16        12.33 
TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0743 
        3.22         4.47         9.67         2.04        23.57        22.32 
TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 
       19.56         5.39         2.70         2.17         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        22.98         5.85         5.42        20.94 
TCGA-06-1084 TCGA-06-1086 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 
        7.43         6.35        26.79         8.65         7.89        13.61 
TCGA-06-1806 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 
       15.32         0.76         4.93         9.27         2.83        30.64 
TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 
        5.95         6.81         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         3.95         5.39 
TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 TCGA-06-6699 
        1.48         0.49         7.36         8.32        12.85         1.55 
TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-08-0244 
        4.77         4.96         1.87         3.12         2.56        22.68 
TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 
       34.75         3.91       108.82         1.74         4.34        13.78 
TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0354 
       10.39         7.59         3.42        53.82         1.28        15.06 
TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 
       22.52        14.70        35.64        19.53         0.95         9.17 
TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 
       10.85        15.72         3.19        10.59         0.30         0.56 
TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 
        3.52        11.77         8.52        18.44        58.19         1.28 
TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 
       10.75         4.80         6.54        15.98        17.33         5.52 
TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 
       14.01        14.43         1.64        10.39         5.95         7.17 
TCGA-12-0656 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 
       65.92        38.17        25.97        24.13         6.12         2.63 
TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 
       18.12        28.41        12.43        53.10        43.10         5.49 
TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 
        9.11        14.86        14.27        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-12-1091 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 
        5.82         6.25        30.54        11.97        11.38        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         3.42        25.28        13.61 
TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3652 
       59.41        43.23        25.78        11.54        10.95        34.52 
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-14-1034 TCGA-14-1037 
        5.39         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-14-1451 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 
        6.15        12.43         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         9.86        50.53 
TCGA-15-1446 TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 TCGA-16-0861 TCGA-16-1045 
       19.10         3.91         9.93        26.07         4.31        29.03 
TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 
        0.82         9.90        13.35         3.65        18.28        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         0.43        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-19-1789 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-19-2631 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 
       11.28         8.02        18.64         4.73         7.96         1.78 
TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A6J4 TCGA-19-A6J5 
        6.51         5.39         5.29         5.42         3.98        16.57 
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-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 
        2.33         4.80        16.60         9.86        18.25        33.14 
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-28-1746 
       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-28-2513 TCGA-28-2514 
        1.55         2.83         0.13         0.66         7.30         5.26 
TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 
        3.91         9.04        15.58        14.53        11.77        31.27 
TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 
       14.20         7.79        13.64         4.21        22.68        10.49 
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-32-1987 TCGA-32-1991 TCGA-32-2491 
       19.50         1.18         4.67        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        21.17 
TCGA-32-4208 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-41-2571 
       21.14         3.72        12.59        19.86        10.85         0.85 
TCGA-41-2572 TCGA-41-3392 TCGA-41-3393 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 
       13.35         0.99         4.44         0.20        11.54         7.76 
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-81-5911 TCGA-87-5896 TCGA-OX-A56R 
        7.79         1.61        17.72        26.30         5.92 

  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 
             10.19              10.03 
[1] "0.1 - 65.0 (10.2)"  "0.1 - 127.6 (10.0)"
[1] "hr=" "1"  
D33V2, continuous
D33V3, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    27  30
  18Q GAIN WILD-TYPE 193 310
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     27   30
  18Q GAIN WILD-TYPE  193  310
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE               27                193
  MALE                 30                310
[1] 2 2
[1] FALSE
D33V4, continuous
                    vv
clus                 GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  18Q GAIN MUTATED                               0                   0
  18Q GAIN WILD-TYPE                            17                  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                 17
  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 341 162
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     41   16
  18Q GAIN WILD-TYPE  341  162
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  NO                41                341
  YES               16                162
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18Q GAIN MUTATED       0                         3    51
  18Q GAIN WILD-TYPE    13                        36   434
D33V7, multiclass
                           clus
vv                          18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  ASIAN                                    0                 13
  BLACK OR AFRICAN AMERICAN                3                 36
  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  11 414
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      1   48
  18Q GAIN WILD-TYPE   11  414
                        clus
vv                       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 11
  NOT HISPANIC OR LATINO               48                414
[1] 2 2
[1] FALSE

Clustering(34) Variable = 19P GAIN MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                  0   1
  19P GAIN MUTATED    37 181
  19P GAIN WILD-TYPE  61 281
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
               218                342 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
               181                281 
$`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        55.86        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-02-2466 TCGA-02-2485 TCGA-06-0119 
       15.95         4.37        10.55        16.80        15.45         2.70 
TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0137 
        0.26         4.04        47.31         0.10         3.58        23.08 
TCGA-06-0145 TCGA-06-0147 TCGA-06-0148 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 
        2.33        16.70         9.80        19.46        46.59        11.80 
TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0164 
       12.79         8.65         3.19         5.46         9.44        56.88 
TCGA-06-0173 TCGA-06-0174 TCGA-06-0177 TCGA-06-0179 TCGA-06-0185 TCGA-06-0190 
        0.23         2.20         2.01        19.00        73.84        10.29 
TCGA-06-0192 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0211 
       18.31         0.39         6.48         5.49         3.91        11.84 
TCGA-06-0216 TCGA-06-0221 TCGA-06-0237 TCGA-06-0394 TCGA-06-0402 TCGA-06-0409 
       22.49        18.02        10.36        10.32         0.26        70.52 
TCGA-06-0410 TCGA-06-0414 TCGA-06-0645 TCGA-06-0650 TCGA-06-0743 TCGA-06-0744 
        4.70        35.01         3.22        23.57        22.32        19.56 
TCGA-06-0747 TCGA-06-0877 TCGA-06-0879 TCGA-06-1086 TCGA-06-1087 TCGA-06-1802 
        2.70         5.65        22.98         6.35         3.58         7.89 
TCGA-06-1806 TCGA-06-2563 TCGA-06-2565 TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 
       15.32        30.64         6.81         8.98         8.55         6.71 
TCGA-06-6388 TCGA-06-6695 TCGA-06-6699 TCGA-06-A6S0 TCGA-08-0246 TCGA-08-0347 
        3.95         8.32         1.55         3.12         3.91        13.78 
TCGA-08-0352 TCGA-08-0353 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0375 
        1.28         6.41        22.52        14.70        35.64         9.17 
TCGA-08-0386 TCGA-08-0390 TCGA-08-0509 TCGA-08-0510 TCGA-08-0514 TCGA-08-0518 
       15.72        10.59         0.56         3.52         8.52         1.28 
TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0657 TCGA-12-0670 
        6.54        15.98        17.33         5.52         0.10        25.97 
TCGA-12-0688 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0780 
       24.13        18.12        28.41        12.43        53.10        14.27 
TCGA-12-0819 TCGA-12-0826 TCGA-12-0829 TCGA-12-1094 TCGA-12-1099 TCGA-12-1598 
       24.79        27.78        20.58        11.38         3.42         9.44 
TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 
       25.28        13.61         6.41        25.78        11.54        10.95 
TCGA-12-3652 TCGA-12-3653 TCGA-14-0783 TCGA-14-0789 TCGA-14-0790 TCGA-14-0817 
       34.52        11.74         6.21        11.24        13.78         5.39 
TCGA-14-0866 TCGA-14-0867 TCGA-14-1034 TCGA-14-1402 TCGA-14-1450 TCGA-14-1452 
       26.33         2.04        15.95        32.05        58.78         7.10 
TCGA-14-1454 TCGA-14-1823 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 TCGA-14-4157 
       30.18        17.85         7.17        17.49         7.96         3.42 
TCGA-15-1446 TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 TCGA-16-1055 TCGA-16-1056 
       19.10         5.52         3.91         9.93         9.90        13.35 
TCGA-16-1062 TCGA-19-0955 TCGA-19-1386 TCGA-19-1388 TCGA-19-1390 TCGA-19-1392 
       18.28        11.77         9.07        12.95        25.38         3.48 
TCGA-19-1786 TCGA-19-1789 TCGA-19-2629 TCGA-19-5950 TCGA-19-5951 TCGA-19-5953 
        7.17         3.25        16.47        11.28         8.02         4.73 
TCGA-19-5955 TCGA-19-5958 TCGA-19-5959 TCGA-26-1799 TCGA-26-5139 TCGA-27-1833 
        1.78         5.39         5.29         9.37         1.58        18.25 
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 
       15.58        14.53        14.20        13.64         4.21         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        21.17        21.14        12.59        10.62 
TCGA-41-2572 TCGA-41-2575 TCGA-41-3393 TCGA-41-3915 TCGA-41-5651 TCGA-74-6578 
       13.35         9.53         4.44        11.84        11.54        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 
       17.72        26.30 

$`19P GAIN WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0010 TCGA-02-0011 TCGA-02-0014 
        9.17         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        10.36        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         0.23        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         0.16 
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-02-2470 
       47.11        11.34         9.27        16.21         3.35        12.92 
TCGA-02-2483 TCGA-02-2486 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 
       15.32        16.21        22.72        32.52        10.52        18.74 
TCGA-06-0133 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 
       14.07        22.16        10.75         0.20         9.21         2.20 
TCGA-06-0143 TCGA-06-0146 TCGA-06-0149 TCGA-06-0160 TCGA-06-0162 TCGA-06-0165 
       11.74        20.09         7.86        11.80         2.56        10.65 
TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0175 TCGA-06-0176 
        5.29        19.04         3.12        13.02         2.73        91.00 
TCGA-06-0178 TCGA-06-0182 TCGA-06-0184 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 
       53.98         2.53        40.37        26.33        28.47        14.93 
TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0210 TCGA-06-0213 TCGA-06-0214 
        4.67         7.04         2.60         4.96         0.20        12.43 
TCGA-06-0219 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0397 TCGA-06-0412 
        0.36        11.80        20.42        14.96         5.52         8.05 
TCGA-06-0413 TCGA-06-0644 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0686 
        0.16        12.33         4.47         9.67         2.04         9.40 
TCGA-06-0745 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0878 
        5.39         2.17         0.92        43.46        46.19         7.17 
TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1800 TCGA-06-1801 
        5.85         5.42        20.94         7.43        26.79         8.65 
TCGA-06-1804 TCGA-06-1805 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 
       13.61        33.90         1.08         0.76         4.93         9.27 
TCGA-06-2562 TCGA-06-2564 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 
        2.83         5.95         5.98         4.37         0.43        31.50 
TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 TCGA-06-5418 
       11.24         3.55         8.35         4.54         8.81         2.73 
TCGA-06-5856 TCGA-06-5858 TCGA-06-5859 TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 
        3.75         6.15         4.57         7.79         5.39         1.48 
TCGA-06-6693 TCGA-06-6694 TCGA-06-6697 TCGA-06-6698 TCGA-06-6700 TCGA-06-6701 
        0.49         7.36        12.85         4.77         4.77         4.96 
TCGA-06-A5U1 TCGA-06-A6S1 TCGA-08-0244 TCGA-08-0245 TCGA-08-0344 TCGA-08-0345 
        1.87         2.56        22.68        34.75       108.82         1.74 
TCGA-08-0346 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0354 
        4.34        10.39         7.59         3.42        53.82        15.06 
TCGA-08-0358 TCGA-08-0359 TCGA-08-0380 TCGA-08-0389 TCGA-08-0392 TCGA-08-0512 
       19.53         0.95        10.85         3.19         0.30        11.77 
TCGA-08-0516 TCGA-08-0517 TCGA-08-0520 TCGA-08-0521 TCGA-12-0615 TCGA-12-0616 
       18.44        58.19        10.75         4.80        14.01        14.43 
TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0662 
        1.64        10.39         5.95         7.17        65.92        38.17 
TCGA-12-0691 TCGA-12-0692 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 
        6.12         2.63        43.10         5.49         9.11        14.86 
TCGA-12-0818 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 TCGA-12-0827 TCGA-12-0828 
       91.76        18.48        10.62        23.51        38.76         8.94 
TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 
      127.59         5.82         6.25        30.54        21.63        11.97 
TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-3644 TCGA-12-3646 
       15.85         9.11        14.53         3.98        59.41        43.23 
TCGA-12-3651 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 
       11.77        13.12         3.22         2.04        15.12        11.97 
TCGA-14-0781 TCGA-14-0786 TCGA-14-0787 TCGA-14-0812 TCGA-14-0813 TCGA-14-0862 
        0.95        23.05         2.24         3.25         1.35         2.89 
TCGA-14-0865 TCGA-14-0871 TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 TCGA-14-1396 
       16.50        28.93        19.30         0.79         1.38         1.12 
TCGA-14-1401 TCGA-14-1451 TCGA-14-1453 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 
        3.75        23.11         1.15         0.92        40.96         6.15 
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-14-3477 TCGA-15-0742 TCGA-15-1444 TCGA-15-1447 TCGA-16-0849 TCGA-16-0850 
        3.78         9.86        50.53        53.19        26.07        16.31 
TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1060 TCGA-16-1063 TCGA-16-1460 
        4.31        29.03         0.82         3.65        13.97         6.41 
TCGA-19-0957 TCGA-19-0960 TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 
       21.90         8.61         0.43        14.27         3.39        10.75 
TCGA-19-1387 TCGA-19-1389 TCGA-19-1787 TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 
        5.95         4.64        12.66         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-19-5952 TCGA-19-5954 TCGA-19-5956 TCGA-19-5960 TCGA-19-A6J4 
        6.64        18.64         7.96         6.51         5.42         3.98 
TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 
       16.57        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         1.22         7.92 
TCGA-26-6174 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1834 TCGA-27-1835 
        2.33         4.80        16.60         9.86        33.14        21.30 
TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2519 TCGA-27-2523 TCGA-27-2526 
       30.05        14.04        11.51        10.39        16.08         2.86 
TCGA-27-2527 TCGA-28-1746 TCGA-28-1747 TCGA-28-1750 TCGA-28-1755 TCGA-28-1756 
       14.40         0.20         2.53         8.35         1.55         2.83 
TCGA-28-1757 TCGA-28-2509 TCGA-28-5204 TCGA-28-5207 TCGA-28-5211 TCGA-28-5213 
        0.13         4.77         3.91         9.04        11.77        31.27 
TCGA-28-5215 TCGA-28-5219 TCGA-28-5220 TCGA-32-1973 TCGA-32-1976 TCGA-32-1980 
        7.79        22.68        10.49        21.07         0.49         1.18 
TCGA-32-1986 TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 TCGA-32-2615 TCGA-32-2616 
       12.69        16.93        12.23        20.78        15.95         7.36 
TCGA-32-2634 TCGA-32-4210 TCGA-32-4213 TCGA-32-4719 TCGA-41-2571 TCGA-41-2573 
       22.78         3.72        19.86        10.85         0.85         8.94 
TCGA-41-3392 TCGA-41-4097 TCGA-41-6646 TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 
        0.99         0.20         7.76         3.45        20.91         4.34 
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-76-6282 
        9.17        10.78        16.70         3.29         2.70        17.06 
TCGA-76-6285 TCGA-76-6286 TCGA-76-6657 TCGA-76-6662 TCGA-81-5910 TCGA-OX-A56R 
        8.35        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 
             11.38               9.17 
[1] "0.1 - 100.0 (11.4)" "0.1 - 127.6 (9.2)" 
[1] "hr=" "1.1"
D34V2, continuous
D34V3, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    87 131
  19P GAIN WILD-TYPE 133 209
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     87  131
  19P GAIN WILD-TYPE  133  209
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE               87                133
  MALE                131                209
[1] 2 2
[1] FALSE
D34V4, continuous
                    vv
clus                 GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  19P GAIN MUTATED                               6                  10
  19P GAIN WILD-TYPE                            11                   8
                    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)                  6                 11
  TREATED PRIMARY GBM                           10                  8
  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   151  67
  19P GAIN WILD-TYPE 231 111
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED    151   67
  19P GAIN WILD-TYPE  231  111
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  NO               151                231
  YES               67                111
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19P GAIN MUTATED       7                        15   189
  19P GAIN WILD-TYPE     6                        24   296
D34V7, multiclass
                           clus
vv                          19P GAIN MUTATED 19P GAIN WILD-TYPE
  ASIAN                                    7                  6
  BLACK OR AFRICAN AMERICAN               15                 24
  WHITE                                  189                296
[1] 3 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     6 179
  19P GAIN WILD-TYPE   6 283
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      6  179
  19P GAIN WILD-TYPE    6  283
                        clus
vv                       19P GAIN MUTATED 19P GAIN WILD-TYPE
  HISPANIC OR LATINO                    6                  6
  NOT HISPANIC OR LATINO              179                283
[1] 2 2
[1] FALSE

Clustering(35) Variable = 19Q GAIN MUTATION ANALYSIS
D35V1, survival
                    sevent
clus2                  0   1
  19Q GAIN MUTATED    33 160
  19Q GAIN WILD-TYPE  65 302
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
               193                367 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
               160                302 
$`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        55.86        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         0.26        47.31         0.10         3.58 
TCGA-06-0137 TCGA-06-0145 TCGA-06-0147 TCGA-06-0148 TCGA-06-0150 TCGA-06-0151 
       23.08         2.33        16.70         9.80        19.46        46.59 
TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0164 TCGA-06-0173 
        8.65         3.19         5.46         9.44        56.88         0.23 
TCGA-06-0174 TCGA-06-0177 TCGA-06-0179 TCGA-06-0182 TCGA-06-0185 TCGA-06-0190 
        2.20         2.01        19.00         2.53        73.84        10.29 
TCGA-06-0192 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0211 
       18.31         0.39         6.48         5.49         3.91        11.84 
TCGA-06-0216 TCGA-06-0237 TCGA-06-0394 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 
       22.49        10.36        10.32         0.26        70.52         4.70 
TCGA-06-0414 TCGA-06-0645 TCGA-06-0650 TCGA-06-0743 TCGA-06-0744 TCGA-06-0877 
       35.01         3.22        23.57        22.32        19.56         5.65 
TCGA-06-0879 TCGA-06-1086 TCGA-06-1087 TCGA-06-1802 TCGA-06-1806 TCGA-06-2563 
       22.98         6.35         3.58         7.89        15.32        30.64 
TCGA-06-2565 TCGA-06-5414 TCGA-06-5415 TCGA-06-6388 TCGA-06-6695 TCGA-06-A6S0 
        6.81         8.98         8.55         3.95         8.32         3.12 
TCGA-08-0246 TCGA-08-0347 TCGA-08-0352 TCGA-08-0355 TCGA-08-0356 TCGA-08-0375 
        3.91        13.78         1.28        22.52        14.70         9.17 
TCGA-08-0386 TCGA-08-0390 TCGA-08-0509 TCGA-08-0510 TCGA-08-0514 TCGA-08-0518 
       15.72        10.59         0.56         3.52         8.52         1.28 
TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0657 TCGA-12-0670 
        6.54        15.98        17.33         5.52         0.10        25.97 
TCGA-12-0688 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0778 
       24.13        18.12        28.41        12.43        53.10        14.86 
TCGA-12-0780 TCGA-12-0819 TCGA-12-0826 TCGA-12-0829 TCGA-12-1094 TCGA-12-1099 
       14.27        24.79        27.78        20.58        11.38         3.42 
TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 
       25.28        13.61         6.41        25.78        11.54        10.95 
TCGA-12-3652 TCGA-12-3653 TCGA-14-0789 TCGA-14-0790 TCGA-14-0817 TCGA-14-0866 
       34.52        11.74        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-19-1388 
        9.93         9.90        18.28        11.77         9.07        12.95 
TCGA-19-1390 TCGA-19-1392 TCGA-19-1786 TCGA-19-1789 TCGA-19-2620 TCGA-19-5950 
       25.38         3.48         7.17         3.25         4.87        11.28 
TCGA-19-5953 TCGA-19-5955 TCGA-26-1799 TCGA-26-5139 TCGA-27-1833 TCGA-27-2518 
        4.73         1.78         9.37         1.58        18.25        24.76 
TCGA-27-2521 TCGA-27-2524 TCGA-27-2528 TCGA-28-1749 TCGA-28-1751 TCGA-28-1752 
       10.39         7.59        15.78         9.21         7.63         8.48 
TCGA-28-1753 TCGA-28-2506 TCGA-28-2513 TCGA-28-2514 TCGA-28-5208 TCGA-28-5209 
        1.22         6.74         7.30         5.26        15.58        14.53 
TCGA-28-5214 TCGA-28-5216 TCGA-28-5218 TCGA-28-6450 TCGA-32-1977 TCGA-32-1978 
       14.20        13.64         4.21         5.42         0.10        15.85 
TCGA-32-1979 TCGA-32-1982 TCGA-32-2495 TCGA-32-2632 TCGA-32-2638 TCGA-32-5222 
       19.50         4.67        15.02         8.84        21.17        10.62 
TCGA-41-2572 TCGA-41-3393 TCGA-41-3915 TCGA-41-5651 TCGA-74-6578 TCGA-76-4934 
       13.35         4.44        11.84        11.54        14.33         2.53 
TCGA-76-6280 TCGA-76-6656 TCGA-76-6661 TCGA-76-6663 TCGA-76-6664 TCGA-81-5911 
       11.38         4.83         0.23         7.73         7.79        17.72 
TCGA-87-5896 
       26.30 

$`19Q GAIN WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0010 TCGA-02-0011 
        9.17         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        10.36        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         0.23        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         0.16        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        16.21 
TCGA-06-0124 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 
        4.04        22.72        32.52        10.52        18.74        14.07 
TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 
       22.16        10.75         0.20         9.21         2.20        11.74 
TCGA-06-0146 TCGA-06-0149 TCGA-06-0152 TCGA-06-0154 TCGA-06-0160 TCGA-06-0162 
       20.09         7.86        11.80        12.79        11.80         2.56 
TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0175 
       10.65         5.29        19.04         3.12        13.02         2.73 
TCGA-06-0176 TCGA-06-0178 TCGA-06-0184 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 
       91.00        53.98        40.37        26.33        28.47        14.93 
TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0210 TCGA-06-0213 TCGA-06-0214 
        4.67         7.04         2.60         4.96         0.20        12.43 
TCGA-06-0219 TCGA-06-0221 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0397 
        0.36        18.02        11.80        20.42        14.96         5.52 
TCGA-06-0412 TCGA-06-0413 TCGA-06-0644 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 
        8.05         0.16        12.33         4.47         9.67         2.04 
TCGA-06-0686 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 
        9.40         5.39         2.70         2.17         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         5.85         5.42        20.94         7.43 
TCGA-06-1800 TCGA-06-1801 TCGA-06-1804 TCGA-06-1805 TCGA-06-2557 TCGA-06-2558 
       26.79         8.65        13.61        33.90         1.08         0.76 
TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2564 TCGA-06-2566 TCGA-06-2567 
        4.93         9.27         2.83         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        11.24         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         0.49         7.36        12.85 
TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U1 TCGA-06-A6S1 
        4.77         1.55         4.77         4.96         1.87         2.56 
TCGA-08-0244 TCGA-08-0245 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0348 
       22.68        34.75       108.82         1.74         4.34        10.39 
TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0353 TCGA-08-0354 TCGA-08-0357 
        7.59         3.42        53.82         6.41        15.06        35.64 
TCGA-08-0358 TCGA-08-0359 TCGA-08-0380 TCGA-08-0389 TCGA-08-0392 TCGA-08-0512 
       19.53         0.95        10.85         3.19         0.30        11.77 
TCGA-08-0516 TCGA-08-0517 TCGA-08-0520 TCGA-08-0521 TCGA-12-0615 TCGA-12-0616 
       18.44        58.19        10.75         4.80        14.01        14.43 
TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0662 
        1.64        10.39         5.95         7.17        65.92        38.17 
TCGA-12-0691 TCGA-12-0692 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0818 
        6.12         2.63        43.10         5.49         9.11        91.76 
TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 TCGA-12-0827 TCGA-12-0828 TCGA-12-1088 
       18.48        10.62        23.51        38.76         8.94       127.59 
TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 TCGA-12-1095 
        5.82         6.25        30.54        21.63        11.97        15.85 
TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1598 TCGA-12-3644 TCGA-12-3646 
        9.11        14.53         3.98         9.44        59.41        43.23 
TCGA-12-3651 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 
       11.77        13.12         3.22         2.04        15.12        11.97 
TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 TCGA-14-0787 TCGA-14-0812 TCGA-14-0813 
        0.95         6.21        23.05         2.24         3.25         1.35 
TCGA-14-0862 TCGA-14-0865 TCGA-14-0871 TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 
        2.89        16.50        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-14-1794 TCGA-14-1795 TCGA-14-1821 
       40.96         6.15        12.43         0.99         1.97        17.79 
TCGA-14-1825 TCGA-14-1827 TCGA-14-4157 TCGA-15-0742 TCGA-15-1444 TCGA-15-1447 
        7.63         5.88         3.42         9.86        50.53        53.19 
TCGA-15-1449 TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 
        5.52        26.07        16.31         4.31        29.03         0.82 
TCGA-16-1056 TCGA-16-1060 TCGA-16-1063 TCGA-16-1460 TCGA-19-0957 TCGA-19-0960 
       13.35         3.65        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 
        0.43        14.27         3.39        10.75         5.95         4.64 
TCGA-19-1787 TCGA-19-1791 TCGA-19-2619 TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 
       12.66         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-19-5951 
        4.08        16.47         7.00         7.04         6.64         8.02 
TCGA-19-5952 TCGA-19-5954 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 
       18.64         7.96         6.51         5.39         5.29         5.42 
TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 
        3.98        16.57        10.03        13.87         9.73        31.33 
TCGA-26-1443 TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 
        7.13         9.40        14.86         5.49         8.88         1.22 
TCGA-26-6173 TCGA-26-6174 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1834 
        7.92         2.33         4.80        16.60         9.86        33.14 
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         3.91         9.04 
TCGA-28-5211 TCGA-28-5213 TCGA-28-5215 TCGA-28-5219 TCGA-28-5220 TCGA-32-1970 
       11.77        31.27         7.79        22.68        10.49        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         7.76         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 
             11.38               9.27 
[1] "0.1 - 92.7 (11.4)" "0.1 - 127.6 (9.3)"
[1] "hr=" "1.1"
D35V2, continuous
D35V3, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    78 115
  19Q GAIN WILD-TYPE 142 225
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     78  115
  19Q GAIN WILD-TYPE  142  225
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE               78                142
  MALE                115                225
[1] 2 2
[1] FALSE
D35V4, continuous
                    vv
clus                 GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  19Q GAIN MUTATED                               6                   7
  19Q GAIN WILD-TYPE                            11                  11
                    vv
clus                 UNTREATED PRIMARY (DE NOVO) GBM
  19Q GAIN MUTATED                               180
  19Q GAIN WILD-TYPE                             345
D35V5, multiclass
                                 clus
vv                                19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                  6                 11
  TREATED PRIMARY GBM                            7                 11
  UNTREATED PRIMARY (DE NOVO) GBM              180                345
[1] 3 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   129  64
  19Q GAIN WILD-TYPE 253 114
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED    129   64
  19Q GAIN WILD-TYPE  253  114
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  NO               129                253
  YES               64                114
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19Q GAIN MUTATED       7                        14   165
  19Q GAIN WILD-TYPE     6                        25   320
D35V7, multiclass
                           clus
vv                          19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  ASIAN                                    7                  6
  BLACK OR AFRICAN AMERICAN               14                 25
  WHITE                                  165                320
[1] 3 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     6 159
  19Q GAIN WILD-TYPE   6 303
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      6  159
  19Q GAIN WILD-TYPE    6  303
                        clus
vv                       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    6                  6
  NOT HISPANIC OR LATINO              159                303
[1] 2 2
[1] FALSE

Clustering(36) Variable = 20P GAIN MUTATION ANALYSIS
D36V1, survival
                    sevent
clus2                  0   1
  20P GAIN MUTATED    30 186
  20P GAIN WILD-TYPE  68 276
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               216                344 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               186                276 
$`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        55.86        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         0.23         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         0.26        47.31 
TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0130 TCGA-06-0137 TCGA-06-0147 
        0.10         3.58        22.72        10.52        23.08        16.70 
TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 
        9.80         7.86        19.46        46.59        11.80        12.79 
TCGA-06-0157 TCGA-06-0158 TCGA-06-0164 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 
        3.19         5.46        56.88         3.12        13.02         0.23 
TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 TCGA-06-0179 TCGA-06-0182 
        2.20         2.73        91.00         2.01        19.00         2.53 
TCGA-06-0185 TCGA-06-0189 TCGA-06-0192 TCGA-06-0195 TCGA-06-0197 TCGA-06-0206 
       73.84        14.93        18.31         7.04         2.60         6.48 
TCGA-06-0209 TCGA-06-0211 TCGA-06-0216 TCGA-06-0237 TCGA-06-0397 TCGA-06-0402 
        3.91        11.84        22.49        10.36         5.52         0.26 
TCGA-06-0409 TCGA-06-0410 TCGA-06-0644 TCGA-06-0645 TCGA-06-0743 TCGA-06-0745 
       70.52         4.70        12.33         3.22        22.32         5.39 
TCGA-06-0747 TCGA-06-0877 TCGA-06-0882 TCGA-06-1087 TCGA-06-1802 TCGA-06-1806 
        2.70         5.65         5.42         3.58         7.89        15.32 
TCGA-06-2557 TCGA-06-2562 TCGA-06-2563 TCGA-06-2565 TCGA-06-2569 TCGA-06-5414 
        1.08         2.83        30.64         6.81         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         3.95         5.39         8.32        12.85 
TCGA-06-6698 TCGA-06-A5U1 TCGA-08-0246 TCGA-08-0352 TCGA-08-0355 TCGA-08-0356 
        4.77         1.87         3.91         1.28        22.52        14.70 
TCGA-08-0357 TCGA-08-0375 TCGA-08-0386 TCGA-08-0510 TCGA-08-0514 TCGA-08-0516 
       35.64         9.17        15.72         3.52         8.52        18.44 
TCGA-08-0518 TCGA-08-0529 TCGA-08-0531 TCGA-12-0656 TCGA-12-0670 TCGA-12-0688 
        1.28        17.33         5.52        65.92        25.97        24.13 
TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0778 TCGA-12-0780 TCGA-12-0819 
        2.63        18.12        28.41        14.86        14.27        24.79 
TCGA-12-0820 TCGA-12-0826 TCGA-12-0827 TCGA-12-0829 TCGA-12-1093 TCGA-12-1094 
       18.48        27.78        38.76        20.58        11.97        11.38 
TCGA-12-1095 TCGA-12-1600 TCGA-12-1602 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 
       15.85        13.61         6.41        43.23        25.78        11.54 
TCGA-12-3652 TCGA-12-3653 TCGA-14-0740 TCGA-14-0783 TCGA-14-0786 TCGA-14-0787 
       34.52        11.74        11.97         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-14-1453 TCGA-14-1823 TCGA-14-2554 TCGA-14-2555 
       32.05         7.10         1.15        17.85        17.49         7.96 
TCGA-15-0742 TCGA-15-1447 TCGA-15-1449 TCGA-16-0846 TCGA-16-0861 TCGA-16-1060 
        9.86        53.19         5.52         3.91         4.31         3.65 
TCGA-16-1062 TCGA-19-0955 TCGA-19-1386 TCGA-19-1388 TCGA-19-1392 TCGA-19-1786 
       18.28        11.77         9.07        12.95         3.48         7.17 
TCGA-19-1789 TCGA-19-2631 TCGA-19-5950 TCGA-19-5951 TCGA-19-5954 TCGA-19-5958 
        3.25         7.00        11.28         8.02         7.96         5.39 
TCGA-19-5959 TCGA-26-1439 TCGA-26-1440 TCGA-26-1799 TCGA-26-6173 TCGA-27-1833 
        5.29        13.87         9.73         9.37         7.92        18.25 
TCGA-27-1834 TCGA-27-1835 TCGA-27-2519 TCGA-27-2523 TCGA-27-2526 TCGA-27-2527 
       33.14        21.30        10.39        16.08         2.86        14.40 
TCGA-27-2528 TCGA-28-1749 TCGA-28-1751 TCGA-28-2506 TCGA-28-2509 TCGA-28-2513 
       15.78         9.21         7.63         6.74         4.77         7.30 
TCGA-28-5215 TCGA-28-5218 TCGA-28-6450 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 
        7.79         4.21         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-32-4210 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2575 
       21.17         3.72        10.62         0.85        13.35         9.53 
TCGA-41-3393 TCGA-41-5651 TCGA-41-6646 TCGA-74-6575 TCGA-74-6581 TCGA-76-4925 
        4.44        11.54         7.76        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 

$`20P GAIN WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 TCGA-02-0011 
        9.17         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        10.36        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         0.16        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        16.21         4.04        32.52 
TCGA-06-0132 TCGA-06-0133 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 
       18.74        14.07        22.16        10.75         0.20         9.21 
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         8.65         9.44 
TCGA-06-0160 TCGA-06-0162 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0178 
       11.80         2.56        10.65         5.29        19.04        53.98 
TCGA-06-0184 TCGA-06-0187 TCGA-06-0188 TCGA-06-0190 TCGA-06-0194 TCGA-06-0201 
       40.37        26.33        28.47        10.29         4.67         0.39 
TCGA-06-0208 TCGA-06-0210 TCGA-06-0213 TCGA-06-0214 TCGA-06-0219 TCGA-06-0221 
        5.49         4.96         0.20        12.43         0.36        18.02 
TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0412 TCGA-06-0413 
       11.80        20.42        14.96        10.32         8.05         0.16 
TCGA-06-0414 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 
       35.01         4.47         9.67         2.04        23.57         9.40 
TCGA-06-0744 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0878 
       19.56         2.17         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 
       22.98         5.85        20.94         7.43         6.35        26.79 
TCGA-06-1801 TCGA-06-1804 TCGA-06-1805 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 
        8.65        13.61        33.90         0.76         4.93         9.27 
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        11.24         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         0.49         7.36         1.55 
TCGA-06-6700 TCGA-06-6701 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-08-0244 TCGA-08-0245 
        4.77         4.96         3.12         2.56        22.68        34.75 
TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 
      108.82         1.74         4.34        13.78        10.39         7.59 
TCGA-08-0350 TCGA-08-0351 TCGA-08-0353 TCGA-08-0354 TCGA-08-0358 TCGA-08-0359 
        3.42        53.82         6.41        15.06        19.53         0.95 
TCGA-08-0380 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0512 
       10.85         3.19        10.59         0.30         0.56        11.77 
TCGA-08-0517 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-12-0615 
       58.19        10.75         4.80         6.54        15.98        14.01 
TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0657 
       14.43         1.64        10.39         5.95         7.17         0.10 
TCGA-12-0662 TCGA-12-0691 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 
       38.17         6.12        12.43        53.10        43.10         5.49 
TCGA-12-0776 TCGA-12-0818 TCGA-12-0821 TCGA-12-0822 TCGA-12-0828 TCGA-12-1088 
        9.11        91.76        10.62        23.51         8.94       127.59 
TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 TCGA-12-1092 TCGA-12-1096 TCGA-12-1097 
        5.82         6.25        30.54        21.63         9.11        14.53 
TCGA-12-1098 TCGA-12-1099 TCGA-12-1598 TCGA-12-1599 TCGA-12-3644 TCGA-12-3650 
        3.98         3.42         9.44        25.28        59.41        10.95 
TCGA-12-3651 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0781 
       11.77        13.12         3.22         2.04        15.12         0.95 
TCGA-14-0789 TCGA-14-0812 TCGA-14-0813 TCGA-14-0862 TCGA-14-0865 TCGA-14-0867 
       11.24         3.25         1.35         2.89        16.50         2.04 
TCGA-14-1034 TCGA-14-1037 TCGA-14-1396 TCGA-14-1401 TCGA-14-1450 TCGA-14-1451 
       15.95        19.30         1.12         3.75        58.78        23.11 
TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 TCGA-14-1794 
       30.18         0.92        40.96         6.15        12.43         0.99 
TCGA-14-1795 TCGA-14-1821 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-3477 
        1.97        17.79         7.63         5.88         7.17         3.78 
TCGA-14-4157 TCGA-15-1444 TCGA-15-1446 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 
        3.42        50.53        19.10         9.93        26.07        16.31 
TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1063 TCGA-16-1460 
       29.03         0.82         9.90        13.35        13.97         6.41 
TCGA-19-0957 TCGA-19-0960 TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 
       21.90         8.61         0.43        14.27         3.39        10.75 
TCGA-19-1387 TCGA-19-1389 TCGA-19-1390 TCGA-19-1787 TCGA-19-1791 TCGA-19-2619 
        5.95         4.64        25.38        12.66         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        16.47 
TCGA-19-4065 TCGA-19-5947 TCGA-19-5952 TCGA-19-5953 TCGA-19-5955 TCGA-19-5956 
        7.04         6.64        18.64         4.73         1.78         6.51 
TCGA-19-5960 TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1442 TCGA-26-1443 
        5.42         3.98        16.57        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         1.22         1.58 
TCGA-26-6174 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1836 TCGA-27-1837 
        2.33         4.80        16.60         9.86        30.05        14.04 
TCGA-27-1838 TCGA-27-2518 TCGA-27-2521 TCGA-27-2524 TCGA-28-1746 TCGA-28-1747 
       11.51        24.76        10.39         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         3.91         9.04        15.58        14.53 
TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5216 TCGA-28-5219 TCGA-28-5220 
       11.77        31.27        14.20        13.64        22.68        10.49 
TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 
       15.39        21.07         0.49         4.67        12.69        14.86 
TCGA-32-1991 TCGA-32-2494 TCGA-32-2616 TCGA-32-4208 TCGA-32-4211 TCGA-32-4213 
       16.93        20.78         7.36        21.14        12.59        19.86 
TCGA-32-4719 TCGA-41-2573 TCGA-41-3392 TCGA-41-3915 TCGA-41-4097 TCGA-74-6573 
       10.85         8.94         0.99        11.84         0.20         3.45 
TCGA-74-6577 TCGA-74-6578 TCGA-74-6584 TCGA-76-4926 TCGA-76-4928 TCGA-76-4931 
        4.34        14.33         7.50         4.54         3.09         9.17 
TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6282 
        2.53        10.78        16.70         3.29         2.70        17.06 
TCGA-76-6285 TCGA-76-6286 TCGA-76-6662 TCGA-76-6663 TCGA-81-5910 TCGA-81-5911 
        8.35        20.98         9.27         7.73         1.61        17.72 
TCGA-87-5896 TCGA-OX-A56R 
       26.30         5.92 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               0.1                0.1 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             92.65             127.59 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            10.455              9.900 
[1] "0.1 - 92.7 (10.5)" "0.1 - 127.6 (9.9)"
[1] "hr=" "1.1"
D36V2, continuous
D36V3, binary
                    cls
clus                   0   1
  20P GAIN MUTATED    91 125
  20P GAIN WILD-TYPE 129 215
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     91  125
  20P GAIN WILD-TYPE  129  215
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE               91                129
  MALE                125                215
[1] 2 2
[1] FALSE
D36V4, continuous
                    vv
clus                 GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  20P GAIN MUTATED                               5                   9
  20P GAIN WILD-TYPE                            12                   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)                  5                 12
  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  65
  20P GAIN WILD-TYPE 231 113
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED    151   65
  20P GAIN WILD-TYPE  231  113
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  NO               151                231
  YES               65                113
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20P GAIN MUTATED       9                        11   191
  20P GAIN WILD-TYPE     4                        28   294
D36V7, multiclass
                           clus
vv                          20P GAIN MUTATED 20P GAIN WILD-TYPE
  ASIAN                                    9                  4
  BLACK OR AFRICAN AMERICAN               11                 28
  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     5 185
  20P GAIN WILD-TYPE   7 277
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      5  185
  20P GAIN WILD-TYPE    7  277
                        clus
vv                       20P GAIN MUTATED 20P GAIN WILD-TYPE
  HISPANIC OR LATINO                    5                  7
  NOT HISPANIC OR LATINO              185                277
[1] 2 2
[1] FALSE

Clustering(37) Variable = 20Q GAIN MUTATION ANALYSIS
D37V1, survival
                    sevent
clus2                  0   1
  20Q GAIN MUTATED    31 183
  20Q GAIN WILD-TYPE  67 279
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               214                346 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               183                279 
$`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        55.86        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 
        0.23         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         0.26 
TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0130 TCGA-06-0137 
       47.31         0.10         3.58        22.72        10.52        23.08 
TCGA-06-0147 TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 
       16.70         9.80         7.86        19.46        46.59        11.80 
TCGA-06-0154 TCGA-06-0157 TCGA-06-0158 TCGA-06-0164 TCGA-06-0169 TCGA-06-0171 
       12.79         3.19         5.46        56.88         3.12        13.02 
TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 TCGA-06-0179 
        0.23         2.20         2.73        91.00         2.01        19.00 
TCGA-06-0182 TCGA-06-0185 TCGA-06-0189 TCGA-06-0192 TCGA-06-0195 TCGA-06-0197 
        2.53        73.84        14.93        18.31         7.04         2.60 
TCGA-06-0206 TCGA-06-0209 TCGA-06-0211 TCGA-06-0216 TCGA-06-0237 TCGA-06-0394 
        6.48         3.91        11.84        22.49        10.36        10.32 
TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 TCGA-06-0644 TCGA-06-0645 
        5.52         0.26        70.52         4.70        12.33         3.22 
TCGA-06-0743 TCGA-06-0745 TCGA-06-0747 TCGA-06-0877 TCGA-06-0879 TCGA-06-0882 
       22.32         5.39         2.70         5.65        22.98         5.42 
TCGA-06-1087 TCGA-06-1802 TCGA-06-1806 TCGA-06-2557 TCGA-06-2562 TCGA-06-2563 
        3.58         7.89        15.32         1.08         2.83        30.64 
TCGA-06-2565 TCGA-06-2569 TCGA-06-5414 TCGA-06-5415 TCGA-06-5856 TCGA-06-6388 
        6.81         0.43         8.98         8.55         3.75         3.95 
TCGA-06-6390 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-A5U1 TCGA-08-0246 
        5.39         8.32        12.85         4.77         1.87         3.91 
TCGA-08-0352 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0375 TCGA-08-0386 
        1.28        22.52        14.70        35.64         9.17        15.72 
TCGA-08-0510 TCGA-08-0514 TCGA-08-0516 TCGA-08-0518 TCGA-08-0529 TCGA-08-0531 
        3.52         8.52        18.44         1.28        17.33         5.52 
TCGA-12-0656 TCGA-12-0670 TCGA-12-0688 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 
       65.92        25.97        24.13         2.63        18.12        28.41 
TCGA-12-0780 TCGA-12-0819 TCGA-12-0820 TCGA-12-0826 TCGA-12-0829 TCGA-12-1093 
       14.27        24.79        18.48        27.78        20.58        11.97 
TCGA-12-1094 TCGA-12-1600 TCGA-12-1602 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 
       11.38        13.61         6.41        43.23        25.78        11.54 
TCGA-12-3652 TCGA-12-3653 TCGA-14-0783 TCGA-14-0786 TCGA-14-0787 TCGA-14-0790 
       34.52        11.74         6.21        23.05         2.24        13.78 
TCGA-14-0817 TCGA-14-0866 TCGA-14-0871 TCGA-14-1043 TCGA-14-1395 TCGA-14-1402 
        5.39        26.33        28.93         0.79         1.38        32.05 
TCGA-14-1452 TCGA-14-1823 TCGA-14-2554 TCGA-14-2555 TCGA-15-0742 TCGA-15-1447 
        7.10        17.85        17.49         7.96         9.86        53.19 
TCGA-15-1449 TCGA-16-0846 TCGA-16-1060 TCGA-19-0955 TCGA-19-0960 TCGA-19-1386 
        5.52         3.91         3.65        11.77         8.61         9.07 
TCGA-19-1388 TCGA-19-1392 TCGA-19-1786 TCGA-19-1789 TCGA-19-2631 TCGA-19-5950 
       12.95         3.48         7.17         3.25         7.00        11.28 
TCGA-19-5951 TCGA-19-5954 TCGA-19-5958 TCGA-19-5959 TCGA-26-1439 TCGA-26-1440 
        8.02         7.96         5.39         5.29        13.87         9.73 
TCGA-26-1799 TCGA-26-6173 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-2519 
        9.37         7.92        18.25        33.14        21.30        10.39 
TCGA-27-2521 TCGA-27-2523 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1749 
       10.39        16.08         2.86        14.40        15.78         9.21 
TCGA-28-1751 TCGA-28-2506 TCGA-28-2509 TCGA-28-2513 TCGA-28-5214 TCGA-28-5215 
        7.63         6.74         4.77         7.30        14.20         7.79 
TCGA-28-5218 TCGA-28-6450 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 TCGA-32-1980 
        4.21         5.42         0.10        15.85        19.50         1.18 
TCGA-32-2491 TCGA-32-2495 TCGA-32-2615 TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 
       12.23        15.02        15.95         8.84        22.78        21.17 
TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2575 TCGA-41-3393 TCGA-41-5651 
       10.62         0.85        13.35         9.53         4.44        11.54 
TCGA-41-6646 TCGA-74-6575 TCGA-74-6581 TCGA-76-4925 TCGA-76-4929 TCGA-76-6280 
        7.76        20.91         8.22         4.80         3.65        11.38 
TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6664 
        4.83         5.03         0.23         7.79 

$`20Q GAIN WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 TCGA-02-0011 
        9.17         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        10.36        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         0.16 
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        16.21         4.04        32.52        18.74 
TCGA-06-0133 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 
       14.07        22.16        10.75         0.20         9.21         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         8.65         9.44        11.80 
TCGA-06-0162 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0178 TCGA-06-0184 
        2.56        10.65         5.29        19.04        53.98        40.37 
TCGA-06-0187 TCGA-06-0188 TCGA-06-0190 TCGA-06-0194 TCGA-06-0201 TCGA-06-0208 
       26.33        28.47        10.29         4.67         0.39         5.49 
TCGA-06-0210 TCGA-06-0213 TCGA-06-0214 TCGA-06-0219 TCGA-06-0221 TCGA-06-0238 
        4.96         0.20        12.43         0.36        18.02        11.80 
TCGA-06-0240 TCGA-06-0241 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0646 
       20.42        14.96         8.05         0.16        35.01         4.47 
TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0744 TCGA-06-0749 
        9.67         2.04        23.57         9.40        19.56         2.17 
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         5.85        20.94 
TCGA-06-1084 TCGA-06-1086 TCGA-06-1800 TCGA-06-1801 TCGA-06-1804 TCGA-06-1805 
        7.43         6.35        26.79         8.65        13.61        33.90 
TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2564 TCGA-06-2566 TCGA-06-2567 
        0.76         4.93         9.27         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        11.24         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-A6S0 
        0.49         7.36         1.55         4.77         4.96         3.12 
TCGA-06-A6S1 TCGA-08-0244 TCGA-08-0245 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 
        2.56        22.68        34.75       108.82         1.74         4.34 
TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0353 
       13.78        10.39         7.59         3.42        53.82         6.41 
TCGA-08-0354 TCGA-08-0358 TCGA-08-0359 TCGA-08-0380 TCGA-08-0389 TCGA-08-0390 
       15.06        19.53         0.95        10.85         3.19        10.59 
TCGA-08-0392 TCGA-08-0509 TCGA-08-0512 TCGA-08-0517 TCGA-08-0520 TCGA-08-0521 
        0.30         0.56        11.77        58.19        10.75         4.80 
TCGA-08-0524 TCGA-08-0525 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 
        6.54        15.98        14.01        14.43         1.64        10.39 
TCGA-12-0620 TCGA-12-0654 TCGA-12-0657 TCGA-12-0662 TCGA-12-0691 TCGA-12-0769 
        5.95         7.17         0.10        38.17         6.12        12.43 
TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0818 
       53.10        43.10         5.49         9.11        14.86        91.76 
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-12-1095 TCGA-12-1096 TCGA-12-1097 
        6.25        30.54        21.63        15.85         9.11        14.53 
TCGA-12-1098 TCGA-12-1099 TCGA-12-1598 TCGA-12-1599 TCGA-12-3644 TCGA-12-3650 
        3.98         3.42         9.44        25.28        59.41        10.95 
TCGA-12-3651 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 
       11.77        13.12         3.22         2.04        15.12        11.97 
TCGA-14-0781 TCGA-14-0789 TCGA-14-0812 TCGA-14-0813 TCGA-14-0862 TCGA-14-0865 
        0.95        11.24         3.25         1.35         2.89        16.50 
TCGA-14-0867 TCGA-14-1034 TCGA-14-1037 TCGA-14-1396 TCGA-14-1401 TCGA-14-1450 
        2.04        15.95        19.30         1.12         3.75        58.78 
TCGA-14-1451 TCGA-14-1453 TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 
       23.11         1.15        30.18         0.92        40.96         6.15 
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         9.93 
TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 
       26.07        16.31         4.31        29.03         0.82         9.90 
TCGA-16-1056 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0957 TCGA-19-0962 
       13.35        18.28        13.97         6.41        21.90         0.43 
TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 TCGA-19-1387 TCGA-19-1389 TCGA-19-1390 
       14.27         3.39        10.75         5.95         4.64        25.38 
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-19-2629 TCGA-19-4065 TCGA-19-5947 TCGA-19-5952 
        0.16         4.08        16.47         7.04         6.64        18.64 
TCGA-19-5953 TCGA-19-5955 TCGA-19-5956 TCGA-19-5960 TCGA-19-A6J4 TCGA-19-A6J5 
        4.73         1.78         6.51         5.42         3.98        16.57 
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-27-1830 TCGA-27-1831 
        8.88         1.22         1.58         2.33         4.80        16.60 
TCGA-27-1832 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2524 
        9.86        30.05        14.04        11.51        24.76         7.59 
TCGA-28-1746 TCGA-28-1747 TCGA-28-1750 TCGA-28-1752 TCGA-28-1753 TCGA-28-1755 
        0.20         2.53         8.35         8.48         1.22         1.55 
TCGA-28-1756 TCGA-28-1757 TCGA-28-2502 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 
        2.83         0.13         0.66         5.26         3.91         9.04 
TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5216 TCGA-28-5219 
       15.58        14.53        11.77        31.27        13.64        22.68 
TCGA-28-5220 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-1982 TCGA-32-1986 
       10.49        15.39        21.07         0.49         4.67        12.69 
TCGA-32-1987 TCGA-32-1991 TCGA-32-2494 TCGA-32-2616 TCGA-32-4208 TCGA-32-4210 
       14.86        16.93        20.78         7.36        21.14         3.72 
TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-41-2573 TCGA-41-3392 TCGA-41-3915 
       12.59        19.86        10.85         8.94         0.99        11.84 
TCGA-41-4097 TCGA-74-6573 TCGA-74-6577 TCGA-74-6578 TCGA-74-6584 TCGA-76-4926 
        0.20         3.45         4.34        14.33         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-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6662 TCGA-76-6663 
        2.70        17.06         8.35        20.98         9.27         7.73 
TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R 
        1.61        17.72        26.30         5.92 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               0.1                0.1 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             92.65             127.59 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             10.39               9.88 
[1] "0.1 - 92.7 (10.4)" "0.1 - 127.6 (9.9)"
[1] "hr=" "1"  
D37V2, continuous
D37V3, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED    91 123
  20Q GAIN WILD-TYPE 129 217
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     91  123
  20Q GAIN WILD-TYPE  129  217
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE               91                129
  MALE                123                217
[1] 2 2
[1] FALSE
D37V4, continuous
                    vv
clus                 GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  20Q GAIN MUTATED                               5                   9
  20Q GAIN WILD-TYPE                            12                   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)                  5                 12
  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  64
  20Q GAIN WILD-TYPE 232 114
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED    150   64
  20Q GAIN WILD-TYPE  232  114
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  NO               150                232
  YES               64                114
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20Q GAIN MUTATED       9                        12   188
  20Q GAIN WILD-TYPE     4                        27   297
D37V7, multiclass
                           clus
vv                          20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  ASIAN                                    9                  4
  BLACK OR AFRICAN AMERICAN               12                 27
  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     5 185
  20Q GAIN WILD-TYPE   7 277
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      5  185
  20Q GAIN WILD-TYPE    7  277
                        clus
vv                       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    5                  7
  NOT HISPANIC OR LATINO              185                277
[1] 2 2
[1] FALSE

Clustering(38) Variable = 21Q GAIN MUTATION ANALYSIS
D38V1, survival
                    sevent
clus2                  0   1
  21Q GAIN MUTATED     8  54
  21Q GAIN WILD-TYPE  90 408
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                62                498 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                54                408 
$`21Q GAIN MUTATED`
TCGA-02-0001 TCGA-02-0006 TCGA-02-0025 TCGA-02-0055 TCGA-02-0069 TCGA-02-0075 
        9.17        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        10.52         0.20         7.86 
TCGA-06-0151 TCGA-06-0159 TCGA-06-0164 TCGA-06-0168 TCGA-06-0176 TCGA-06-0177 
       46.59         9.44        56.88        19.04        91.00         2.01 
TCGA-06-0188 TCGA-06-0189 TCGA-06-0197 TCGA-06-0216 TCGA-06-0237 TCGA-06-0644 
       28.47        14.93         2.60        22.49        10.36        12.33 
TCGA-06-0743 TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 TCGA-06-1806 TCGA-06-2565 
       22.32         7.43         6.35         3.58        15.32         6.81 
TCGA-06-2567 TCGA-06-5415 TCGA-06-6698 TCGA-08-0246 TCGA-08-0386 TCGA-08-0510 
        4.37         8.55         4.77         3.91        15.72         3.52 
TCGA-12-0619 TCGA-12-0822 TCGA-12-1095 TCGA-12-1602 TCGA-12-3646 TCGA-14-0871 
       10.39        23.51        15.85         6.41        43.23        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         3.48        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 
        9.04         7.79        13.64         4.21        15.95         8.84 
TCGA-41-2575 TCGA-41-3915 
        9.53        11.84 

$`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        55.86        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 
       10.36        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         0.23        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         0.16        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        16.21         2.70         0.26 
TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 
        4.04        47.31         0.10         3.58        22.72        32.52 
TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0141 
       18.74        14.07        23.08        22.16        10.75         9.21 
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        16.70         9.80 
TCGA-06-0150 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 
       19.46        11.80        12.79         8.65         3.19         5.46 
TCGA-06-0160 TCGA-06-0162 TCGA-06-0165 TCGA-06-0166 TCGA-06-0169 TCGA-06-0171 
       11.80         2.56        10.65         5.29         3.12        13.02 
TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 
        0.23         2.20         2.73        53.98        19.00         2.53 
TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 
       40.37        73.84        26.33        10.29        18.31         4.67 
TCGA-06-0195 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 
        7.04         0.39         6.48         5.49         3.91         4.96 
TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0219 TCGA-06-0221 TCGA-06-0238 
       11.84         0.20        12.43         0.36        18.02        11.80 
TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 
       20.42        14.96        10.32         5.52         0.26        70.52 
TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0645 TCGA-06-0646 
        4.70         8.05         0.16        35.01         3.22         4.47 
TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0744 TCGA-06-0745 
        9.67         2.04        23.57         9.40        19.56         5.39 
TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 
        2.70         2.17         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        22.98         5.85         5.42        20.94        26.79 
TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-2557 TCGA-06-2558 
        8.65         7.89        13.61        33.90         1.08         0.76 
TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2566 
        4.93         9.27         2.83        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        11.24         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         3.95         7.79         5.39         1.48         0.49 
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-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-08-0244 TCGA-08-0245 TCGA-08-0344 
        1.87         3.12         2.56        22.68        34.75       108.82 
TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 
        1.74         4.34        13.78        10.39         7.59         3.42 
TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 
       53.82         1.28         6.41        15.06        22.52        14.70 
TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0389 
       35.64        19.53         0.95         9.17        10.85         3.19 
TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 
       10.59         0.30         0.56        11.77         8.52        18.44 
TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 
       58.19         1.28        10.75         4.80         6.54        15.98 
TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0620 
       17.33         5.52        14.01        14.43         1.64         5.95 
TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 
        7.17        65.92         0.10        38.17        25.97        24.13 
TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 
        6.12         2.63        18.12        28.41        12.43        53.10 
TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 
       43.10         5.49         9.11        14.86        14.27        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-12-0829 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 TCGA-12-1092 
       20.58       127.59         5.82         6.25        30.54        21.63 
TCGA-12-1093 TCGA-12-1094 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 
       11.97        11.38         9.11        14.53         3.98         3.42 
TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 TCGA-12-3644 TCGA-12-3648 TCGA-12-3649 
        9.44        25.28        13.61        59.41        25.78        11.54 
TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 
       10.95        11.77        34.52        11.74        13.12         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-14-1037 TCGA-14-1043 
        2.89        16.50        26.33         2.04        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-14-1459 
        7.10         1.15         0.92        40.96         6.15        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         9.86 
TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 TCGA-16-0848 TCGA-16-0849 
       50.53        19.10        53.19         5.52         9.93        26.07 
TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 
       16.31         4.31        29.03         0.82         9.90        13.35 
TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 
        3.65        18.28        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         0.43        14.27         3.39        10.75         9.07 
TCGA-19-1387 TCGA-19-1389 TCGA-19-1390 TCGA-19-1786 TCGA-19-1789 TCGA-19-1791 
        5.95         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-19-2629 TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 
       16.47         7.00         7.04         6.64        11.28         8.02 
TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 
       18.64         4.73         7.96         1.78         6.51         5.39 
TCGA-19-5959 TCGA-19-5960 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 
        5.29         5.42        16.57        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-27-1830 
        8.88         1.22         1.58         7.92         2.33         4.80 
TCGA-27-1831 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 
       16.60        18.25        33.14        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-27-2528 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         3.91        15.58        14.53        11.77 
TCGA-28-5213 TCGA-28-5214 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 
       31.27        14.20        22.68        10.49         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-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4210 
       15.02         7.36        22.78        21.17        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        10.62         0.85        13.35 
TCGA-41-2573 TCGA-41-3392 TCGA-41-3393 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 
        8.94         0.99         4.44         0.20        11.54         7.76 
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 

  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 
            10.455              9.915 
[1] "0.2 - 92.7 (10.5)" "0.1 - 127.6 (9.9)"
[1] "hr=" "1.1"
D38V2, continuous
D38V3, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    24  38
  21Q GAIN WILD-TYPE 196 302
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     24   38
  21Q GAIN WILD-TYPE  196  302
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE               24                196
  MALE                 38                302
[1] 2 2
[1] FALSE
D38V4, continuous
                    vv
clus                 GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  21Q GAIN MUTATED                               5                   1
  21Q GAIN WILD-TYPE                            12                  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)                  5                 12
  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  20
  21Q GAIN WILD-TYPE 340 158
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     42   20
  21Q GAIN WILD-TYPE  340  158
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  NO                42                340
  YES               20                158
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  21Q GAIN MUTATED       4                         4    53
  21Q GAIN WILD-TYPE     9                        35   432
D38V7, multiclass
                           clus
vv                          21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  ASIAN                                    4                  9
  BLACK OR AFRICAN AMERICAN                4                 35
  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  55
  21Q GAIN WILD-TYPE  12 407
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      0   55
  21Q GAIN WILD-TYPE   12  407
                        clus
vv                       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 12
  NOT HISPANIC OR LATINO               55                407
[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  91 435
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                34                526 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                27                435 
$`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        10.52         3.91        70.52        35.01         6.35 
TCGA-06-1087 TCGA-06-2569 TCGA-08-0510 TCGA-12-0618 TCGA-12-0827 TCGA-12-1099 
        3.58         0.43         3.52         1.64        38.76         3.42 
TCGA-12-1602 TCGA-14-0813 TCGA-14-0871 TCGA-15-1449 TCGA-16-0846 TCGA-19-1387 
        6.41         1.35        28.93         5.52         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         7.79 
TCGA-28-5216 TCGA-28-5218 TCGA-32-2616 TCGA-32-4211 
       13.64         4.21         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 
        9.17         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        55.86        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        10.36        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         0.23        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         0.16 
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        16.21 
TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 
        2.70         0.26         4.04        47.31         0.10         3.58 
TCGA-06-0128 TCGA-06-0129 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 
       22.72        32.52        18.74        14.07        23.08        22.16 
TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 
       10.75         0.20         9.21         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        16.70         9.80         7.86        19.46        46.59 
TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 
       11.80        12.79         8.65         3.19         5.46         9.44 
TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 
       11.80         2.56        56.88        10.65         5.29        19.04 
TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 
        3.12        13.02         0.23         2.20         2.73        91.00 
TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 
        2.01        53.98        19.00         2.53        40.37        73.84 
TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 
       26.33        28.47        14.93        10.29        18.31         4.67 
TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0210 
        7.04         2.60         0.39         6.48         5.49         4.96 
TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 
       11.84         0.20        12.43        22.49         0.36        18.02 
TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 
       10.36        11.80        20.42        14.96        10.32         5.52 
TCGA-06-0402 TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0644 TCGA-06-0645 
        0.26         4.70         8.05         0.16        12.33         3.22 
TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 
        4.47         9.67         2.04        23.57         9.40        22.32 
TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 
       19.56         5.39         2.70         2.17         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        22.98         5.85         5.42 
TCGA-06-0939 TCGA-06-1084 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 
       20.94         7.43        26.79         8.65         7.89        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         0.76         4.93         9.27 
TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 
        2.83        30.64         5.95         6.81         5.98         4.37 
TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 
       31.50        11.24         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         3.95         7.79         5.39         1.48         0.49 
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-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-08-0244 TCGA-08-0245 
        4.96         1.87         3.12         2.56        22.68        34.75 
TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 
        3.91       108.82         1.74         4.34        13.78        10.39 
TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 
        7.59         3.42        53.82         1.28         6.41        15.06 
TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 
       22.52        14.70        35.64        19.53         0.95         9.17 
TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 
       10.85        15.72         3.19        10.59         0.30         0.56 
TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 
       11.77         8.52        18.44        58.19         1.28        10.75 
TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 
        4.80         6.54        15.98        17.33         5.52        14.01 
TCGA-12-0616 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 
       14.43        10.39         5.95         7.17        65.92         0.10 
TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 
       38.17        25.97        24.13         6.12         2.63        18.12 
TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 
       28.41        12.43        53.10        43.10         5.49         9.11 
TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 
       14.86        14.27        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 
        6.25        30.54        21.63        11.97        11.38        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         9.44        25.28        13.61 
TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 
       59.41        43.23        25.78        11.54        10.95        11.77 
TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 
       34.52        11.74        13.12         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-14-0817 TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 
       13.78         3.25         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-14-1458 TCGA-14-1459 TCGA-14-1794 
       30.18         0.92        40.96         6.15        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         9.86        50.53 
TCGA-15-1446 TCGA-15-1447 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 
       19.10        53.19         9.93        26.07        16.31         4.31 
TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 
       29.03         0.82         9.90        13.35         3.65        18.28 
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         0.43 
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         3.48 
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        16.47         7.00 
TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 
        6.64        11.28         8.02        18.64         4.73         7.96 
TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A6J4 
        1.78         6.51         5.39         5.29         5.42         3.98 
TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 
       16.57        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         1.22 
TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 
        1.58         7.92         2.33         4.80        16.60         9.86 
TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 
       18.25        33.14        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-28-2506 
        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         3.91         9.04        15.58 
TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5219 TCGA-28-5220 
       14.53        11.77        31.27        14.20        22.68        10.49 
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-32-2632 TCGA-32-2634 
       12.23        20.78        15.02        15.95         8.84        22.78 
TCGA-32-2638 TCGA-32-4208 TCGA-32-4210 TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 
       21.17        21.14         3.72        19.86        10.85        10.62 
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-74-6573 TCGA-74-6575 
       11.84         0.20        11.54         7.76         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 
        1.61        17.72        26.30         5.92 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
               0.2                0.1 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             70.52             127.59 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              7.20              10.36 
[1] "0.2 - 70.5 (7.2)"   "0.1 - 127.6 (10.4)"
[1] "hr=" "1.2"
D39V2, continuous
D39V3, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    13  21
  22Q GAIN WILD-TYPE 207 319
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     13   21
  22Q GAIN WILD-TYPE  207  319
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE               13                207
  MALE                 21                319
[1] 2 2
[1] FALSE
D39V4, continuous
                    vv
clus                 GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  22Q GAIN MUTATED                               0                   0
  22Q GAIN WILD-TYPE                            17                  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                 17
  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 359 167
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     23   11
  22Q GAIN WILD-TYPE  359  167
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  NO                23                359
  YES               11                167
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  22Q GAIN MUTATED       1                         3    29
  22Q GAIN WILD-TYPE    12                        36   456
D39V7, multiclass
                           clus
vv                          22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  ASIAN                                    1                 12
  BLACK OR AFRICAN AMERICAN                3                 36
  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  10 436
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      2   26
  22Q GAIN WILD-TYPE   10  436
                        clus
vv                       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                 10
  NOT HISPANIC OR LATINO               26                436
[1] 2 2
[1] FALSE

Clustering(40) Variable = XQ GAIN MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                 0   1
  XQ GAIN MUTATED     2  14
  XQ GAIN WILD-TYPE  96 448
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               16               544 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               14               448 
$`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        22.32 
TCGA-06-6698 TCGA-12-0773 TCGA-14-1455 TCGA-14-1823 TCGA-19-1787 TCGA-26-1799 
        4.77        43.10         0.92        17.85        12.66         9.37 
TCGA-28-5209 TCGA-28-5218 TCGA-32-2632 TCGA-32-4210 
       14.53         4.21         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 
        9.17         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        55.86        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        10.36        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         0.23        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         0.16        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        16.21         2.70         0.26         4.04 
TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 
       47.31         0.10         3.58        22.72        32.52        10.52 
TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 
       18.74        14.07        23.08        22.16        10.75         0.20 
TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 
        9.21         2.20        11.74         2.33        20.09        16.70 
TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 
        9.80         7.86        19.46        11.80        12.79         8.65 
TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 
        3.19         5.46         9.44        11.80         2.56        56.88 
TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 
       10.65         5.29        19.04         3.12        13.02         0.23 
TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 
        2.20         2.73        91.00         2.01        53.98        19.00 
TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 
        2.53        40.37        73.84        26.33        28.47        14.93 
TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 
       10.29        18.31         4.67         7.04         2.60         0.39 
TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 
        6.48         5.49         3.91         4.96        11.84         0.20 
TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 
       12.43        22.49         0.36        18.02        10.36        11.80 
TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 
       20.42        14.96        10.32         5.52         0.26        70.52 
TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 
        4.70         8.05         0.16        35.01        12.33         3.22 
TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0744 
        4.47         9.67         2.04        23.57         9.40        19.56 
TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 
        5.39         2.70         2.17         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        22.98         5.85         5.42        20.94 
TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 
        7.43         6.35         3.58        26.79         8.65         7.89 
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         0.76         4.93 
TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 
        9.27         2.83        30.64         5.95         6.81         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        11.24         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         3.95         7.79         5.39 
TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 TCGA-06-6699 
        1.48         0.49         7.36         8.32        12.85         1.55 
TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-08-0244 
        4.77         4.96         1.87         3.12         2.56        22.68 
TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 
       34.75         3.91       108.82         1.74         4.34        13.78 
TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 
       10.39         7.59         3.42        53.82         1.28         6.41 
TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 
       15.06        22.52        14.70        35.64        19.53         0.95 
TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 
        9.17        10.85        15.72         3.19        10.59         0.30 
TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 
        0.56         3.52        11.77         8.52        18.44        58.19 
TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 
        1.28        10.75         4.80         6.54        15.98        17.33 
TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 
        5.52        14.01        14.43         1.64        10.39         5.95 
TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 
        7.17        65.92         0.10        38.17        25.97        24.13 
TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 
        6.12         2.63        18.12        28.41        12.43        53.10 
TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 
        5.49         9.11        14.86        14.27        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         6.25        30.54        21.63 
TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 
       11.97        11.38        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 
        3.42         9.44        25.28        13.61         6.41        59.41 
TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 
       43.23        25.78        11.54        10.95        11.77        34.52 
TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 
       11.74        13.12         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-14-1456 TCGA-14-1458 TCGA-14-1459 TCGA-14-1794 
        1.15        30.18        40.96         6.15        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         9.86        50.53        19.10 
TCGA-15-1447 TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 
       53.19         5.52         3.91         9.93        26.07        16.31 
TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 
        4.31        29.03         0.82         9.90        13.35         3.65 
TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 
       18.28        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 
        0.43        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-19-1789 
       12.95         4.64        25.38         3.48         7.17         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        16.47         7.00         7.04         6.64        11.28 
TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 
        8.02        18.64         4.73         7.96         1.78         6.51 
TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 
        5.39         5.29         5.42         3.98        16.57        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-26-5139 TCGA-26-6173 TCGA-26-6174 
        5.49         8.88         1.22         1.58         7.92         2.33 
TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 
        4.80        16.60         9.86        18.25        33.14        21.30 
TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 
       30.05        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-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5211 
        7.30         5.26         3.91         9.04        15.58        11.77 
TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5219 TCGA-28-5220 
       31.27        14.20         7.79        13.64        22.68        10.49 
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-32-2634 
       12.23        20.78        15.02        15.95         7.36        22.78 
TCGA-32-2638 TCGA-32-4208 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 
       21.17        21.14        12.59        19.86        10.85        10.62 
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-74-6573 TCGA-74-6575 
       11.84         0.20        11.54         7.76         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 
        1.61        17.72        26.30         5.92 

  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            10.110 
[1] "0.9 - 46.6 (11.0)"  "0.1 - 127.6 (10.1)"
[1] "hr=" "1"  
D40V2, continuous
D40V3, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     6  10
  XQ GAIN WILD-TYPE 214 330
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      6   10
  XQ GAIN WILD-TYPE  214  330
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE               6               214
  MALE                10               330
[1] 2 2
[1] FALSE
D40V4, continuous
                   vv
clus                GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  XQ GAIN MUTATED                               1                   1
  XQ GAIN WILD-TYPE                            16                  17
                   vv
clus                UNTREATED PRIMARY (DE NOVO) GBM
  XQ GAIN MUTATED                                14
  XQ GAIN WILD-TYPE                             511
D40V5, multiclass
                                 clus
vv                                XQ GAIN MUTATED XQ GAIN WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                 1                16
  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"
D40V6, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     8   8
  XQ GAIN WILD-TYPE 374 170
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      8    8
  XQ GAIN WILD-TYPE  374  170
     clus
vv    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  NO                8               374
  YES               8               170
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XQ GAIN MUTATED       0                         0    14
  XQ GAIN WILD-TYPE    13                        39   471
D40V7, multiclass
                           clus
vv                          XQ GAIN MUTATED XQ GAIN WILD-TYPE
  ASIAN                                   0                13
  BLACK OR AFRICAN AMERICAN               0                39
  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"
D40V8, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     1  10
  XQ GAIN WILD-TYPE  11 452
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      1   10
  XQ GAIN WILD-TYPE   11  452
                        clus
vv                       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                11
  NOT HISPANIC OR LATINO              10               452
[1] 2 2
[1] FALSE

Clustering(41) Variable = 1P LOSS MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                 0   1
  1P LOSS MUTATED     2  13
  1P LOSS WILD-TYPE  96 449
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               15               545 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               13               449 
$`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       108.82 
TCGA-08-0392 TCGA-08-0510 TCGA-14-0740 TCGA-19-1387 TCGA-19-1388 TCGA-19-1390 
        0.30         3.52        11.97         5.95        12.95        25.38 
TCGA-19-2629 TCGA-41-4097 TCGA-74-6575 
       16.47         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 
        9.17         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        55.86        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        10.36         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         0.23        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         0.16        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        16.21         2.70         0.26 
TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 
        4.04        47.31         0.10         3.58        22.72        32.52 
TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 
       10.52        18.74        14.07        23.08        22.16        10.75 
TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 
        0.20         9.21         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 
       16.70         9.80         7.86        19.46        46.59        11.80 
TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 
       12.79         8.65         3.19         5.46         9.44        11.80 
TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 
        2.56        56.88        10.65         5.29        19.04         3.12 
TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 
       13.02         0.23         2.20         2.73        91.00         2.01 
TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 
       53.98        19.00         2.53        40.37        73.84        26.33 
TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 
       28.47        14.93        10.29        18.31         4.67         7.04 
TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 
        2.60         0.39         6.48         5.49         3.91         4.96 
TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 
       11.84         0.20        12.43        22.49         0.36        18.02 
TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 
       10.36        11.80        20.42        14.96        10.32         5.52 
TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 
        0.26        70.52         4.70         8.05         0.16        35.01 
TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 
       12.33         3.22         4.47         9.67         2.04        23.57 
TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 
        9.40        22.32        19.56         5.39         2.70         2.17 
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        22.98 
TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 
        5.85         5.42        20.94         7.43         6.35         3.58 
TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 
       26.79         8.65         7.89        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         0.76         4.93         9.27         2.83        30.64 
TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 
        5.95         6.81         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 
       11.24         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         3.95 
TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 
        7.79         5.39         1.48         0.49         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-08-0245 TCGA-08-0246 TCGA-08-0345 TCGA-08-0346 
        3.12         2.56        34.75         3.91         1.74         4.34 
TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 
       13.78        10.39         7.59         3.42        53.82         1.28 
TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 
        6.41        15.06        22.52        14.70        35.64        19.53 
TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 
        0.95         9.17        10.85        15.72         3.19        10.59 
TCGA-08-0509 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 
        0.56        11.77         8.52        18.44        58.19         1.28 
TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 
       10.75         4.80         6.54        15.98        17.33         5.52 
TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 
       14.01        14.43         1.64        10.39         5.95         7.17 
TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 
       65.92         0.10        38.17        25.97        24.13         6.12 
TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 
        2.63        18.12        28.41        12.43        53.10        43.10 
TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 
        5.49         9.11        14.86        14.27        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         6.25        30.54        21.63 
TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 
       11.97        11.38        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 
        3.42         9.44        25.28        13.61         6.41        59.41 
TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 
       43.23        25.78        11.54        10.95        11.77        34.52 
TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0781 
       11.74        13.12         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-14-0817 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         6.15        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         9.86        50.53 
TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 
       19.10        53.19         5.52         3.91         9.93        26.07 
TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 
       16.31         4.31        29.03         0.82         9.90        13.35 
TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 
        3.65        18.28        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         0.43        14.27         3.39        10.75         9.07 
TCGA-19-1389 TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 
        4.64         3.48         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-19-4065 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 
        7.00         7.04         6.64        11.28         8.02        18.64 
TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 
        4.73         7.96         1.78         6.51         5.39         5.29 
TCGA-19-5960 TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 
        5.42         3.98        16.57        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-27-1830 
        8.88         1.22         1.58         7.92         2.33         4.80 
TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 
       16.60         9.86        18.25        33.14        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         3.91         9.04        15.58        14.53        11.77 
TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 
       31.27        14.20         7.79        13.64         4.21        22.68 
TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 
       10.49         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        21.17        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        10.62         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        11.54         7.76 
TCGA-74-6573 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 TCGA-76-4925 
        3.45         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 
        7.79         1.61        17.72        26.30         5.92 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
              0.2               0.1 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           108.82            127.59 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            11.97              9.93 
[1] "0.2 - 108.8 (12.0)" "0.1 - 127.6 (9.9)" 
[1] "hr=" "1.4"
D41V2, continuous
D41V3, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     4  11
  1P LOSS WILD-TYPE 216 329
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      4   11
  1P LOSS WILD-TYPE  216  329
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE               4               216
  MALE                11               329
[1] 2 2
[1] FALSE
D41V4, continuous
                   vv
clus                GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  1P LOSS MUTATED                               0                   1
  1P LOSS WILD-TYPE                            17                  17
                   vv
clus                UNTREATED PRIMARY (DE NOVO) GBM
  1P LOSS MUTATED                                14
  1P LOSS WILD-TYPE                             511
D41V5, multiclass
                                 clus
vv                                1P LOSS MUTATED 1P LOSS WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                 0                17
  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
  1P LOSS MUTATED     9   6
  1P LOSS WILD-TYPE 373 172
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      9    6
  1P LOSS WILD-TYPE  373  172
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  NO                9               373
  YES               6               172
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1P LOSS MUTATED       0                         0    14
  1P LOSS WILD-TYPE    13                        39   471
D41V7, multiclass
                           clus
vv                          1P LOSS MUTATED 1P LOSS WILD-TYPE
  ASIAN                                   0                13
  BLACK OR AFRICAN AMERICAN               0                39
  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
  1P LOSS MUTATED     0  13
  1P LOSS WILD-TYPE  12 449
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      0   13
  1P LOSS WILD-TYPE   12  449
                        clus
vv                       1P LOSS MUTATED 1P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                12
  NOT HISPANIC OR LATINO              13               449
[1] 2 2
[1] FALSE

Clustering(42) Variable = 1Q LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                 0   1
  1Q LOSS MUTATED     2  12
  1Q LOSS WILD-TYPE  96 450
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               14               546 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               12               450 
$`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         0.30         3.52 
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        16.47 
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 
        9.17         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        55.86        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        10.36        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         0.23        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         0.16        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        16.21         2.70 
TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 
        0.26         4.04        47.31         0.10         3.58        22.72 
TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 
       32.52        10.52        18.74        14.07        23.08        22.16 
TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 
       10.75         0.20         9.21         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        16.70         9.80         7.86        19.46        46.59 
TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 
       11.80        12.79         8.65         3.19         5.46         9.44 
TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 
       11.80         2.56        56.88        10.65         5.29        19.04 
TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 
        3.12        13.02         0.23         2.20         2.73        91.00 
TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 
        2.01        53.98        19.00         2.53        40.37        73.84 
TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 
       26.33        28.47        14.93        10.29        18.31         4.67 
TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 
        7.04         2.60         0.39         6.48         5.49         3.91 
TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 
        4.96        11.84         0.20        12.43        22.49         0.36 
TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 
       18.02        10.36        11.80        20.42        14.96        10.32 
TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 
        5.52         0.26        70.52         4.70         8.05         0.16 
TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 
       35.01        12.33         3.22         4.47         9.67         2.04 
TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 
       23.57         9.40        22.32        19.56         5.39         2.70 
TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 
        2.17         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 
       22.98         5.85         5.42        20.94         7.43         6.35 
TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 
        3.58        26.79         8.65         7.89        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         0.76         4.93         9.27         2.83 
TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 
       30.64         5.95         6.81         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        11.24         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 
        3.95         7.79         5.39         1.48         0.49         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-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 
        1.87         3.12         2.56        34.75         3.91       108.82 
TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 
        1.74         4.34        13.78        10.39         7.59         3.42 
TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 
       53.82         1.28         6.41        15.06        22.52        14.70 
TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 
       35.64        19.53         0.95         9.17        10.85        15.72 
TCGA-08-0389 TCGA-08-0390 TCGA-08-0509 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 
        3.19        10.59         0.56        11.77         8.52        18.44 
TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 
       58.19         1.28        10.75         4.80         6.54        15.98 
TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 
       17.33         5.52        14.01        14.43         1.64        10.39 
TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 
        5.95         7.17        65.92         0.10        38.17        25.97 
TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 
       24.13         6.12         2.63        18.12        28.41        12.43 
TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 
       53.10        43.10         5.49         9.11        14.86        14.27 
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         6.25 
TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 
       30.54        21.63        11.97        11.38        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         3.42         9.44        25.28        13.61 
TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 
        6.41        59.41        43.23        25.78        11.54        10.95 
TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 
       11.77        34.52        11.74        13.12         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-14-0812 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-14-1037 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-14-1450 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         6.15        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         9.86 
TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 
       50.53        19.10        53.19         5.52         3.91         9.93 
TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 
       26.07        16.31         4.31        29.03         0.82         9.90 
TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 
       13.35         3.65        18.28        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         0.43        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         3.48         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-19-2631 TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 
        4.08         7.00         7.04         6.64        11.28         8.02 
TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 
       18.64         4.73         7.96         1.78         6.51         5.39 
TCGA-19-5959 TCGA-19-5960 TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 
        5.29         5.42         3.98        16.57        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         1.22         1.58         7.92         2.33 
TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 
        4.80        16.60         9.86        18.25        33.14        21.30 
TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 
       30.05        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-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 
        7.30         5.26         3.91         9.04        15.58        14.53 
TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 
       11.77        31.27        14.20         7.79        13.64         4.21 
TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 
       22.68        10.49         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        21.17        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        10.62         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        11.54 
TCGA-41-6646 TCGA-74-6573 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 
        7.76         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 

  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              9.98 
[1] "0.2 - 25.4 (11.4)"  "0.1 - 127.6 (10.0)"
[1] "hr=" "1.2"
D42V2, continuous
D42V3, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     5   9
  1Q LOSS WILD-TYPE 215 331
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      5    9
  1Q LOSS WILD-TYPE  215  331
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE               5               215
  MALE                 9               331
[1] 2 2
[1] FALSE
D42V4, continuous
                   vv
clus                GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  1Q LOSS MUTATED                               0                   0
  1Q LOSS WILD-TYPE                            17                  18
                   vv
clus                UNTREATED PRIMARY (DE NOVO) GBM
  1Q LOSS MUTATED                                14
  1Q LOSS WILD-TYPE                             511
D42V5, multiclass
                                 clus
vv                                1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                 0                17
  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"
D42V6, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     8   6
  1Q LOSS WILD-TYPE 374 172
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      8    6
  1Q LOSS WILD-TYPE  374  172
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  NO                8               374
  YES               6               172
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1Q LOSS MUTATED       0                         0    12
  1Q LOSS WILD-TYPE    13                        39   473
D42V7, multiclass
                           clus
vv                          1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  ASIAN                                   0                13
  BLACK OR AFRICAN AMERICAN               0                39
  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"
D42V8, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     0  11
  1Q LOSS WILD-TYPE  12 451
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      0   11
  1Q LOSS WILD-TYPE   12  451
                        clus
vv                       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                12
  NOT HISPANIC OR LATINO              11               451
[1] 2 2
[1] FALSE

Clustering(43) Variable = 2P LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                 0   1
  2P LOSS MUTATED     4  28
  2P LOSS WILD-TYPE  94 434
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               32               528 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               28               434 
$`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        11.80         2.53 
TCGA-06-0188 TCGA-06-0414 TCGA-06-1087 TCGA-06-1802 TCGA-06-5416 TCGA-06-5856 
       28.47        35.01         3.58         7.89         6.71         3.75 
TCGA-06-6389 TCGA-06-6694 TCGA-06-A6S0 TCGA-12-0826 TCGA-12-1600 TCGA-12-3646 
        7.79         7.36         3.12        27.78        13.61        43.23 
TCGA-14-0783 TCGA-14-0812 TCGA-14-0867 TCGA-15-1447 TCGA-16-0850 TCGA-19-1388 
        6.21         3.25         2.04        53.19        16.31        12.95 
TCGA-19-1390 TCGA-19-1392 TCGA-19-2625 TCGA-19-5956 TCGA-28-2509 TCGA-28-5215 
       25.38         3.48         4.08         6.51         4.77         7.79 
TCGA-32-2615 TCGA-76-4934 
       15.95         2.53 

$`2P LOSS WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 
        9.17         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        55.86        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        10.36        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         0.23        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         0.16        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        16.21         2.70         0.26         4.04 
TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 
       47.31         0.10         3.58        22.72        32.52        10.52 
TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 
       18.74        14.07        23.08        22.16        10.75         0.20 
TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 
        9.21         2.20        11.74         2.33        20.09        16.70 
TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0154 TCGA-06-0155 
        9.80         7.86        19.46        46.59        12.79         8.65 
TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 
        3.19         5.46         9.44        11.80         2.56        56.88 
TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 
       10.65         5.29        19.04         3.12        13.02         0.23 
TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 
        2.20         2.73        91.00         2.01        53.98        19.00 
TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 
       40.37        73.84        26.33        14.93        10.29        18.31 
TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 
        4.67         7.04         2.60         0.39         6.48         5.49 
TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 
        3.91         4.96        11.84         0.20        12.43        22.49 
TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 
        0.36        18.02        10.36        11.80        20.42        14.96 
TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 
       10.32         5.52         0.26        70.52         4.70         8.05 
TCGA-06-0413 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 
        0.16        12.33         3.22         4.47         9.67         2.04 
TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 
       23.57         9.40        22.32        19.56         5.39         2.70 
TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 
        2.17         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 
       22.98         5.85         5.42        20.94         7.43         6.35 
TCGA-06-1800 TCGA-06-1801 TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 TCGA-06-2557 
       26.79         8.65        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 
        0.76         4.93         9.27         2.83        30.64         5.95 
TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-5408 
        6.81         5.98         4.37         0.43        31.50        11.24 
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-06-5858 TCGA-06-5859 TCGA-06-6388 TCGA-06-6390 TCGA-06-6391 
        2.73         6.15         4.57         3.95         5.39         1.48 
TCGA-06-6693 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 
        0.49         8.32        12.85         4.77         1.55         4.77 
TCGA-06-6701 TCGA-06-A5U1 TCGA-06-A6S1 TCGA-08-0244 TCGA-08-0245 TCGA-08-0246 
        4.96         1.87         2.56        22.68        34.75         3.91 
TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 
      108.82         1.74         4.34        13.78        10.39         7.59 
TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 
        3.42        53.82         1.28         6.41        15.06        22.52 
TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 
       14.70        35.64        19.53         0.95         9.17        10.85 
TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 
       15.72         3.19        10.59         0.30         0.56         3.52 
TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 
       11.77         8.52        18.44        58.19         1.28        10.75 
TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 
        4.80         6.54        15.98        17.33         5.52        14.01 
TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 
       14.43         1.64        10.39         5.95         7.17        65.92 
TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 
        0.10        38.17        25.97        24.13         6.12         2.63 
TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 
       18.12        28.41        12.43        53.10        43.10         5.49 
TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 
        9.11        14.86        14.27        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         6.25        30.54        21.63        11.97        11.38 
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         3.42         9.44 
TCGA-12-1599 TCGA-12-1602 TCGA-12-3644 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 
       25.28         6.41        59.41        25.78        11.54        10.95 
TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 
       11.77        34.52        11.74        13.12         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-14-0813 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-14-0871 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         6.15        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         9.86        50.53 
TCGA-15-1446 TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 TCGA-16-0861 
       19.10         5.52         3.91         9.93        26.07         4.31 
TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 
       29.03         0.82         9.90        13.35         3.65        18.28 
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         0.43 
TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 TCGA-19-1389 
       14.27         3.39        10.75         9.07         5.95         4.64 
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-19-2629 TCGA-19-2631 TCGA-19-4065 
        1.08         7.53         0.16        16.47         7.00         7.04 
TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 
        6.64        11.28         8.02        18.64         4.73         7.96 
TCGA-19-5955 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A6J4 TCGA-19-A6J5 
        1.78         5.39         5.29         5.42         3.98        16.57 
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         1.22         1.58 
TCGA-26-6173 TCGA-26-6174 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 
        7.92         2.33         4.80        16.60         9.86        18.25 
TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 
       33.14        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         3.91         9.04        15.58 
TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5216 TCGA-28-5218 
       14.53        11.77        31.27        14.20        13.64         4.21 
TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 
       22.68        10.49         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        21.17        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        10.62         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        11.54 
TCGA-41-6646 TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 
        7.76         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 

  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 
             7.84             10.34 
[1] "2.0 - 53.2 (7.8)"   "0.1 - 127.6 (10.3)"
[1] "hr=" "1.1"
D43V2, continuous
D43V3, binary
                   cls
clus                  0   1
  2P LOSS MUTATED    17  15
  2P LOSS WILD-TYPE 203 325
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     17   15
  2P LOSS WILD-TYPE  203  325
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE              17               203
  MALE                15               325
[1] 2 2
[1] FALSE
D43V4, continuous
                   vv
clus                GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  2P LOSS MUTATED                               1                   1
  2P LOSS WILD-TYPE                            16                  17
                   vv
clus                UNTREATED PRIMARY (DE NOVO) GBM
  2P LOSS MUTATED                                30
  2P LOSS WILD-TYPE                             495
D43V5, multiclass
                                 clus
vv                                2P LOSS MUTATED 2P LOSS WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                 1                16
  TREATED PRIMARY GBM                           1                17
  UNTREATED PRIMARY (DE NOVO) GBM              30               495
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V6, binary
                   cls
clus                  0   1
  2P LOSS MUTATED    18  14
  2P LOSS WILD-TYPE 364 164
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     18   14
  2P LOSS WILD-TYPE  364  164
     clus
vv    2P LOSS MUTATED 2P LOSS WILD-TYPE
  NO               18               364
  YES              14               164
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2P LOSS MUTATED       0                         1    31
  2P LOSS WILD-TYPE    13                        38   454
D43V7, multiclass
                           clus
vv                          2P LOSS MUTATED 2P LOSS WILD-TYPE
  ASIAN                                   0                13
  BLACK OR AFRICAN AMERICAN               1                38
  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"
D43V8, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     0  26
  2P LOSS WILD-TYPE  12 436
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      0   26
  2P LOSS WILD-TYPE   12  436
                        clus
vv                       2P LOSS MUTATED 2P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                12
  NOT HISPANIC OR LATINO              26               436
[1] 2 2
[1] FALSE

Clustering(44) Variable = 2Q LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                 0   1
  2Q LOSS MUTATED     3  29
  2Q LOSS WILD-TYPE  95 433
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               32               528 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               29               433 
$`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        11.80         2.53 
TCGA-06-0188 TCGA-06-0414 TCGA-06-1087 TCGA-06-1802 TCGA-06-5416 TCGA-06-5856 
       28.47        35.01         3.58         7.89         6.71         3.75 
TCGA-06-6694 TCGA-06-A6S0 TCGA-12-0826 TCGA-12-1600 TCGA-12-3646 TCGA-14-0783 
        7.36         3.12        27.78        13.61        43.23         6.21 
TCGA-14-0812 TCGA-14-0867 TCGA-15-1444 TCGA-15-1447 TCGA-16-0850 TCGA-19-1388 
        3.25         2.04        50.53        53.19        16.31        12.95 
TCGA-19-1390 TCGA-19-1392 TCGA-19-2625 TCGA-19-5956 TCGA-28-2509 TCGA-28-5215 
       25.38         3.48         4.08         6.51         4.77         7.79 
TCGA-32-2615 TCGA-76-4934 
       15.95         2.53 

$`2Q LOSS WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 
        9.17         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        55.86        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        10.36        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         0.23        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         0.16        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        16.21         2.70         0.26         4.04 
TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 
       47.31         0.10         3.58        22.72        32.52        10.52 
TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 
       18.74        14.07        23.08        22.16        10.75         0.20 
TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 
        9.21         2.20        11.74         2.33        20.09        16.70 
TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0154 TCGA-06-0155 
        9.80         7.86        19.46        46.59        12.79         8.65 
TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 
        3.19         5.46         9.44        11.80         2.56        56.88 
TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 
       10.65         5.29        19.04         3.12        13.02         0.23 
TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 
        2.20         2.73        91.00         2.01        53.98        19.00 
TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 
       40.37        73.84        26.33        14.93        10.29        18.31 
TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 
        4.67         7.04         2.60         0.39         6.48         5.49 
TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 
        3.91         4.96        11.84         0.20        12.43        22.49 
TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 
        0.36        18.02        10.36        11.80        20.42        14.96 
TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 
       10.32         5.52         0.26        70.52         4.70         8.05 
TCGA-06-0413 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 
        0.16        12.33         3.22         4.47         9.67         2.04 
TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 
       23.57         9.40        22.32        19.56         5.39         2.70 
TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 
        2.17         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 
       22.98         5.85         5.42        20.94         7.43         6.35 
TCGA-06-1800 TCGA-06-1801 TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 TCGA-06-2557 
       26.79         8.65        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 
        0.76         4.93         9.27         2.83        30.64         5.95 
TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-5408 
        6.81         5.98         4.37         0.43        31.50        11.24 
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-06-5858 TCGA-06-5859 TCGA-06-6388 TCGA-06-6389 TCGA-06-6390 
        2.73         6.15         4.57         3.95         7.79         5.39 
TCGA-06-6391 TCGA-06-6693 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 
        1.48         0.49         8.32        12.85         4.77         1.55 
TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U1 TCGA-06-A6S1 TCGA-08-0244 TCGA-08-0245 
        4.77         4.96         1.87         2.56        22.68        34.75 
TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 
        3.91       108.82         1.74         4.34        13.78        10.39 
TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 
        7.59         3.42        53.82         1.28         6.41        15.06 
TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 
       22.52        14.70        35.64        19.53         0.95         9.17 
TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 
       10.85        15.72         3.19        10.59         0.30         0.56 
TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 
        3.52        11.77         8.52        18.44        58.19         1.28 
TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 
       10.75         4.80         6.54        15.98        17.33         5.52 
TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 
       14.01        14.43         1.64        10.39         5.95         7.17 
TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 
       65.92         0.10        38.17        25.97        24.13         6.12 
TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 
        2.63        18.12        28.41        12.43        53.10        43.10 
TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 
        5.49         9.11        14.86        14.27        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         6.25        30.54        21.63        11.97 
TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 
       11.38        15.85         9.11        14.53         3.98         3.42 
TCGA-12-1598 TCGA-12-1599 TCGA-12-1602 TCGA-12-3644 TCGA-12-3648 TCGA-12-3649 
        9.44        25.28         6.41        59.41        25.78        11.54 
TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 
       10.95        11.77        34.52        11.74        13.12         3.22 
TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 TCGA-14-0781 TCGA-14-0786 TCGA-14-0787 
        2.04        15.12        11.97         0.95        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-14-0871 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         6.15        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         9.86 
TCGA-15-1446 TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 TCGA-16-0861 
       19.10         5.52         3.91         9.93        26.07         4.31 
TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 
       29.03         0.82         9.90        13.35         3.65        18.28 
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         0.43 
TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 TCGA-19-1389 
       14.27         3.39        10.75         9.07         5.95         4.64 
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-19-2629 TCGA-19-2631 TCGA-19-4065 
        1.08         7.53         0.16        16.47         7.00         7.04 
TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 
        6.64        11.28         8.02        18.64         4.73         7.96 
TCGA-19-5955 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A6J4 TCGA-19-A6J5 
        1.78         5.39         5.29         5.42         3.98        16.57 
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         1.22         1.58 
TCGA-26-6173 TCGA-26-6174 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 
        7.92         2.33         4.80        16.60         9.86        18.25 
TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 
       33.14        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         3.91         9.04        15.58 
TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5216 TCGA-28-5218 
       14.53        11.77        31.27        14.20        13.64         4.21 
TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 
       22.68        10.49         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        21.17        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        10.62         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        11.54 
TCGA-41-6646 TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 
        7.76         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 

  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 
            8.730            10.305 
[1] "2.0 - 53.2 (8.7)"   "0.1 - 127.6 (10.3)"
[1] "hr=" "1"  
D44V2, continuous
D44V3, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED    16  16
  2Q LOSS WILD-TYPE 204 324
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     16   16
  2Q LOSS WILD-TYPE  204  324
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE              16               204
  MALE                16               324
[1] 2 2
[1] FALSE
D44V4, continuous
                   vv
clus                GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  2Q LOSS MUTATED                               2                   1
  2Q LOSS WILD-TYPE                            15                  17
                   vv
clus                UNTREATED PRIMARY (DE NOVO) GBM
  2Q LOSS MUTATED                                29
  2Q LOSS WILD-TYPE                             496
D44V5, multiclass
                                 clus
vv                                2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                 2                15
  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
  2Q LOSS MUTATED    17  15
  2Q LOSS WILD-TYPE 365 163
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     17   15
  2Q LOSS WILD-TYPE  365  163
     clus
vv    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  NO               17               365
  YES              15               163
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2Q LOSS MUTATED       0                         1    31
  2Q LOSS WILD-TYPE    13                        38   454
D44V7, multiclass
                           clus
vv                          2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  ASIAN                                   0                13
  BLACK OR AFRICAN AMERICAN               1                38
  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"
D44V8, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     0  26
  2Q LOSS WILD-TYPE  12 436
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      0   26
  2Q LOSS WILD-TYPE   12  436
                        clus
vv                       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                12
  NOT HISPANIC OR LATINO              26               436
[1] 2 2
[1] FALSE

Clustering(45) Variable = 3P LOSS MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                 0   1
  3P LOSS MUTATED     7  33
  3P LOSS WILD-TYPE  91 429
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               40               520 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               33               429 
$`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         0.23        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        16.21        22.72        11.80        22.49 
TCGA-06-0221 TCGA-06-0409 TCGA-06-0878 TCGA-06-1806 TCGA-06-5416 TCGA-06-5859 
       18.02        70.52         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         3.91        15.72        10.59        18.44         9.11 
TCGA-12-0826 TCGA-12-3653 TCGA-14-0862 TCGA-14-0871 TCGA-14-1458 TCGA-14-1823 
       27.78        11.74         2.89        28.93         6.15        17.85 
TCGA-14-3477 TCGA-15-1447 TCGA-15-1449 TCGA-19-1388 TCGA-19-A6J4 TCGA-26-1439 
        3.78        53.19         5.52        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 
        9.17         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        55.86        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        10.36        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 
        0.16        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         0.26 
TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0129 TCGA-06-0130 
        4.04        47.31         0.10         3.58        32.52        10.52 
TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 
       18.74        14.07        23.08        22.16        10.75         0.20 
TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 
        9.21         2.20        11.74         2.33        20.09        16.70 
TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0154 TCGA-06-0155 
        9.80         7.86        19.46        46.59        12.79         8.65 
TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 
        3.19         5.46         9.44        11.80         2.56        56.88 
TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 
       10.65         5.29        19.04         3.12        13.02         0.23 
TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 
        2.20         2.73        91.00         2.01        53.98        19.00 
TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 
        2.53        40.37        73.84        26.33        28.47        14.93 
TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 
       10.29        18.31         4.67         7.04         2.60         0.39 
TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 
        6.48         5.49         3.91         4.96        11.84         0.20 
TCGA-06-0214 TCGA-06-0219 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 
       12.43         0.36        10.36        11.80        20.42        14.96 
TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 
       10.32         5.52         0.26         4.70         8.05         0.16 
TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 
       35.01        12.33         3.22         4.47         9.67         2.04 
TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 
       23.57         9.40        22.32        19.56         5.39         2.70 
TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 TCGA-06-0879 
        2.17         0.92        43.46        46.19         5.65        22.98 
TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 
        5.85         5.42        20.94         7.43         6.35         3.58 
TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-2557 
       26.79         8.65         7.89        13.61        33.90         1.08 
TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 
        0.76         4.93         9.27         2.83        30.64         5.95 
TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-5408 
        6.81         5.98         4.37         0.43        31.50        11.24 
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         3.95         7.79         1.48 
TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 
        0.49         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-08-0244 
        4.77         4.96         1.87         3.12         2.56        22.68 
TCGA-08-0245 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 
       34.75       108.82         1.74         4.34        13.78        10.39 
TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 
        7.59         3.42        53.82         1.28         6.41        15.06 
TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 
       22.52        14.70        35.64        19.53         0.95         9.17 
TCGA-08-0380 TCGA-08-0389 TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 
       10.85         3.19         0.30         0.56         3.52        11.77 
TCGA-08-0514 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 
        8.52        58.19         1.28        10.75         4.80         6.54 
TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 
       15.98        17.33         5.52        14.01        14.43         1.64 
TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 
       10.39         5.95         7.17        65.92         0.10        38.17 
TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 
       25.97        24.13         6.12         2.63        18.12        28.41 
TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0778 TCGA-12-0780 
       12.43        53.10        43.10         5.49        14.86        14.27 
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         6.25        30.54 
TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 
       21.63        11.97        11.38        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         3.42         9.44        25.28        13.61         6.41 
TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 
       59.41        43.23        25.78        11.54        10.95        11.77 
TCGA-12-3652 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 
       34.52        13.12         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-14-0865 TCGA-14-0866 TCGA-14-0867 
        3.25         1.35         5.39        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-14-1453 TCGA-14-1454 
       32.05        58.78        23.11         7.10         1.15        30.18 
TCGA-14-1455 TCGA-14-1456 TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 
        0.92        40.96        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-16-0846 TCGA-16-0848 TCGA-16-0849 
        9.86        50.53        19.10         3.91         9.93        26.07 
TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 
       16.31         4.31        29.03         0.82         9.90        13.35 
TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 
        3.65        18.28        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         0.43        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         3.48         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        16.47         7.00         7.04         6.64 
TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 
       11.28         8.02        18.64         4.73         7.96         1.78 
TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A6J5 TCGA-26-1438 
        6.51         5.39         5.29         5.42        16.57        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         1.22         1.58         7.92         2.33 
TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 
        4.80        16.60         9.86        18.25        33.14        21.30 
TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 
       30.05        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-28-1753 TCGA-28-1755 
        2.53         9.21         8.35         7.63         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         3.91         9.04        15.58        14.53        11.77 
TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 
       31.27        14.20         7.79        13.64         4.21        22.68 
TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 
       10.49         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-32-2616 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 
       21.17        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 
       10.62         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-74-6573 
        4.44        11.84         0.20        11.54         7.76         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-76-4931 TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 
        4.54         3.09         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 
        1.61        17.72        26.30         5.92 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             0.23              0.10 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            92.65            127.59 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            13.41              9.86 
[1] "0.2 - 92.7 (13.4)" "0.1 - 127.6 (9.9)"
[1] "hr=" "1.2"
D45V2, continuous
D45V3, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    16  24
  3P LOSS WILD-TYPE 204 316
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     16   24
  3P LOSS WILD-TYPE  204  316
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE              16               204
  MALE                24               316
[1] 2 2
[1] FALSE
D45V4, continuous
                   vv
clus                GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  3P LOSS MUTATED                               2                   2
  3P LOSS WILD-TYPE                            15                  16
                   vv
clus                UNTREATED PRIMARY (DE NOVO) GBM
  3P LOSS MUTATED                                36
  3P LOSS WILD-TYPE                             489
D45V5, multiclass
                                 clus
vv                                3P LOSS MUTATED 3P LOSS WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                 2                15
  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"
D45V6, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    32   8
  3P LOSS WILD-TYPE 350 170
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     32    8
  3P LOSS WILD-TYPE  350  170
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  NO               32               350
  YES               8               170
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3P LOSS MUTATED       0                         4    35
  3P LOSS WILD-TYPE    13                        35   450
D45V7, multiclass
                           clus
vv                          3P LOSS MUTATED 3P LOSS WILD-TYPE
  ASIAN                                   0                13
  BLACK OR AFRICAN AMERICAN               4                35
  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"
D45V8, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     2  32
  3P LOSS WILD-TYPE  10 430
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      2   32
  3P LOSS WILD-TYPE   10  430
                        clus
vv                       3P LOSS MUTATED 3P LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                10
  NOT HISPANIC OR LATINO              32               430
[1] 2 2
[1] FALSE

Clustering(46) Variable = 3Q LOSS MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                 0   1
  3Q LOSS MUTATED     4  30
  3Q LOSS WILD-TYPE  94 432
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               34               526 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               30               432 
$`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         0.23        92.65        15.91        22.72 
TCGA-06-0152 TCGA-06-0214 TCGA-06-0216 TCGA-06-0221 TCGA-06-0409 TCGA-06-1806 
       11.80        12.43        22.49        18.02        70.52        15.32 
TCGA-06-5859 TCGA-06-6390 TCGA-08-0246 TCGA-08-0386 TCGA-08-0390 TCGA-08-0516 
        4.57         5.39         3.91        15.72        10.59        18.44 
TCGA-12-0691 TCGA-12-0826 TCGA-12-1099 TCGA-12-3653 TCGA-14-0812 TCGA-14-0871 
        6.12        27.78         3.42        11.74         3.25        28.93 
TCGA-14-1458 TCGA-14-1823 TCGA-15-1447 TCGA-15-1449 TCGA-19-1388 TCGA-19-A6J4 
        6.15        17.85        53.19         5.52        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 
        9.17         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        55.86        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        10.36        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         0.16        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        16.21         2.70         0.26         4.04        47.31 
TCGA-06-0126 TCGA-06-0127 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 
        0.10         3.58        32.52        10.52        18.74        14.07 
TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 
       23.08        22.16        10.75         0.20         9.21         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        16.70         9.80         7.86 
TCGA-06-0150 TCGA-06-0151 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 
       19.46        46.59        12.79         8.65         3.19         5.46 
TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 
        9.44        11.80         2.56        56.88        10.65         5.29 
TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 
       19.04         3.12        13.02         0.23         2.20         2.73 
TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 
       91.00         2.01        53.98        19.00         2.53        40.37 
TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 
       73.84        26.33        28.47        14.93        10.29        18.31 
TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 
        4.67         7.04         2.60         0.39         6.48         5.49 
TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0219 TCGA-06-0237 
        3.91         4.96        11.84         0.20         0.36        10.36 
TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 
       11.80        20.42        14.96        10.32         5.52         0.26 
TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 
        4.70         8.05         0.16        35.01        12.33         3.22 
TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 
        4.47         9.67         2.04        23.57         9.40        22.32 
TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 
       19.56         5.39         2.70         2.17         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        22.98         5.85         5.42 
TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 
       20.94         7.43         6.35         3.58        26.79         8.65 
TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 
        7.89        13.61        33.90         1.08         0.76         4.93 
TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 
        9.27         2.83        30.64         5.95         6.81         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        11.24         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         3.95         7.79         1.48         0.49 
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-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-08-0244 TCGA-08-0245 
        4.96         1.87         3.12         2.56        22.68        34.75 
TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 
      108.82         1.74         4.34        13.78        10.39         7.59 
TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 
        3.42        53.82         1.28         6.41        15.06        22.52 
TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 
       14.70        35.64        19.53         0.95         9.17        10.85 
TCGA-08-0389 TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 
        3.19         0.30         0.56         3.52        11.77         8.52 
TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 
       58.19         1.28        10.75         4.80         6.54        15.98 
TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 
       17.33         5.52        14.01        14.43         1.64        10.39 
TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 
        5.95         7.17        65.92         0.10        38.17        25.97 
TCGA-12-0688 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 
       24.13         2.63        18.12        28.41        12.43        53.10 
TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 
       43.10         5.49         9.11        14.86        14.27        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         6.25        30.54        21.63 
TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 
       11.97        11.38        15.85         9.11        14.53         3.98 
TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 
        9.44        25.28        13.61         6.41        59.41        43.23 
TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-5295 
       25.78        11.54        10.95        11.77        34.52        13.12 
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-14-0817 
       23.05         2.24        11.24        13.78         1.35         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-14-1459 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         9.86 
TCGA-15-1444 TCGA-15-1446 TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 
       50.53        19.10         3.91         9.93        26.07        16.31 
TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 
        4.31        29.03         0.82         9.90        13.35         3.65 
TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 
       18.28        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 
        0.43        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         3.48         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        16.47         7.00         7.04         6.64        11.28 
TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 
        8.02        18.64         4.73         7.96         1.78         6.51 
TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1440 
        5.39         5.29         5.42        16.57        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-27-1830 
        8.88         1.22         1.58         7.92         2.33         4.80 
TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 
       16.60         9.86        18.25        33.14        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 
        3.91         9.04        15.58        14.53        11.77        31.27 
TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 
       14.20         7.79        13.64         4.21        22.68        10.49 
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-32-4210 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 
       21.17        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 
       10.62         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-74-6573 
        4.44        11.84         0.20        11.54         7.76         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-76-4931 TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 
        4.54         3.09         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 
        1.61        17.72        26.30         5.92 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             0.23              0.10 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            92.65            127.59 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
           12.115             9.900 
[1] "0.2 - 92.7 (12.1)" "0.1 - 127.6 (9.9)"
[1] "hr=" "1.1"
D46V2, continuous
D46V3, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    15  19
  3Q LOSS WILD-TYPE 205 321
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     15   19
  3Q LOSS WILD-TYPE  205  321
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE              15               205
  MALE                19               321
[1] 2 2
[1] FALSE
D46V4, continuous
                   vv
clus                GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  3Q LOSS MUTATED                               2                   1
  3Q LOSS WILD-TYPE                            15                  17
                   vv
clus                UNTREATED PRIMARY (DE NOVO) GBM
  3Q LOSS MUTATED                                31
  3Q LOSS WILD-TYPE                             494
D46V5, multiclass
                                 clus
vv                                3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                 2                15
  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"
D46V6, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    25   9
  3Q LOSS WILD-TYPE 357 169
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     25    9
  3Q LOSS WILD-TYPE  357  169
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  NO               25               357
  YES               9               169
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3Q LOSS MUTATED       1                         3    30
  3Q LOSS WILD-TYPE    12                        36   455
D46V7, multiclass
                           clus
vv                          3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  ASIAN                                   1                12
  BLACK OR AFRICAN AMERICAN               3                36
  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"
D46V8, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     1  27
  3Q LOSS WILD-TYPE  11 435
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      1   27
  3Q LOSS WILD-TYPE   11  435
                        clus
vv                       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                11
  NOT HISPANIC OR LATINO              27               435
[1] 2 2
[1] FALSE

Clustering(47) Variable = 4P LOSS MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                 0   1
  4P LOSS MUTATED     7  46
  4P LOSS WILD-TYPE  91 416
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               53               507 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               46               416 
$`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 
       22.16        11.80         5.29         0.23         2.73         2.01 
TCGA-06-0216 TCGA-06-0414 TCGA-06-0645 TCGA-06-0744 TCGA-06-1087 TCGA-06-1800 
       22.49        35.01         3.22        19.56         3.58        26.79 
TCGA-06-2557 TCGA-06-5416 TCGA-06-6693 TCGA-06-A6S0 TCGA-08-0351 TCGA-08-0386 
        1.08         6.71         0.49         3.12        53.82        15.72 
TCGA-08-0525 TCGA-12-0619 TCGA-12-0827 TCGA-12-1598 TCGA-12-3644 TCGA-12-3646 
       15.98        10.39        38.76         9.44        59.41        43.23 
TCGA-12-3653 TCGA-14-0867 TCGA-14-1454 TCGA-14-1458 TCGA-14-1823 TCGA-15-1449 
       11.74         2.04        30.18         6.15        17.85         5.52 
TCGA-16-0848 TCGA-16-0849 TCGA-19-1387 TCGA-19-2629 TCGA-19-4065 TCGA-27-1830 
        9.93        26.07         5.95        16.47         7.04         4.80 
TCGA-27-1837 TCGA-27-1838 TCGA-28-2514 TCGA-28-5207 TCGA-28-5214 TCGA-32-1973 
       14.04        11.51         5.26         9.04        14.20        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 
        9.17         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        55.86        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        10.36        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         0.23        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         0.16        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 
       16.21         2.70         0.26         4.04        47.31         0.10 
TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 
        3.58        22.72        32.52        10.52        18.74        14.07 
TCGA-06-0137 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 
       23.08        10.75         0.20         9.21         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        16.70         9.80         7.86        19.46 
TCGA-06-0151 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 
       46.59        12.79         8.65         3.19         5.46         9.44 
TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0168 TCGA-06-0169 
       11.80         2.56        56.88        10.65        19.04         3.12 
TCGA-06-0171 TCGA-06-0174 TCGA-06-0176 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 
       13.02         2.20        91.00        53.98        19.00         2.53 
TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 
       40.37        73.84        26.33        28.47        14.93        10.29 
TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 
       18.31         4.67         7.04         2.60         0.39         6.48 
TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 
        5.49         3.91         4.96        11.84         0.20        12.43 
TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 
        0.36        18.02        10.36        11.80        20.42        14.96 
TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 
       10.32         5.52         0.26        70.52         4.70         8.05 
TCGA-06-0413 TCGA-06-0644 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 
        0.16        12.33         4.47         9.67         2.04        23.57 
TCGA-06-0686 TCGA-06-0743 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 
        9.40        22.32         5.39         2.70         2.17         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        22.98         5.85 
TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1801 TCGA-06-1802 
        5.42        20.94         7.43         6.35         8.65         7.89 
TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 
       13.61        33.90        15.32         0.76         4.93         9.27 
TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 
        2.83        30.64         5.95         6.81         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        11.24         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         3.95         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-A5U1 TCGA-06-A6S1 TCGA-08-0244 TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 
        1.87         2.56        22.68        34.75         3.91       108.82 
TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 
        1.74         4.34        13.78        10.39         7.59         3.42 
TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 
        1.28         6.41        15.06        22.52        14.70        35.64 
TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0389 TCGA-08-0390 
       19.53         0.95         9.17        10.85         3.19        10.59 
TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 
        0.30         0.56         3.52        11.77         8.52        18.44 
TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0529 
       58.19         1.28        10.75         4.80         6.54        17.33 
TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0620 TCGA-12-0654 
        5.52        14.01        14.43         1.64         5.95         7.17 
TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 
       65.92         0.10        38.17        25.97        24.13         6.12 
TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 
        2.63        18.12        28.41        12.43        53.10        43.10 
TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 
        5.49         9.11        14.86        14.27        91.76        24.79 
TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 TCGA-12-0826 TCGA-12-0828 TCGA-12-0829 
       18.48        10.62        23.51        27.78         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         6.25        30.54        21.63        11.97 
TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 
       11.38        15.85         9.11        14.53         3.98         3.42 
TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 
       25.28        13.61         6.41        25.78        11.54        10.95 
TCGA-12-3651 TCGA-12-3652 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 
       11.77        34.52        13.12         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-14-1455 TCGA-14-1456 TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 
        1.15         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-15-1447 
        3.78         3.42         9.86        50.53        19.10        53.19 
TCGA-16-0846 TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 
        3.91        16.31         4.31        29.03         0.82         9.90 
TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 
       13.35         3.65        18.28        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         0.43        14.27         3.39        10.75 
TCGA-19-1386 TCGA-19-1388 TCGA-19-1389 TCGA-19-1390 TCGA-19-1392 TCGA-19-1786 
        9.07        12.95         4.64        25.38         3.48         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-19-5947 TCGA-19-5950 
        7.53         0.16         4.08         7.00         6.64        11.28 
TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 
        8.02        18.64         4.73         7.96         1.78         6.51 
TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 
        5.39         5.29         5.42         3.98        16.57        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         1.22         1.58         7.92 
TCGA-26-6174 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 
        2.33        16.60         9.86        18.25        33.14        21.30 
TCGA-27-1836 TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 
       30.05        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-28-5204 
        0.13         0.66         6.74         4.77         7.30         3.91 
TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5215 TCGA-28-5216 
       15.58        14.53        11.77        31.27         7.79        13.64 
TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1976 
        4.21        22.68        10.49         5.42        15.39         0.49 
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        21.17        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        10.62         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        11.54         7.76 
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-76-4929 TCGA-76-4931 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 
        4.54         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 
       17.72        26.30         5.92 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             0.23              0.10 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            82.59            127.59 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            11.51              9.90 
[1] "0.2 - 82.6 (11.5)" "0.1 - 127.6 (9.9)"
[1] "hr=" "1.1"
D47V2, continuous
D47V3, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    16  37
  4P LOSS WILD-TYPE 204 303
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     16   37
  4P LOSS WILD-TYPE  204  303
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE              16               204
  MALE                37               303
[1] 2 2
[1] FALSE
D47V4, continuous
                   vv
clus                GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  4P LOSS MUTATED                               1                   0
  4P LOSS WILD-TYPE                            16                  18
                   vv
clus                UNTREATED PRIMARY (DE NOVO) GBM
  4P LOSS MUTATED                                52
  4P LOSS WILD-TYPE                             473
D47V5, multiclass
                                 clus
vv                                4P LOSS MUTATED 4P LOSS WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                 1                16
  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"
D47V6, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    38  15
  4P LOSS WILD-TYPE 344 163
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     38   15
  4P LOSS WILD-TYPE  344  163
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  NO               38               344
  YES              15               163
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4P LOSS MUTATED       2                         3    47
  4P LOSS WILD-TYPE    11                        36   438
D47V7, multiclass
                           clus
vv                          4P LOSS MUTATED 4P LOSS WILD-TYPE
  ASIAN                                   2                11
  BLACK OR AFRICAN AMERICAN               3                36
  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"
D47V8, binary
                   cls
clus                  0   1
  4P LOSS MUTATED     2  42
  4P LOSS WILD-TYPE  10 420
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      2   42
  4P LOSS WILD-TYPE   10  420
                        clus
vv                       4P LOSS MUTATED 4P LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                10
  NOT HISPANIC OR LATINO              42               420
[1] 2 2
[1] FALSE

Clustering(48) Variable = 4Q LOSS MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                 0   1
  4Q LOSS MUTATED    12  41
  4Q LOSS WILD-TYPE  86 421
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               53               507 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               41               421 
$`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 
       22.16        11.80         5.29         2.01        22.49        35.01 
TCGA-06-0645 TCGA-06-0744 TCGA-06-1087 TCGA-06-1800 TCGA-06-1805 TCGA-06-2557 
        3.22        19.56         3.58        26.79        33.90         1.08 
TCGA-06-2569 TCGA-06-5416 TCGA-06-6389 TCGA-06-6693 TCGA-08-0386 TCGA-12-0619 
        0.43         6.71         7.79         0.49        15.72        10.39 
TCGA-12-0827 TCGA-12-1598 TCGA-12-3644 TCGA-12-3646 TCGA-12-3653 TCGA-14-0740 
       38.76         9.44        59.41        43.23        11.74        11.97 
TCGA-14-0867 TCGA-14-1453 TCGA-14-1454 TCGA-14-1458 TCGA-14-1823 TCGA-15-1447 
        2.04         1.15        30.18         6.15        17.85        53.19 
TCGA-15-1449 TCGA-16-0848 TCGA-19-1387 TCGA-19-2629 TCGA-19-4065 TCGA-19-A6J5 
        5.52         9.93         5.95        16.47         7.04        16.57 
TCGA-26-1442 TCGA-27-1830 TCGA-27-1838 TCGA-28-2514 TCGA-28-5207 TCGA-28-5214 
       31.33         4.80        11.51         5.26         9.04        14.20 
TCGA-32-1973 TCGA-32-2632 TCGA-76-4925 TCGA-76-4934 TCGA-76-6285 
       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 
        9.17         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        55.86        77.65        20.12 
TCGA-02-0025 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 
       42.74        10.36        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         0.23        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         0.16        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 
       16.21         2.70         0.26         4.04        47.31         0.10 
TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 
        3.58        22.72        32.52        10.52        18.74        14.07 
TCGA-06-0137 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 
       23.08        10.75         0.20         9.21         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        16.70         9.80         7.86        19.46 
TCGA-06-0151 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 
       46.59        12.79         8.65         3.19         5.46         9.44 
TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0168 TCGA-06-0169 
       11.80         2.56        56.88        10.65        19.04         3.12 
TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0178 
       13.02         0.23         2.20         2.73        91.00        53.98 
TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 
       19.00         2.53        40.37        73.84        26.33        28.47 
TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 
       14.93        10.29        18.31         4.67         7.04         2.60 
TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 
        0.39         6.48         5.49         3.91         4.96        11.84 
TCGA-06-0213 TCGA-06-0214 TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 
        0.20        12.43         0.36        18.02        10.36        11.80 
TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 
       20.42        14.96        10.32         5.52         0.26        70.52 
TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0644 TCGA-06-0646 TCGA-06-0648 
        4.70         8.05         0.16        12.33         4.47         9.67 
TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0745 TCGA-06-0747 
        2.04        23.57         9.40        22.32         5.39         2.70 
TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 
        2.17         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 
       22.98         5.85         5.42        20.94         7.43         6.35 
TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1806 TCGA-06-2558 TCGA-06-2559 
        8.65         7.89        13.61        15.32         0.76         4.93 
TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 
        9.27         2.83        30.64         5.95         6.81         5.98 
TCGA-06-2567 TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 
        4.37        31.50        11.24         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         3.95         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-08-0244 TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 
        3.12         2.56        22.68        34.75         3.91       108.82 
TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 
        1.74         4.34        13.78        10.39         7.59         3.42 
TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 
       53.82         1.28         6.41        15.06        22.52        14.70 
TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0389 
       35.64        19.53         0.95         9.17        10.85         3.19 
TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 
       10.59         0.30         0.56         3.52        11.77         8.52 
TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 
       18.44        58.19         1.28        10.75         4.80         6.54 
TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 
       15.98        17.33         5.52        14.01        14.43         1.64 
TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 
        5.95         7.17        65.92         0.10        38.17        25.97 
TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 
       24.13         6.12         2.63        18.12        28.41        12.43 
TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 
       53.10        43.10         5.49         9.11        14.86        14.27 
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         6.25        30.54 
TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 
       21.63        11.97        11.38        15.85         9.11        14.53 
TCGA-12-1098 TCGA-12-1099 TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 TCGA-12-3648 
        3.98         3.42        25.28        13.61         6.41        25.78 
TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-5295 TCGA-12-5299 
       11.54        10.95        11.77        34.52        13.12         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-14-0871 TCGA-14-1034 TCGA-14-1037 TCGA-14-1043 
       16.50        26.33        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-14-1455 TCGA-14-1456 TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 
        7.10         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         9.86        50.53        19.10         3.91 
TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 
       26.07        16.31         4.31        29.03         0.82         9.90 
TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 
       13.35         3.65        18.28        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         0.43        14.27         3.39        10.75 
TCGA-19-1386 TCGA-19-1388 TCGA-19-1389 TCGA-19-1390 TCGA-19-1392 TCGA-19-1786 
        9.07        12.95         4.64        25.38         3.48         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-19-5947 TCGA-19-5950 
        7.53         0.16         4.08         7.00         6.64        11.28 
TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 
        8.02        18.64         4.73         7.96         1.78         6.51 
TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A6J4 TCGA-26-1438 TCGA-26-1439 
        5.39         5.29         5.42         3.98        10.03        13.87 
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-26-6174 TCGA-27-1831 
        8.88         1.22         1.58         7.92         2.33        16.60 
TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 
        9.86        18.25        33.14        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-28-1756 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         3.91        15.58 
TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 
       14.53        11.77        31.27         7.79        13.64         4.21 
TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1976 TCGA-32-1977 
       22.68        10.49         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-32-2615 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        21.17        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        10.62         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        11.54         7.76 
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 
       17.72        26.30         5.92 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             0.43              0.10 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            59.41            127.59 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            11.51              9.90 
[1] "0.4 - 59.4 (11.5)" "0.1 - 127.6 (9.9)"
[1] "hr=" "1.2"
D48V2, continuous
D48V3, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED    19  34
  4Q LOSS WILD-TYPE 201 306
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     19   34
  4Q LOSS WILD-TYPE  201  306
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE              19               201
  MALE                34               306
[1] 2 2
[1] FALSE
D48V4, continuous
                   vv
clus                GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  4Q LOSS MUTATED                               1                   1
  4Q LOSS WILD-TYPE                            16                  17
                   vv
clus                UNTREATED PRIMARY (DE NOVO) GBM
  4Q LOSS MUTATED                                51
  4Q LOSS WILD-TYPE                             474
D48V5, multiclass
                                 clus
vv                                4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                 1                16
  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"
D48V6, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED    38  15
  4Q LOSS WILD-TYPE 344 163
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     38   15
  4Q LOSS WILD-TYPE  344  163
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  NO               38               344
  YES              15               163
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4Q LOSS MUTATED       2                         4    47
  4Q LOSS WILD-TYPE    11                        35   438
D48V7, multiclass
                           clus
vv                          4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  ASIAN                                   2                11
  BLACK OR AFRICAN AMERICAN               4                35
  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
  4Q LOSS MUTATED     2  39
  4Q LOSS WILD-TYPE  10 423
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      2   39
  4Q LOSS WILD-TYPE   10  423
                        clus
vv                       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                10
  NOT HISPANIC OR LATINO              39               423
[1] 2 2
[1] FALSE

Clustering(49) Variable = 5P LOSS MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                 0   1
  5P LOSS MUTATED     8  34
  5P LOSS WILD-TYPE  90 428
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               42               518 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               34               428 
$`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         0.23        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        28.47        35.01        12.33         9.40 
TCGA-06-1087 TCGA-06-6389 TCGA-08-0245 TCGA-08-0344 TCGA-08-0386 TCGA-08-0516 
        3.58         7.79        34.75       108.82        15.72        18.44 
TCGA-08-0517 TCGA-12-0818 TCGA-12-3652 TCGA-12-3653 TCGA-14-0740 TCGA-14-0817 
       58.19        91.76        34.52        11.74        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 
       16.31         5.95         7.04         7.96        14.86        33.14 
TCGA-27-2521 TCGA-28-1755 TCGA-28-5215 TCGA-41-5651 TCGA-76-4925 TCGA-76-4929 
       10.39         1.55         7.79        11.54         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 
        9.17         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        55.86        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        10.36        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         0.16        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        16.21 
TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 
        2.70         0.26         4.04        47.31         0.10         3.58 
TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 
       32.52        10.52        18.74        14.07        23.08        22.16 
TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 
       10.75         0.20         9.21         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        16.70         9.80         7.86        19.46        46.59 
TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 
       11.80        12.79         8.65         3.19         5.46         9.44 
TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 
       11.80         2.56        56.88        10.65         5.29        19.04 
TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 
        3.12        13.02         0.23         2.20         2.73        91.00 
TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 
        2.01        53.98        19.00         2.53        40.37        73.84 
TCGA-06-0187 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 
       26.33        14.93        10.29        18.31         4.67         7.04 
TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 
        2.60         0.39         6.48         5.49         3.91         4.96 
TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 
       11.84         0.20        12.43        22.49         0.36        18.02 
TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 
       10.36        11.80        20.42        14.96        10.32         5.52 
TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0645 
        0.26        70.52         4.70         8.05         0.16         3.22 
TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0743 TCGA-06-0744 
        4.47         9.67         2.04        23.57        22.32        19.56 
TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 
        5.39         2.70         2.17         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        22.98         5.85         5.42        20.94 
TCGA-06-1084 TCGA-06-1086 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 
        7.43         6.35        26.79         8.65         7.89        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         0.76         4.93         9.27 
TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 
        2.83        30.64         5.95         6.81         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        11.24         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         3.95         5.39         1.48         0.49 
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-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-08-0244 TCGA-08-0246 
        4.96         1.87         3.12         2.56        22.68         3.91 
TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 
        1.74         4.34        13.78        10.39         7.59         3.42 
TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 
       53.82         1.28         6.41        15.06        22.52        14.70 
TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0389 
       35.64        19.53         0.95         9.17        10.85         3.19 
TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 
       10.59         0.30         0.56         3.52        11.77         8.52 
TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 
        1.28        10.75         4.80         6.54        15.98        17.33 
TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 
        5.52        14.01        14.43         1.64        10.39         5.95 
TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 
        7.17        65.92         0.10        38.17        25.97        24.13 
TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 
        6.12         2.63        18.12        28.41        12.43        53.10 
TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0819 
       43.10         5.49         9.11        14.86        14.27        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         6.25        30.54        21.63 
TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 
       11.97        11.38        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 
        3.42         9.44        25.28        13.61         6.41        59.41 
TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-5295 
       43.23        25.78        11.54        10.95        11.77        13.12 
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-14-0862 
        2.24        11.24        13.78         3.25         1.35         2.89 
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-14-1454 
        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         6.15        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         9.86        50.53        19.10        53.19         5.52 
TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 
        3.91         9.93        26.07         4.31        29.03         0.82 
TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 
        9.90        13.35         3.65        18.28        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         0.43        14.27         3.39 
TCGA-19-1385 TCGA-19-1386 TCGA-19-1388 TCGA-19-1389 TCGA-19-1390 TCGA-19-1392 
       10.75         9.07        12.95         4.64        25.38         3.48 
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        16.47         7.00 
TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5955 
        6.64        11.28         8.02        18.64         4.73         1.78 
TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A6J4 TCGA-19-A6J5 
        6.51         5.39         5.29         5.42         3.98        16.57 
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-26-5134 TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 
        9.40         5.49         8.88         1.22         1.58         7.92 
TCGA-26-6174 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1835 
        2.33         4.80        16.60         9.86        18.25        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-28-1756 
        9.21         8.35         7.63         8.48         1.22         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 
        3.91         9.04        15.58        14.53        11.77        31.27 
TCGA-28-5214 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 
       14.20        13.64         4.21        22.68        10.49         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 
       21.17        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 
       10.62         0.85        13.35         8.94         9.53         0.99 
TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-41-6646 TCGA-74-6573 TCGA-74-6575 
        4.44        11.84         0.20         7.76         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 
       26.30         5.92 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             0.23              0.10 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
           108.82            127.59 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            12.49              9.83 
[1] "0.2 - 108.8 (12.5)" "0.1 - 127.6 (9.8)" 
[1] "hr=" "1.4"
D49V2, continuous
D49V3, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    16  26
  5P LOSS WILD-TYPE 204 314
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     16   26
  5P LOSS WILD-TYPE  204  314
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE              16               204
  MALE                26               314
[1] 2 2
[1] FALSE
D49V4, continuous
                   vv
clus                GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  5P LOSS MUTATED                               0                   1
  5P LOSS WILD-TYPE                            17                  17
                   vv
clus                UNTREATED PRIMARY (DE NOVO) GBM
  5P LOSS MUTATED                                41
  5P LOSS WILD-TYPE                             484
D49V5, multiclass
                                 clus
vv                                5P LOSS MUTATED 5P LOSS WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                 0                17
  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"
D49V6, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    35   7
  5P LOSS WILD-TYPE 347 171
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     35    7
  5P LOSS WILD-TYPE  347  171
     clus
vv    5P LOSS MUTATED 5P LOSS WILD-TYPE
  NO               35               347
  YES               7               171
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5P LOSS MUTATED       3                         4    35
  5P LOSS WILD-TYPE    10                        35   450
D49V7, multiclass
                           clus
vv                          5P LOSS MUTATED 5P LOSS WILD-TYPE
  ASIAN                                   3                10
  BLACK OR AFRICAN AMERICAN               4                35
  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"
D49V8, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     2  32
  5P LOSS WILD-TYPE  10 430
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      2   32
  5P LOSS WILD-TYPE   10  430
                        clus
vv                       5P LOSS MUTATED 5P LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                10
  NOT HISPANIC OR LATINO              32               430
[1] 2 2
[1] FALSE

Clustering(50) Variable = 5Q LOSS MUTATION ANALYSIS
D50V1, survival
                   sevent
clus2                 0   1
  5Q LOSS MUTATED    10  33
  5Q LOSS WILD-TYPE  88 429
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               43               517 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               33               429 
$`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         0.23 
TCGA-02-2483 TCGA-06-0128 TCGA-06-0188 TCGA-06-0237 TCGA-06-0414 TCGA-06-0644 
       15.32        22.72        28.47        10.36        35.01        12.33 
TCGA-06-0686 TCGA-06-1087 TCGA-06-2569 TCGA-06-6389 TCGA-08-0344 TCGA-08-0350 
        9.40         3.58         0.43         7.79       108.82         3.42 
TCGA-08-0386 TCGA-08-0516 TCGA-12-0818 TCGA-12-3652 TCGA-12-3653 TCGA-14-0740 
       15.72        18.44        91.76        34.52        11.74        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        16.31         8.61         5.95         7.04         7.96 
TCGA-26-5133 TCGA-27-1834 TCGA-27-2521 TCGA-28-5215 TCGA-41-5651 TCGA-76-4925 
       14.86        33.14        10.39         7.79        11.54         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 
        9.17         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        55.86        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        10.36        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 
        0.16        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        16.21 
TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 
        2.70         0.26         4.04        47.31         0.10         3.58 
TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 
       32.52        10.52        18.74        14.07        23.08        22.16 
TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 
       10.75         0.20         9.21         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        16.70         9.80         7.86        19.46        46.59 
TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 
       11.80        12.79         8.65         3.19         5.46         9.44 
TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 
       11.80         2.56        56.88        10.65         5.29        19.04 
TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 
        3.12        13.02         0.23         2.20         2.73        91.00 
TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 
        2.01        53.98        19.00         2.53        40.37        73.84 
TCGA-06-0187 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 
       26.33        14.93        10.29        18.31         4.67         7.04 
TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 
        2.60         0.39         6.48         5.49         3.91         4.96 
TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 
       11.84         0.20        12.43        22.49         0.36        18.02 
TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 
       11.80        20.42        14.96        10.32         5.52         0.26 
TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0645 TCGA-06-0646 
       70.52         4.70         8.05         0.16         3.22         4.47 
TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 
        9.67         2.04        23.57        22.32        19.56         5.39 
TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 
        2.70         2.17         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        22.98         5.85         5.42        20.94         7.43 
TCGA-06-1086 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 
        6.35        26.79         8.65         7.89        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         0.76         4.93         9.27         2.83 
TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2570 
       30.64         5.95         6.81         5.98         4.37        31.50 
TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 
       11.24         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 
        3.95         5.39         1.48         0.49         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-08-0244 TCGA-08-0245 TCGA-08-0246 TCGA-08-0345 
        3.12         2.56        22.68        34.75         3.91         1.74 
TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0351 TCGA-08-0352 
        4.34        13.78        10.39         7.59        53.82         1.28 
TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 
        6.41        15.06        22.52        14.70        35.64        19.53 
TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 
        0.95         9.17        10.85         3.19        10.59         0.30 
TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 TCGA-08-0517 TCGA-08-0518 
        0.56         3.52        11.77         8.52        58.19         1.28 
TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 
       10.75         4.80         6.54        15.98        17.33         5.52 
TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 
       14.01        14.43         1.64        10.39         5.95         7.17 
TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 
       65.92         0.10        38.17        25.97        24.13         6.12 
TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 
        2.63        18.12        28.41        12.43        53.10        43.10 
TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0819 TCGA-12-0820 
        5.49         9.11        14.86        14.27        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         6.25        30.54        21.63        11.97 
TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 
       11.38        15.85         9.11        14.53         3.98         3.42 
TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 
        9.44        25.28        13.61         6.41        59.41        43.23 
TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-5295 TCGA-12-5299 
       25.78        11.54        10.95        11.77        13.12         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-14-0866 
       11.24        13.78         3.25         1.35         2.89        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-14-1454 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-14-1823 
       40.96         6.15        12.43         0.99         1.97        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 
        9.86        50.53        19.10        53.19         5.52         3.91 
TCGA-16-0848 TCGA-16-0849 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 
        9.93        26.07         4.31        29.03         0.82         9.90 
TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 
       13.35         3.65        18.28        13.97         6.41        11.77 
TCGA-19-0957 TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 
       21.90         0.43        14.27         3.39        10.75         9.07 
TCGA-19-1388 TCGA-19-1389 TCGA-19-1390 TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 
       12.95         4.64        25.38         3.48         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        16.47         7.00         6.64        11.28 
TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 
        8.02        18.64         4.73         1.78         6.51         5.39 
TCGA-19-5959 TCGA-19-5960 TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 
        5.29         5.42         3.98        16.57        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-27-1830 
        8.88         1.22         1.58         7.92         2.33         4.80 
TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 
       16.60         9.86        18.25        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         3.91 
TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 
        9.04        15.58        14.53        11.77        31.27        14.20 
TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 
       13.64         4.21        22.68        10.49         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        21.17 
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        10.62 
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-74-6573 TCGA-74-6575 TCGA-74-6577 
       11.84         0.20         7.76         3.45        20.91         4.34 
TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 TCGA-76-4926 TCGA-76-4928 TCGA-76-4931 
       14.33         8.22         7.50         4.54         3.09         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 
        5.92 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             0.23              0.10 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
           108.82            127.59 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            11.97              9.86 
[1] "0.2 - 108.8 (12.0)" "0.1 - 127.6 (9.9)" 
[1] "hr=" "1.3"
D50V2, continuous
D50V3, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    17  26
  5Q LOSS WILD-TYPE 203 314
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     17   26
  5Q LOSS WILD-TYPE  203  314
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE              17               203
  MALE                26               314
[1] 2 2
[1] FALSE
D50V4, continuous
                   vv
clus                GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  5Q LOSS MUTATED                               0                   0
  5Q LOSS WILD-TYPE                            17                  18
                   vv
clus                UNTREATED PRIMARY (DE NOVO) GBM
  5Q LOSS MUTATED                                43
  5Q LOSS WILD-TYPE                             482
D50V5, multiclass
                                 clus
vv                                5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                 0                17
  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"
D50V6, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    34   9
  5Q LOSS WILD-TYPE 348 169
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     34    9
  5Q LOSS WILD-TYPE  348  169
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  NO               34               348
  YES               9               169
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5Q LOSS MUTATED       2                         4    37
  5Q LOSS WILD-TYPE    11                        35   448
D50V7, multiclass
                           clus
vv                          5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  ASIAN                                   2                11
  BLACK OR AFRICAN AMERICAN               4                35
  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"
D50V8, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED     3  32
  5Q LOSS WILD-TYPE   9 430
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      3   32
  5Q LOSS WILD-TYPE    9  430
                        clus
vv                       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                 9
  NOT HISPANIC OR LATINO              32               430
[1] 2 2
[1] FALSE

Clustering(51) Variable = 6P LOSS MUTATION ANALYSIS
D51V1, survival
                   sevent
clus2                 0   1
  6P LOSS MUTATED     9  77
  6P LOSS WILD-TYPE  89 385
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               86               474 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               77               385 
$`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        32.52 
TCGA-06-0130 TCGA-06-0138 TCGA-06-0141 TCGA-06-0162 TCGA-06-0166 TCGA-06-0184 
       10.52        22.16         9.21         2.56         5.29        40.37 
TCGA-06-0192 TCGA-06-0209 TCGA-06-0216 TCGA-06-0402 TCGA-06-0644 TCGA-06-0649 
       18.31         3.91        22.49         0.26        12.33         2.04 
TCGA-06-1806 TCGA-06-2561 TCGA-06-5410 TCGA-06-5416 TCGA-06-5856 TCGA-06-6390 
       15.32         9.27         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         3.91         6.41         0.30         3.52        11.77 
TCGA-12-0616 TCGA-12-0691 TCGA-12-0692 TCGA-12-0822 TCGA-12-1098 TCGA-12-1099 
       14.43         6.12         2.63        23.51         3.98         3.42 
TCGA-12-1602 TCGA-12-3646 TCGA-12-3653 TCGA-14-0736 TCGA-14-0817 TCGA-14-0865 
        6.41        43.23        11.74        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         0.43         3.48        16.47 
TCGA-19-4065 TCGA-19-5947 TCGA-19-5960 TCGA-19-A6J4 TCGA-26-1439 TCGA-27-1832 
        7.04         6.64         5.42         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        10.49 
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        11.54         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 
        9.17         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        55.86        77.65        53.10 
TCGA-02-0025 TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 
       42.74        10.36        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         0.23        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         0.16        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        16.21         2.70         0.26         4.04        47.31 
TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 
        0.10         3.58        22.72        18.74        14.07        23.08 
TCGA-06-0139 TCGA-06-0140 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 
       10.75         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 
       16.70         9.80         7.86        19.46        46.59        11.80 
TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 
       12.79         8.65         3.19         5.46         9.44        11.80 
TCGA-06-0164 TCGA-06-0165 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 
       56.88        10.65        19.04         3.12        13.02         0.23 
TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 
        2.20         2.73        91.00         2.01        53.98        19.00 
TCGA-06-0182 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 
        2.53        73.84        26.33        28.47        14.93        10.29 
TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 
        4.67         7.04         2.60         0.39         6.48         5.49 
TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0219 TCGA-06-0221 
        4.96        11.84         0.20        12.43         0.36        18.02 
TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 
       10.36        11.80        20.42        14.96        10.32         5.52 
TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0645 
       70.52         4.70         8.05         0.16        35.01         3.22 
TCGA-06-0646 TCGA-06-0648 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 
        4.47         9.67        23.57         9.40        22.32        19.56 
TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 
        5.39         2.70         2.17         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        22.98         5.85         5.42        20.94 
TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 
        7.43         6.35         3.58        26.79         8.65         7.89 
TCGA-06-1804 TCGA-06-1805 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2562 
       13.61        33.90         1.08         0.76         4.93         2.83 
TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 
       30.64         5.95         6.81         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        11.24         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         3.95         7.79 
TCGA-06-6391 TCGA-06-6693 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 
        1.48         0.49         8.32        12.85         4.77         1.55 
TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-08-0244 
        4.77         4.96         1.87         3.12         2.56        22.68 
TCGA-08-0245 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 
       34.75       108.82         1.74         4.34        13.78        10.39 
TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0354 TCGA-08-0355 
        7.59         3.42        53.82         1.28        15.06        22.52 
TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 
       14.70        35.64        19.53         0.95         9.17        10.85 
TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0509 TCGA-08-0514 TCGA-08-0516 
       15.72         3.19        10.59         0.56         8.52        18.44 
TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 
       58.19         1.28        10.75         4.80         6.54        15.98 
TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 
       17.33         5.52        14.01         1.64        10.39         5.95 
TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 
        7.17        65.92         0.10        38.17        25.97        24.13 
TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 
       18.12        28.41        12.43        53.10        43.10         5.49 
TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 
        9.11        14.86        14.27        91.76        24.79        18.48 
TCGA-12-0821 TCGA-12-0826 TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 
       10.62        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         6.25        30.54        21.63        11.97        11.38 
TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 
       15.85         9.11        14.53         9.44        25.28        13.61 
TCGA-12-3644 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 
       59.41        25.78        11.54        10.95        11.77        34.52 
TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0740 TCGA-14-0781 TCGA-14-0783 
       13.12         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-14-0862 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-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 
       23.11         7.10        30.18         0.92        40.96         6.15 
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         9.86 
TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 TCGA-16-0848 TCGA-16-0849 
       50.53        19.10        53.19         5.52         9.93        26.07 
TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 
       16.31         4.31        29.03         0.82         9.90        13.35 
TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 
        3.65        18.28        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-19-1786 TCGA-19-1787 TCGA-19-1789 
       12.95         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-19-2631 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 
        4.08         7.00        11.28         8.02        18.64         4.73 
TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-A6J5 
        7.96         1.78         6.51         5.39         5.29        16.57 
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         1.22         1.58         7.92 
TCGA-26-6174 TCGA-27-1830 TCGA-27-1831 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 
        2.33         4.80        16.60        18.25        33.14        21.30 
TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 
       30.05        14.04        11.51        24.76        10.39        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-28-2513 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 
        0.13         0.66         7.30         3.91         9.04        15.58 
TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 
       14.53        11.77        31.27        14.20         7.79        13.64 
TCGA-28-5218 TCGA-28-5219 TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 TCGA-32-1977 
        4.21        22.68         5.42        15.39        21.07         0.10 
TCGA-32-1978 TCGA-32-1979 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 TCGA-32-1991 
       15.85        19.50         4.67        12.69        14.86        16.93 
TCGA-32-2491 TCGA-32-2494 TCGA-32-2616 TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 
       12.23        20.78         7.36         8.84        22.78        21.17 
TCGA-32-4208 TCGA-32-4213 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 
       21.14        19.86        10.62         0.85        13.35         8.94 
TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 TCGA-41-6646 TCGA-74-6577 
        9.53         0.99         4.44        11.84         7.76         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-76-6285 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 

  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 
             8.58             10.39 
[1] "0.2 - 92.7 (8.6)"   "0.1 - 127.6 (10.4)"
[1] "hr=" "1.4"
D51V2, continuous
D51V3, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    35  51
  6P LOSS WILD-TYPE 185 289
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     35   51
  6P LOSS WILD-TYPE  185  289
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE              35               185
  MALE                51               289
[1] 2 2
[1] FALSE
D51V4, continuous
                   vv
clus                GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  6P LOSS MUTATED                               3                   4
  6P LOSS WILD-TYPE                            14                  14
                   vv
clus                UNTREATED PRIMARY (DE NOVO) GBM
  6P LOSS MUTATED                                79
  6P LOSS WILD-TYPE                             446
D51V5, multiclass
                                 clus
vv                                6P LOSS MUTATED 6P LOSS WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                 3                14
  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"
D51V6, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    56  30
  6P LOSS WILD-TYPE 326 148
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     56   30
  6P LOSS WILD-TYPE  326  148
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  NO               56               326
  YES              30               148
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6P LOSS MUTATED       4                         7    71
  6P LOSS WILD-TYPE     9                        32   414
D51V7, multiclass
                           clus
vv                          6P LOSS MUTATED 6P LOSS WILD-TYPE
  ASIAN                                   4                 9
  BLACK OR AFRICAN AMERICAN               7                32
  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"
D51V8, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     1  74
  6P LOSS WILD-TYPE  11 388
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      1   74
  6P LOSS WILD-TYPE   11  388
                        clus
vv                       6P LOSS MUTATED 6P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                11
  NOT HISPANIC OR LATINO              74               388
[1] 2 2
[1] FALSE

Clustering(52) Variable = 6Q LOSS MUTATION ANALYSIS
D52V1, survival
                   sevent
clus2                 0   1
  6Q LOSS MUTATED    17 106
  6Q LOSS WILD-TYPE  81 356
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              123               437 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              106               356 
$`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 
       32.52        10.52        22.16         9.21         2.56         5.29 
TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0192 TCGA-06-0209 TCGA-06-0214 
       40.37        73.84        26.33        18.31         3.91        12.43 
TCGA-06-0216 TCGA-06-0402 TCGA-06-0644 TCGA-06-0649 TCGA-06-0750 TCGA-06-1806 
       22.49         0.26        12.33         2.04         0.92        15.32 
TCGA-06-2561 TCGA-06-5408 TCGA-06-5410 TCGA-06-5413 TCGA-06-5416 TCGA-06-5856 
        9.27        11.24         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         3.91         6.41        19.53 
TCGA-08-0380 TCGA-08-0392 TCGA-08-0510 TCGA-08-0512 TCGA-08-0517 TCGA-08-0525 
       10.85         0.30         3.52        11.77        58.19        15.98 
TCGA-12-0615 TCGA-12-0616 TCGA-12-0654 TCGA-12-0656 TCGA-12-0691 TCGA-12-0692 
       14.01        14.43         7.17        65.92         6.12         2.63 
TCGA-12-0772 TCGA-12-0822 TCGA-12-1095 TCGA-12-1099 TCGA-12-1602 TCGA-12-3646 
       53.10        23.51        15.85         3.42         6.41        43.23 
TCGA-12-3653 TCGA-12-5299 TCGA-14-0736 TCGA-14-0817 TCGA-14-0865 TCGA-14-1037 
       11.74         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         9.86         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         0.43         3.48        16.47         7.04 
TCGA-19-5947 TCGA-19-5952 TCGA-19-5960 TCGA-19-A6J4 TCGA-26-1439 TCGA-26-1443 
        6.64        18.64         5.42         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 
        3.91        14.53        31.27        10.49         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-74-6573 TCGA-74-6575 TCGA-76-4928 
        0.99         0.20        11.54         3.45        20.91         3.09 
TCGA-76-4931 TCGA-76-6285 TCGA-OX-A56R 
        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 
        9.17         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        55.86        77.65        53.10        42.74 
TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 
       10.36        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         0.23 
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 
        0.16        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 
       16.21         2.70         0.26         4.04        47.31         0.10 
TCGA-06-0127 TCGA-06-0128 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0139 
        3.58        22.72        18.74        14.07        23.08        10.75 
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        16.70 
TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 
        9.80         7.86        19.46        46.59        11.80        12.79 
TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0164 
        8.65         3.19         5.46         9.44        11.80        56.88 
TCGA-06-0165 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 
       10.65        19.04         3.12        13.02         0.23         2.20 
TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 
        2.73        91.00         2.01        53.98        19.00         2.53 
TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 
       28.47        14.93        10.29         4.67         7.04         2.60 
TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 
        0.39         6.48         5.49         4.96        11.84         0.20 
TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 
        0.36        18.02        10.36        11.80        20.42        14.96 
TCGA-06-0394 TCGA-06-0397 TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 
       10.32         5.52        70.52         4.70         8.05         0.16 
TCGA-06-0414 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0650 TCGA-06-0686 
       35.01         3.22         4.47         9.67        23.57         9.40 
TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0875 
       22.32        19.56         5.39         2.70         2.17        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        22.98         5.85         5.42 
TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 
       20.94         7.43         6.35         3.58        26.79         8.65 
TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 
        7.89        13.61        33.90         1.08         0.76         4.93 
TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 
        2.83        30.64         5.95         6.81         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         3.95         7.79         1.48 
TCGA-06-6693 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 
        0.49         8.32        12.85         4.77         1.55         4.77 
TCGA-06-6701 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-08-0244 TCGA-08-0245 TCGA-08-0344 
        4.96         1.87         3.12        22.68        34.75       108.82 
TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 
        1.74         4.34        13.78        10.39         7.59         3.42 
TCGA-08-0351 TCGA-08-0352 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 
       53.82         1.28        15.06        22.52        14.70        35.64 
TCGA-08-0359 TCGA-08-0375 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0509 
        0.95         9.17        15.72         3.19        10.59         0.56 
TCGA-08-0514 TCGA-08-0516 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 
        8.52        18.44         1.28        10.75         4.80         6.54 
TCGA-08-0529 TCGA-08-0531 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0657 
       17.33         5.52         1.64        10.39         5.95         0.10 
TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 
       38.17        25.97        24.13        18.12        28.41        12.43 
TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 
       43.10         5.49         9.11        14.86        14.27        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-12-0829 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 TCGA-12-1092 
       20.58       127.59         5.82         6.25        30.54        21.63 
TCGA-12-1093 TCGA-12-1094 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1598 
       11.97        11.38         9.11        14.53         3.98         9.44 
TCGA-12-1599 TCGA-12-1600 TCGA-12-3644 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 
       25.28        13.61        59.41        25.78        11.54        10.95 
TCGA-12-3651 TCGA-12-3652 TCGA-12-5295 TCGA-12-5301 TCGA-14-0740 TCGA-14-0781 
       11.77        34.52        13.12         2.04        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-14-0867 TCGA-14-0871 TCGA-14-1034 
        1.35         2.89        26.33         2.04        28.93        15.95 
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         6.15 
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-15-1444 TCGA-15-1446 
        7.17        17.49         7.96         3.78        50.53        19.10 
TCGA-15-1447 TCGA-15-1449 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 TCGA-16-1047 
       53.19         5.52         9.93        26.07        16.31         0.82 
TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1460 TCGA-19-0955 
        9.90        13.35         3.65        18.28         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-19-2631 TCGA-19-5950 TCGA-19-5951 TCGA-19-5953 
        0.16         4.08         7.00        11.28         8.02         4.73 
TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-A6J5 
        7.96         1.78         6.51         5.39         5.29        16.57 
TCGA-26-1438 TCGA-26-1440 TCGA-26-1442 TCGA-26-1799 TCGA-26-5132 TCGA-26-5133 
       10.03         9.73        31.33         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         1.22         1.58         7.92         2.33 
TCGA-27-1830 TCGA-27-1831 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 
        4.80        16.60        18.25        33.14        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-28-5207 TCGA-28-5208 TCGA-28-5211 TCGA-28-5214 
        0.66         7.30         9.04        15.58        11.77        14.20 
TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-6450 TCGA-32-1970 
        7.79        13.64         4.21        22.68         5.42        15.39 
TCGA-32-1973 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 TCGA-32-1982 TCGA-32-1986 
       21.07         0.10        15.85        19.50         4.67        12.69 
TCGA-32-1987 TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 TCGA-32-2616 TCGA-32-2632 
       14.86        16.93        12.23        20.78         7.36         8.84 
TCGA-32-2634 TCGA-32-2638 TCGA-32-4213 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 
       22.78        21.17        19.86        10.62         0.85        13.35 
TCGA-41-2573 TCGA-41-2575 TCGA-41-3393 TCGA-41-3915 TCGA-41-6646 TCGA-74-6577 
        8.94         9.53         4.44        11.84         7.76         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 
        7.73         7.79         1.61        17.72        26.30 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              0.2               0.1 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            92.65            127.59 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            10.49              9.93 
[1] "0.2 - 92.7 (10.5)" "0.1 - 127.6 (9.9)"
[1] "hr=" "1.1"
D52V2, continuous
D52V3, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    53  70
  6Q LOSS WILD-TYPE 167 270
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     53   70
  6Q LOSS WILD-TYPE  167  270
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE              53               167
  MALE                70               270
[1] 2 2
[1] FALSE
D52V4, continuous
                   vv
clus                GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  6Q LOSS MUTATED                               4                   5
  6Q LOSS WILD-TYPE                            13                  13
                   vv
clus                UNTREATED PRIMARY (DE NOVO) GBM
  6Q LOSS MUTATED                               114
  6Q LOSS WILD-TYPE                             411
D52V5, multiclass
                                 clus
vv                                6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                 4                13
  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"
D52V6, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    84  39
  6Q LOSS WILD-TYPE 298 139
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     84   39
  6Q LOSS WILD-TYPE  298  139
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  NO               84               298
  YES              39               139
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6Q LOSS MUTATED       5                        11   101
  6Q LOSS WILD-TYPE     8                        28   384
D52V7, multiclass
                           clus
vv                          6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  ASIAN                                   5                 8
  BLACK OR AFRICAN AMERICAN              11                28
  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"
D52V8, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED     1 103
  6Q LOSS WILD-TYPE  11 359
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      1  103
  6Q LOSS WILD-TYPE   11  359
                        clus
vv                       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                11
  NOT HISPANIC OR LATINO             103               359
[1] 2 2
[1] FALSE

Clustering(53) Variable = 7P LOSS MUTATION ANALYSIS
D53V1, survival
                   sevent
clus2                 0   1
  7P LOSS MUTATED     2   6
  7P LOSS WILD-TYPE  96 456
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                8               552 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                6               456 
$`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        18.02         4.70        18.44 
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 
        9.17         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        55.86        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        10.36        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 
        0.23        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         0.16        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        16.21         2.70         0.26 
TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 
        4.04        47.31         0.10         3.58        22.72        32.52 
TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 
       10.52        18.74        14.07        23.08        22.16        10.75 
TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 
        0.20         9.21         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 
       16.70         9.80         7.86        19.46        46.59        11.80 
TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 
       12.79         8.65         3.19         5.46         9.44        11.80 
TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 
        2.56        56.88        10.65         5.29        19.04         3.12 
TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 
       13.02         0.23         2.20         2.73        91.00         2.01 
TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 
       53.98        19.00         2.53        40.37        73.84        26.33 
TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 
       28.47        14.93        10.29        18.31         4.67         7.04 
TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 
        2.60         0.39         6.48         5.49         3.91         4.96 
TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0237 
       11.84         0.20        12.43        22.49         0.36        10.36 
TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 
       11.80        20.42        14.96        10.32         5.52         0.26 
TCGA-06-0409 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 
       70.52         8.05         0.16        35.01        12.33         3.22 
TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 
        4.47         9.67         2.04        23.57         9.40        22.32 
TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 
       19.56         5.39         2.70         2.17         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        22.98         5.85         5.42 
TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 
       20.94         7.43         6.35         3.58        26.79         8.65 
TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 TCGA-06-2557 TCGA-06-2558 
        7.89        13.61        33.90        15.32         1.08         0.76 
TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 
        4.93         9.27         2.83        30.64         5.95         6.81 
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        11.24         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         3.95         7.79 
TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 
        5.39         1.48         0.49         7.36         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-08-0244 TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 
        2.56        22.68        34.75         3.91       108.82         1.74 
TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 
        4.34        13.78        10.39         7.59         3.42        53.82 
TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 
        1.28         6.41        15.06        22.52        14.70        35.64 
TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 
       19.53         0.95         9.17        10.85        15.72         3.19 
TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 
       10.59         0.30         0.56         3.52        11.77         8.52 
TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 
       58.19         1.28        10.75         4.80         6.54        15.98 
TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 
       17.33         5.52        14.01        14.43         1.64        10.39 
TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 
        5.95         7.17        65.92         0.10        38.17        25.97 
TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 
       24.13         6.12         2.63        18.12        28.41        12.43 
TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 
       53.10        43.10         5.49         9.11        14.86        14.27 
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         6.25 
TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 
       30.54        21.63        11.97        11.38        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         3.42         9.44        25.28        13.61 
TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 
        6.41        59.41        43.23        25.78        11.54        10.95 
TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 
       11.77        34.52        11.74        13.12         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-14-1454 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 
        6.15        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 
        9.86        50.53        19.10        53.19         5.52         3.91 
TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 
        9.93        26.07        16.31         4.31        29.03         0.82 
TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 
        9.90        13.35         3.65        18.28        13.97         6.41 
TCGA-19-0955 TCGA-19-0957 TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 
       11.77        21.90         0.43        14.27         3.39        10.75 
TCGA-19-1386 TCGA-19-1387 TCGA-19-1388 TCGA-19-1389 TCGA-19-1390 TCGA-19-1392 
        9.07         5.95        12.95         4.64        25.38         3.48 
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        16.47         7.00 
TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 
        7.04         6.64        11.28         8.02        18.64         4.73 
TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 
        7.96         1.78         6.51         5.39         5.29         5.42 
TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 
        3.98        16.57        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-27-1830 TCGA-27-1831 
        1.22         1.58         7.92         2.33         4.80        16.60 
TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 
        9.86        18.25        33.14        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 
        3.91         9.04        15.58        14.53        11.77        31.27 
TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 
       14.20         7.79        13.64         4.21        22.68        10.49 
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        21.17        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        10.62         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        11.54         7.76 
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 

  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 
            18.23              9.98 
[1] "3.8 - 47.1 (18.2)"  "0.1 - 127.6 (10.0)"
[1] "hr=" "1.5"
D53V2, continuous
D53V3, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     3   5
  7P LOSS WILD-TYPE 217 335
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      3    5
  7P LOSS WILD-TYPE  217  335
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  FEMALE               3               217
  MALE                 5               335
[1] 2 2
[1] FALSE
D53V4, continuous
                   vv
clus                GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  7P LOSS MUTATED                               0                   0
  7P LOSS WILD-TYPE                            17                  18
                   vv
clus                UNTREATED PRIMARY (DE NOVO) GBM
  7P LOSS MUTATED                                 8
  7P LOSS WILD-TYPE                             517
D53V5, multiclass
                                 clus
vv                                7P LOSS MUTATED 7P LOSS WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                 0                17
  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"
D53V6, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     7   1
  7P LOSS WILD-TYPE 375 177
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      7    1
  7P LOSS WILD-TYPE  375  177
     clus
vv    7P LOSS MUTATED 7P LOSS WILD-TYPE
  NO                7               375
  YES               1               177
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7P LOSS MUTATED       0                         1     7
  7P LOSS WILD-TYPE    13                        38   478
D53V7, multiclass
                           clus
vv                          7P LOSS MUTATED 7P LOSS WILD-TYPE
  ASIAN                                   0                13
  BLACK OR AFRICAN AMERICAN               1                38
  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"
D53V8, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     0   8
  7P LOSS WILD-TYPE  12 454
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      0    8
  7P LOSS WILD-TYPE   12  454
                        clus
vv                       7P LOSS MUTATED 7P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                12
  NOT HISPANIC OR LATINO               8               454
[1] 2 2
[1] FALSE

Clustering(54) Variable = 7Q LOSS MUTATION ANALYSIS
D54V1, survival
                   sevent
clus2                 0   1
  7Q LOSS MUTATED     1   5
  7Q LOSS WILD-TYPE  97 457
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                6               554 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                5               457 
$`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        18.02         4.70        18.44         3.78 

$`7Q LOSS WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 
        9.17         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        55.86        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        10.36        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         0.23        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         0.16 
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        16.21         2.70 
TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 
        0.26         4.04        47.31         0.10         3.58        22.72 
TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 
       32.52        10.52        18.74        14.07        23.08        22.16 
TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 
       10.75         0.20         9.21         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        16.70         9.80         7.86        19.46        46.59 
TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 
       11.80        12.79         8.65         3.19         5.46         9.44 
TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 
       11.80         2.56        56.88        10.65         5.29        19.04 
TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 
        3.12        13.02         0.23         2.20         2.73        91.00 
TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 
        2.01        53.98        19.00         2.53        40.37        73.84 
TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 
       26.33        28.47        14.93        10.29        18.31         4.67 
TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 
        7.04         2.60         0.39         6.48         5.49         3.91 
TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 
        4.96        11.84         0.20        12.43        22.49         0.36 
TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 
       10.36        11.80        20.42        14.96        10.32         5.52 
TCGA-06-0402 TCGA-06-0409 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 
        0.26        70.52         8.05         0.16        35.01        12.33 
TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 
        3.22         4.47         9.67         2.04        23.57         9.40 
TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 
       22.32        19.56         5.39         2.70         2.17         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        22.98         5.85 
TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 
        5.42        20.94         7.43         6.35         3.58        26.79 
TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 TCGA-06-2557 
        8.65         7.89        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 
        0.76         4.93         9.27         2.83        30.64         5.95 
TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-5408 
        6.81         5.98         4.37         0.43        31.50        11.24 
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         3.95 
TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 
        7.79         5.39         1.48         0.49         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-08-0244 TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 
        3.12         2.56        22.68        34.75         3.91       108.82 
TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 
        1.74         4.34        13.78        10.39         7.59         3.42 
TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 
       53.82         1.28         6.41        15.06        22.52        14.70 
TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 
       35.64        19.53         0.95         9.17        10.85        15.72 
TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 
        3.19        10.59         0.30         0.56         3.52        11.77 
TCGA-08-0514 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 
        8.52        58.19         1.28        10.75         4.80         6.54 
TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 
       15.98        17.33         5.52        14.01        14.43         1.64 
TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 
       10.39         5.95         7.17        65.92         0.10        38.17 
TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 
       25.97        24.13         6.12         2.63        18.12        28.41 
TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 
       12.43        53.10        43.10         5.49         9.11        14.86 
TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 
       14.27        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 
        6.25        30.54        21.63        11.97        11.38        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         3.42         9.44        25.28 
TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 
       13.61         6.41        59.41        43.23        25.78        11.54 
TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 
       10.95        11.77        34.52        11.74        13.12         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         6.15        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-14-4157 TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 
        3.42         9.86        50.53        19.10        53.19         5.52 
TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 
        3.91         9.93        26.07        16.31         4.31        29.03 
TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 
        0.82         9.90        13.35         3.65        18.28        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         0.43        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         3.48         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 
       16.47         7.00         7.04         6.64        11.28         8.02 
TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 
       18.64         4.73         7.96         1.78         6.51         5.39 
TCGA-19-5959 TCGA-19-5960 TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 
        5.29         5.42         3.98        16.57        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         1.22         1.58         7.92         2.33 
TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 
        4.80        16.60         9.86        18.25        33.14        21.30 
TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 
       30.05        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-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 
        7.30         5.26         3.91         9.04        15.58        14.53 
TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 
       11.77        31.27        14.20         7.79        13.64         4.21 
TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 
       22.68        10.49         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        21.17        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        10.62         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-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 
       11.54         7.76         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 
       26.30         5.92 

  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 
            18.23              9.98 
[1] "3.8 - 47.1 (18.2)"  "0.1 - 127.6 (10.0)"
[1] "hr=" "1.3"
D54V2, continuous
D54V3, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     2   4
  7Q LOSS WILD-TYPE 218 336
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      2    4
  7Q LOSS WILD-TYPE  218  336
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  FEMALE               2               218
  MALE                 4               336
[1] 2 2
[1] FALSE
D54V4, continuous
                   vv
clus                GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  7Q LOSS MUTATED                               0                   0
  7Q LOSS WILD-TYPE                            17                  18
                   vv
clus                UNTREATED PRIMARY (DE NOVO) GBM
  7Q LOSS MUTATED                                 6
  7Q LOSS WILD-TYPE                             519
D54V5, multiclass
                                 clus
vv                                7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                 0                17
  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"
D54V6, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     5   1
  7Q LOSS WILD-TYPE 377 177
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      5    1
  7Q LOSS WILD-TYPE  377  177
     clus
vv    7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  NO                5               377
  YES               1               177
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7Q LOSS MUTATED       0                         1     5
  7Q LOSS WILD-TYPE    13                        38   480
D54V7, multiclass
                           clus
vv                          7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  ASIAN                                   0                13
  BLACK OR AFRICAN AMERICAN               1                38
  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"
D54V8, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     0   6
  7Q LOSS WILD-TYPE  12 456
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      0    6
  7Q LOSS WILD-TYPE   12  456
                        clus
vv                       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                12
  NOT HISPANIC OR LATINO               6               456
[1] 2 2
[1] FALSE

Clustering(55) Variable = 8P LOSS MUTATION ANALYSIS
D55V1, survival
                   sevent
clus2                 0   1
  8P LOSS MUTATED    13  45
  8P LOSS WILD-TYPE  85 417
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               58               502 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               45               417 
$`8P LOSS MUTATED`
TCGA-02-0001 TCGA-02-0025 TCGA-02-0059 TCGA-02-0060 TCGA-02-0086 TCGA-02-0106 
        9.17        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        16.21 
TCGA-06-0159 TCGA-06-0171 TCGA-06-0195 TCGA-06-0216 TCGA-06-0410 TCGA-06-0743 
        9.44        13.02         7.04        22.49         4.70        22.32 
TCGA-06-2570 TCGA-06-5408 TCGA-06-5411 TCGA-06-5413 TCGA-06-6693 TCGA-08-0246 
       31.50        11.24         8.35         8.81         0.49         3.91 
TCGA-08-0392 TCGA-08-0510 TCGA-08-0525 TCGA-12-0776 TCGA-12-0826 TCGA-12-0827 
        0.30         3.52        15.98         9.11        27.78        38.76 
TCGA-12-1098 TCGA-12-1598 TCGA-14-0736 TCGA-14-0862 TCGA-14-1034 TCGA-14-1450 
        3.98         9.44        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         1.22         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         3.91        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        55.86        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        10.36        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         0.23        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         0.16        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         0.26         4.04        47.31         0.10 
TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 
        3.58        22.72        32.52        10.52        18.74        14.07 
TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 
       23.08        22.16        10.75         0.20         9.21         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        16.70         9.80         7.86 
TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 
       19.46        46.59        11.80        12.79         8.65         3.19 
TCGA-06-0158 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 
        5.46        11.80         2.56        56.88        10.65         5.29 
TCGA-06-0168 TCGA-06-0169 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 
       19.04         3.12         0.23         2.20         2.73        91.00 
TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 
        2.01        53.98        19.00         2.53        40.37        73.84 
TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 
       26.33        28.47        14.93        10.29        18.31         4.67 
TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 
        2.60         0.39         6.48         5.49         3.91         4.96 
TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 
       11.84         0.20        12.43         0.36        18.02        10.36 
TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 
       11.80        20.42        14.96        10.32         5.52         0.26 
TCGA-06-0409 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 
       70.52         8.05         0.16        35.01        12.33         3.22 
TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0744 
        4.47         9.67         2.04        23.57         9.40        19.56 
TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 
        5.39         2.70         2.17         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        22.98         5.85         5.42        20.94 
TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 
        7.43         6.35         3.58        26.79         8.65         7.89 
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         0.76         4.93 
TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 
        9.27         2.83        30.64         5.95         6.81         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         3.95 
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-A5U1 TCGA-06-A6S0 
        4.77         1.55         4.77         4.96         1.87         3.12 
TCGA-06-A6S1 TCGA-08-0244 TCGA-08-0245 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 
        2.56        22.68        34.75       108.82         1.74         4.34 
TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 
       13.78        10.39         7.59         3.42        53.82         1.28 
TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 
        6.41        15.06        22.52        14.70        35.64        19.53 
TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 
        0.95         9.17        10.85        15.72         3.19        10.59 
TCGA-08-0509 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 
        0.56        11.77         8.52        18.44        58.19         1.28 
TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 
       10.75         4.80         6.54        17.33         5.52        14.01 
TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 
       14.43         1.64        10.39         5.95         7.17        65.92 
TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 
        0.10        38.17        25.97        24.13         6.12         2.63 
TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 
       18.12        28.41        12.43        53.10        43.10         5.49 
TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 
       14.86        14.27        91.76        24.79        18.48        10.62 
TCGA-12-0822 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 
       23.51         8.94        20.58       127.59         5.82         6.25 
TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 
       30.54        21.63        11.97        11.38        15.85         9.11 
TCGA-12-1097 TCGA-12-1099 TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 
       14.53         3.42        25.28        13.61         6.41        59.41 
TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 
       43.23        25.78        11.54        10.95        11.77        34.52 
TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0740 TCGA-14-0781 
       11.74        13.12         3.22         2.04        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-14-0865 TCGA-14-0866 TCGA-14-0867 TCGA-14-0871 
        1.35         5.39        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 
        6.15        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         9.86 
TCGA-15-1444 TCGA-15-1446 TCGA-15-1449 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 
       50.53        19.10         5.52         9.93        26.07        16.31 
TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 
        4.31        29.03         0.82         9.90        13.35         3.65 
TCGA-16-1062 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 TCGA-19-0962 TCGA-19-0963 
       18.28         6.41        11.77        21.90         0.43        14.27 
TCGA-19-0964 TCGA-19-1386 TCGA-19-1387 TCGA-19-1388 TCGA-19-1389 TCGA-19-1390 
        3.39         9.07         5.95        12.95         4.64        25.38 
TCGA-19-1392 TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 
        3.48        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        16.47         7.00 
TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 
        7.04         6.64        11.28         8.02        18.64         4.73 
TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 
        7.96         1.78         6.51         5.39         5.29         5.42 
TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 
        3.98        16.57        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-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 
        7.92         2.33         4.80        16.60         9.86        18.25 
TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 
       33.14        21.30        30.05        14.04        11.51        24.76 
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-28-1746 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-28-2506 TCGA-28-2513 TCGA-28-5207 
        1.55         2.83         0.13         6.74         7.30         9.04 
TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 
       15.58        14.53        11.77        31.27        14.20         7.79 
TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 
       13.64         4.21        22.68        10.49         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        21.17 
TCGA-32-4211 TCGA-32-4213 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 
       12.59        19.86        10.62         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        11.54         7.76 
TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-76-4925 
        3.45        20.91         4.34        14.33         8.22         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 
        1.61        17.72        26.30         5.92 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              0.3               0.1 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            58.78            127.59 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             9.14             10.36 
[1] "0.3 - 58.8 (9.1)"   "0.1 - 127.6 (10.4)"
[1] "hr=" "1.1"
D55V2, continuous
D55V3, binary
                   cls
clus                  0   1
  8P LOSS MUTATED    28  30
  8P LOSS WILD-TYPE 192 310
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     28   30
  8P LOSS WILD-TYPE  192  310
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE              28               192
  MALE                30               310
[1] 2 2
[1] FALSE
D55V4, continuous
                   vv
clus                GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  8P LOSS MUTATED                               1                   1
  8P LOSS WILD-TYPE                            16                  17
                   vv
clus                UNTREATED PRIMARY (DE NOVO) GBM
  8P LOSS MUTATED                                56
  8P LOSS WILD-TYPE                             469
D55V5, multiclass
                                 clus
vv                                8P LOSS MUTATED 8P LOSS WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                 1                16
  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"
D55V6, binary
                   cls
clus                  0   1
  8P LOSS MUTATED    42  16
  8P LOSS WILD-TYPE 340 162
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     42   16
  8P LOSS WILD-TYPE  340  162
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  NO               42               340
  YES              16               162
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8P LOSS MUTATED       5                         2    46
  8P LOSS WILD-TYPE     8                        37   439
D55V7, multiclass
                           clus
vv                          8P LOSS MUTATED 8P LOSS WILD-TYPE
  ASIAN                                   5                 8
  BLACK OR AFRICAN AMERICAN               2                37
  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"
D55V8, binary
                   cls
clus                  0   1
  8P LOSS MUTATED     0  48
  8P LOSS WILD-TYPE  12 414
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      0   48
  8P LOSS WILD-TYPE   12  414
                        clus
vv                       8P LOSS MUTATED 8P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                12
  NOT HISPANIC OR LATINO              48               414
[1] 2 2
[1] FALSE

Clustering(56) Variable = 8Q LOSS MUTATION ANALYSIS
D56V1, survival
                   sevent
clus2                 0   1
  8Q LOSS MUTATED     8  34
  8Q LOSS WILD-TYPE  90 428
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               42               518 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               34               428 
$`8Q LOSS MUTATED`
TCGA-02-0001 TCGA-02-0025 TCGA-02-0059 TCGA-02-0086 TCGA-02-0115 TCGA-02-0281 
        9.17        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        16.21         9.44        13.02         7.04        22.49 
TCGA-06-0410 TCGA-06-0743 TCGA-06-5408 TCGA-06-5411 TCGA-06-5413 TCGA-08-0246 
        4.70        22.32        11.24         8.35         8.81         3.91 
TCGA-08-0392 TCGA-08-0510 TCGA-08-0525 TCGA-12-0776 TCGA-12-0826 TCGA-12-1598 
        0.30         3.52        15.98         9.11        27.78         9.44 
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         1.22         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        55.86        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        10.36        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         0.23 
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         0.16 
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 
        0.26         4.04        47.31         0.10         3.58        22.72 
TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 
       32.52        10.52        18.74        14.07        23.08        22.16 
TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 
       10.75         0.20         9.21         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        16.70         9.80         7.86        19.46        46.59 
TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0160 
       11.80        12.79         8.65         3.19         5.46        11.80 
TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 
        2.56        56.88        10.65         5.29        19.04         3.12 
TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 
        0.23         2.20         2.73        91.00         2.01        53.98 
TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 
       19.00         2.53        40.37        73.84        26.33        28.47 
TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0197 TCGA-06-0201 
       14.93        10.29        18.31         4.67         2.60         0.39 
TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 
        6.48         5.49         3.91         4.96        11.84         0.20 
TCGA-06-0214 TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 
       12.43         0.36        18.02        10.36        11.80        20.42 
TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0412 
       14.96        10.32         5.52         0.26        70.52         8.05 
TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 
        0.16        35.01        12.33         3.22         4.47         9.67 
TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 
        2.04        23.57         9.40        19.56         5.39         2.70 
TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 
        2.17         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 
       22.98         5.85         5.42        20.94         7.43         6.35 
TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 
        3.58        26.79         8.65         7.89        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         0.76         4.93         9.27         2.83 
TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 
       30.64         5.95         6.81         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         3.95         7.79 
TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 
        5.39         1.48         0.49         7.36         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-08-0244 TCGA-08-0245 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 
        2.56        22.68        34.75       108.82         1.74         4.34 
TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 
       13.78        10.39         7.59         3.42        53.82         1.28 
TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 
        6.41        15.06        22.52        14.70        35.64        19.53 
TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 
        0.95         9.17        10.85        15.72         3.19        10.59 
TCGA-08-0509 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 
        0.56        11.77         8.52        18.44        58.19         1.28 
TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 
       10.75         4.80         6.54        17.33         5.52        14.01 
TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 
       14.43         1.64        10.39         5.95         7.17        65.92 
TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 
        0.10        38.17        25.97        24.13         6.12         2.63 
TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 
       18.12        28.41        12.43        53.10        43.10         5.49 
TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 
       14.86        14.27        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 
        6.25        30.54        21.63        11.97        11.38        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         3.42        25.28        13.61 
TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 
        6.41        59.41        43.23        25.78        11.54        10.95 
TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 
       11.77        34.52        11.74        13.12         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-14-0817 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-14-1037 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         6.15        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-15-1447 
        3.78         3.42         9.86        50.53        19.10        53.19 
TCGA-15-1449 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 
        5.52         9.93        26.07        16.31         4.31        29.03 
TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 
        0.82         9.90        13.35         3.65        18.28        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         0.43        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         3.48         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 
       16.47         7.00         7.04         6.64        11.28         8.02 
TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 
       18.64         4.73         7.96         1.78         6.51         5.39 
TCGA-19-5959 TCGA-19-5960 TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1440 
        5.29         5.42         3.98        16.57        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-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-27-1830 TCGA-27-1831 
        8.88         1.58         7.92         2.33         4.80        16.60 
TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 
        9.86        18.25        33.14        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-28-2506 
        8.48         1.22         1.55         2.83         0.13         6.74 
TCGA-28-2513 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 
        7.30         3.91         9.04        15.58        14.53        11.77 
TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 
       31.27        14.20         7.79        13.64         4.21        22.68 
TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 
       10.49         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-32-4211 TCGA-32-4213 
        8.84        22.78        21.17        21.14        12.59        19.86 
TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 
       10.62         0.85        13.35         8.94         9.53         0.99 
TCGA-41-3393 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 TCGA-74-6573 TCGA-74-6575 
        4.44         0.20        11.54         7.76         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-76-4935 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 
       26.30         5.92 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
              0.3               0.1 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            58.78            127.59 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            8.960            10.375 
[1] "0.3 - 58.8 (9.0)"   "0.1 - 127.6 (10.4)"
[1] "hr=" "1.2"
D56V2, continuous
D56V3, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    19  23
  8Q LOSS WILD-TYPE 201 317
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     19   23
  8Q LOSS WILD-TYPE  201  317
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE              19               201
  MALE                23               317
[1] 2 2
[1] FALSE
D56V4, continuous
                   vv
clus                GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  8Q LOSS MUTATED                               1                   1
  8Q LOSS WILD-TYPE                            16                  17
                   vv
clus                UNTREATED PRIMARY (DE NOVO) GBM
  8Q LOSS MUTATED                                40
  8Q LOSS WILD-TYPE                             485
D56V5, multiclass
                                 clus
vv                                8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                 1                16
  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"
D56V6, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    29  13
  8Q LOSS WILD-TYPE 353 165
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     29   13
  8Q LOSS WILD-TYPE  353  165
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  NO               29               353
  YES              13               165
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8Q LOSS MUTATED       2                         2    33
  8Q LOSS WILD-TYPE    11                        37   452
D56V7, multiclass
                           clus
vv                          8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  ASIAN                                   2                11
  BLACK OR AFRICAN AMERICAN               2                37
  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"
D56V8, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     0  35
  8Q LOSS WILD-TYPE  12 427
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      0   35
  8Q LOSS WILD-TYPE   12  427
                        clus
vv                       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                12
  NOT HISPANIC OR LATINO              35               427
[1] 2 2
[1] FALSE

Clustering(57) Variable = 9P LOSS MUTATION ANALYSIS
D57V1, survival
                   sevent
clus2                 0   1
  9P LOSS MUTATED    33 162
  9P LOSS WILD-TYPE  65 300
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              195               365 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              162               300 
$`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        55.86        10.36         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         0.26         4.04        22.72        18.74 
TCGA-06-0141 TCGA-06-0145 TCGA-06-0150 TCGA-06-0154 TCGA-06-0158 TCGA-06-0162 
        9.21         2.33        19.46        12.79         5.46         2.56 
TCGA-06-0164 TCGA-06-0166 TCGA-06-0171 TCGA-06-0173 TCGA-06-0175 TCGA-06-0177 
       56.88         5.29        13.02         0.23         2.73         2.01 
TCGA-06-0185 TCGA-06-0188 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 
       73.84        28.47         5.49         3.91         4.96        11.84 
TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0394 TCGA-06-0409 TCGA-06-0412 
        0.36        18.02        10.36        10.32        70.52         8.05 
TCGA-06-0649 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0750 
        2.04        22.32        19.56         5.39         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        22.98         5.42         7.43         6.35 
TCGA-06-1800 TCGA-06-1802 TCGA-06-1806 TCGA-06-2557 TCGA-06-2561 TCGA-06-2562 
       26.79         7.89        15.32         1.08         9.27         2.83 
TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-5412 TCGA-06-5415 TCGA-06-5418 
        6.81         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         0.49         7.36         8.32 
TCGA-06-6697 TCGA-06-6699 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-08-0246 TCGA-08-0348 
       12.85         1.55         3.12         2.56         3.91        10.39 
TCGA-08-0353 TCGA-08-0355 TCGA-08-0358 TCGA-08-0375 TCGA-08-0390 TCGA-08-0510 
        6.41        22.52        19.53         9.17        10.59         3.52 
TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0525 TCGA-12-0615 TCGA-12-0654 
        8.52        18.44        58.19        15.98        14.01         7.17 
TCGA-12-0656 TCGA-12-0670 TCGA-12-0707 TCGA-12-0778 TCGA-12-0818 TCGA-12-0821 
       65.92        25.97        28.41        14.86        91.76        10.62 
TCGA-12-0826 TCGA-12-0827 TCGA-12-1088 TCGA-12-1092 TCGA-12-1093 TCGA-12-1095 
       27.78        38.76       127.59        21.63        11.97        15.85 
TCGA-12-1097 TCGA-12-1599 TCGA-12-1602 TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 
       14.53        25.28         6.41        11.77        34.52        11.74 
TCGA-14-0736 TCGA-14-0740 TCGA-14-0783 TCGA-14-0786 TCGA-14-0787 TCGA-14-0813 
       15.12        11.97         6.21        23.05         2.24         1.35 
TCGA-14-0862 TCGA-14-1037 TCGA-14-1395 TCGA-14-1396 TCGA-14-1402 TCGA-14-1453 
        2.89        19.30         1.38         1.12        32.05         1.15 
TCGA-14-1458 TCGA-15-1444 TCGA-15-1447 TCGA-16-0846 TCGA-16-0861 TCGA-16-1045 
        6.15        50.53        53.19         3.91         4.31        29.03 
TCGA-16-1047 TCGA-16-1056 TCGA-16-1063 TCGA-19-0955 TCGA-19-0960 TCGA-19-0963 
        0.82        13.35        13.97        11.77         8.61        14.27 
TCGA-19-1388 TCGA-19-1786 TCGA-19-2619 TCGA-19-2620 TCGA-19-2625 TCGA-19-2629 
       12.95         7.17         9.67         4.87         4.08        16.47 
TCGA-19-5947 TCGA-19-5950 TCGA-19-5952 TCGA-19-5955 TCGA-19-5958 TCGA-19-5959 
        6.64        11.28        18.64         1.78         5.39         5.29 
TCGA-19-A6J4 TCGA-26-1439 TCGA-26-1442 TCGA-26-6174 TCGA-27-1833 TCGA-27-2521 
        3.98        13.87        31.33         2.33        18.25        10.39 
TCGA-27-2526 TCGA-28-1750 TCGA-28-1756 TCGA-28-1757 TCGA-28-2502 TCGA-28-2506 
        2.86         8.35         2.83         0.13         0.66         6.74 
TCGA-28-2513 TCGA-28-5208 TCGA-28-5209 TCGA-28-5213 TCGA-28-5220 TCGA-32-1970 
        7.30        15.58        14.53        31.27        10.49        15.39 
TCGA-32-1973 TCGA-32-1976 TCGA-32-1991 TCGA-32-4208 TCGA-32-4211 TCGA-32-4213 
       21.07         0.49        16.93        21.14        12.59        19.86 
TCGA-32-4719 TCGA-41-2572 TCGA-41-2573 TCGA-41-3392 TCGA-41-3393 TCGA-41-4097 
       10.85        13.35         8.94         0.99         4.44         0.20 
TCGA-74-6575 TCGA-74-6584 TCGA-76-4928 TCGA-76-4931 TCGA-76-4935 TCGA-76-6282 
       20.91         7.50         3.09         9.17        10.78        17.06 
TCGA-76-6657 TCGA-76-6664 TCGA-OX-A56R 
        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 
        9.17         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         0.23 
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         0.16        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        16.21 
TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0129 TCGA-06-0130 TCGA-06-0133 
       47.31         0.10         3.58        32.52        10.52        14.07 
TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0142 TCGA-06-0143 
       23.08        22.16        10.75         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        16.70         9.80         7.86        46.59        11.80 
TCGA-06-0155 TCGA-06-0157 TCGA-06-0159 TCGA-06-0160 TCGA-06-0165 TCGA-06-0168 
        8.65         3.19         9.44        11.80        10.65        19.04 
TCGA-06-0169 TCGA-06-0174 TCGA-06-0176 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 
        3.12         2.20        91.00        53.98        19.00         2.53 
TCGA-06-0184 TCGA-06-0187 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 
       40.37        26.33        14.93        10.29        18.31         4.67 
TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0213 TCGA-06-0214 
        7.04         2.60         0.39         6.48         0.20        12.43 
TCGA-06-0216 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0397 TCGA-06-0402 
       22.49        11.80        20.42        14.96         5.52         0.26 
TCGA-06-0410 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 
        4.70         0.16        35.01        12.33         3.22         4.47 
TCGA-06-0648 TCGA-06-0650 TCGA-06-0686 TCGA-06-0749 TCGA-06-0877 TCGA-06-0878 
        9.67        23.57         9.40         2.17         5.65         7.17 
TCGA-06-0881 TCGA-06-0939 TCGA-06-1087 TCGA-06-1801 TCGA-06-1804 TCGA-06-1805 
        5.85        20.94         3.58         8.65        13.61        33.90 
TCGA-06-2558 TCGA-06-2559 TCGA-06-2563 TCGA-06-2564 TCGA-06-2569 TCGA-06-2570 
        0.76         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 
       11.24         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         3.95         5.39         1.48         4.77         4.77 
TCGA-06-6701 TCGA-06-A5U1 TCGA-08-0244 TCGA-08-0245 TCGA-08-0344 TCGA-08-0345 
        4.96         1.87        22.68        34.75       108.82         1.74 
TCGA-08-0346 TCGA-08-0347 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 
        4.34        13.78         7.59         3.42        53.82         1.28 
TCGA-08-0354 TCGA-08-0356 TCGA-08-0357 TCGA-08-0359 TCGA-08-0380 TCGA-08-0386 
       15.06        14.70        35.64         0.95        10.85        15.72 
TCGA-08-0389 TCGA-08-0392 TCGA-08-0509 TCGA-08-0512 TCGA-08-0518 TCGA-08-0520 
        3.19         0.30         0.56        11.77         1.28        10.75 
TCGA-08-0521 TCGA-08-0524 TCGA-08-0529 TCGA-08-0531 TCGA-12-0616 TCGA-12-0618 
        4.80         6.54        17.33         5.52        14.43         1.64 
TCGA-12-0619 TCGA-12-0620 TCGA-12-0657 TCGA-12-0662 TCGA-12-0688 TCGA-12-0691 
       10.39         5.95         0.10        38.17        24.13         6.12 
TCGA-12-0692 TCGA-12-0703 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 
        2.63        18.12        12.43        53.10        43.10         5.49 
TCGA-12-0776 TCGA-12-0780 TCGA-12-0819 TCGA-12-0820 TCGA-12-0822 TCGA-12-0828 
        9.11        14.27        24.79        18.48        23.51         8.94 
TCGA-12-0829 TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 TCGA-12-1094 TCGA-12-1096 
       20.58         5.82         6.25        30.54        11.38         9.11 
TCGA-12-1098 TCGA-12-1099 TCGA-12-1598 TCGA-12-1600 TCGA-12-3644 TCGA-12-3646 
        3.98         3.42         9.44        13.61        59.41        43.23 
TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 
       25.78        11.54        10.95        13.12         3.22         2.04 
TCGA-14-0781 TCGA-14-0789 TCGA-14-0790 TCGA-14-0812 TCGA-14-0817 TCGA-14-0865 
        0.95        11.24        13.78         3.25         5.39        16.50 
TCGA-14-0866 TCGA-14-0867 TCGA-14-0871 TCGA-14-1034 TCGA-14-1043 TCGA-14-1401 
       26.33         2.04        28.93        15.95         0.79         3.75 
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-14-1459 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-15-1446 TCGA-15-1449 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 
        9.86        19.10         5.52         9.93        26.07        16.31 
TCGA-16-1055 TCGA-16-1060 TCGA-16-1062 TCGA-16-1460 TCGA-19-0957 TCGA-19-0962 
        9.90         3.65        18.28         6.41        21.90         0.43 
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 
        3.48        12.66         3.25         0.13         1.08         7.53 
TCGA-19-2624 TCGA-19-2631 TCGA-19-4065 TCGA-19-5951 TCGA-19-5953 TCGA-19-5954 
        0.16         7.00         7.04         8.02         4.73         7.96 
TCGA-19-5956 TCGA-19-5960 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1440 TCGA-26-1443 
        6.51         5.42        16.57        10.03         9.73         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         1.22 
TCGA-26-5139 TCGA-26-6173 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1834 
        1.58         7.92         4.80        16.60         9.86        33.14 
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-27-2527 TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 
       16.08         7.59        14.40        15.78         0.20         2.53 
TCGA-28-1749 TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 TCGA-28-1755 TCGA-28-2509 
        9.21         7.63         8.48         1.22         1.55         4.77 
TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5211 TCGA-28-5214 TCGA-28-5215 
        5.26         3.91         9.04        11.77        14.20         7.79 
TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-6450 TCGA-32-1977 TCGA-32-1978 
       13.64         4.21        22.68         5.42         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-32-2615 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-32-4210 TCGA-32-5222 TCGA-41-2571 TCGA-41-2575 TCGA-41-3915 
       21.17         3.72        10.62         0.85         9.53        11.84 
TCGA-41-5651 TCGA-41-6646 TCGA-74-6573 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 
       11.54         7.76         3.45         4.34        14.33         8.22 
TCGA-76-4925 TCGA-76-4926 TCGA-76-4929 TCGA-76-4934 TCGA-76-6191 TCGA-76-6192 
        4.80         4.54         3.65         2.53        16.70         3.29 
TCGA-76-6193 TCGA-76-6280 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6661 
        2.70        11.38         8.35        20.98         4.83         0.23 
TCGA-76-6662 TCGA-76-6663 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
        9.27         7.73         1.61        17.72        26.30 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             0.13              0.10 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           127.59            108.82 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            10.36              9.90 
[1] "0.1 - 127.6 (10.4)" "0.1 - 108.8 (9.9)" 
[1] "hr=" "1.1"
D57V2, continuous
D57V3, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    79 116
  9P LOSS WILD-TYPE 141 224
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     79  116
  9P LOSS WILD-TYPE  141  224
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE              79               141
  MALE               116               224
[1] 2 2
[1] FALSE
D57V4, continuous
                   vv
clus                GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  9P LOSS MUTATED                               8                   6
  9P LOSS WILD-TYPE                             9                  12
                   vv
clus                UNTREATED PRIMARY (DE NOVO) GBM
  9P LOSS MUTATED                               181
  9P LOSS WILD-TYPE                             344
D57V5, multiclass
                                 clus
vv                                9P LOSS MUTATED 9P LOSS WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                 8                 9
  TREATED PRIMARY GBM                           6                12
  UNTREATED PRIMARY (DE NOVO) GBM             181               344
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V6, binary
                   cls
clus                  0   1
  9P LOSS MUTATED   135  60
  9P LOSS WILD-TYPE 247 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED    135   60
  9P LOSS WILD-TYPE  247  118
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  NO              135               247
  YES              60               118
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9P LOSS MUTATED       6                        17   166
  9P LOSS WILD-TYPE     7                        22   319
D57V7, multiclass
                           clus
vv                          9P LOSS MUTATED 9P LOSS WILD-TYPE
  ASIAN                                   6                 7
  BLACK OR AFRICAN AMERICAN              17                22
  WHITE                                 166               319
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V8, binary
                   cls
clus                  0   1
  9P LOSS MUTATED     1 167
  9P LOSS WILD-TYPE  11 295
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      1  167
  9P LOSS WILD-TYPE   11  295
                        clus
vv                       9P LOSS MUTATED 9P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                11
  NOT HISPANIC OR LATINO             167               295
[1] 2 2
[1] FALSE

Clustering(58) Variable = 9Q LOSS MUTATION ANALYSIS
D58V1, survival
                   sevent
clus2                 0   1
  9Q LOSS MUTATED    13  77
  9Q LOSS WILD-TYPE  85 385
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               90               470 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               77               385 
$`9Q LOSS MUTATED`
TCGA-02-0016 TCGA-02-0021 TCGA-02-0057 TCGA-02-0064 TCGA-02-0086 TCGA-02-0104 
       55.86        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        18.74         9.21        12.79         5.46 
TCGA-06-0162 TCGA-06-0173 TCGA-06-0177 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 
        2.56         0.23         2.01         5.49         3.91         4.96 
TCGA-06-0237 TCGA-06-0409 TCGA-06-0412 TCGA-06-0743 TCGA-06-0745 TCGA-06-0876 
       10.36        70.52         8.05        22.32         5.39        46.19 
TCGA-06-1086 TCGA-06-1802 TCGA-06-1806 TCGA-06-2557 TCGA-06-2561 TCGA-06-5412 
        6.35         7.89        15.32         1.08         9.27         4.54 
TCGA-06-5418 TCGA-06-5859 TCGA-06-6694 TCGA-06-A6S1 TCGA-08-0246 TCGA-08-0355 
        2.73         4.57         7.36         2.56         3.91        22.52 
TCGA-08-0358 TCGA-08-0375 TCGA-08-0510 TCGA-08-0516 TCGA-08-0517 TCGA-12-0615 
       19.53         9.17         3.52        18.44        58.19        14.01 
TCGA-12-0707 TCGA-12-0821 TCGA-12-0826 TCGA-12-1091 TCGA-12-1093 TCGA-12-1602 
       28.41        10.62        27.78        30.54        11.97         6.41 
TCGA-12-3652 TCGA-12-3653 TCGA-14-0736 TCGA-14-0740 TCGA-14-1395 TCGA-14-1396 
       34.52        11.74        15.12        11.97         1.38         1.12 
TCGA-14-1453 TCGA-15-1444 TCGA-15-1447 TCGA-16-0846 TCGA-16-1045 TCGA-16-1047 
        1.15        50.53        53.19         3.91        29.03         0.82 
TCGA-19-0963 TCGA-19-1388 TCGA-19-1786 TCGA-19-2619 TCGA-19-2620 TCGA-19-5950 
       14.27        12.95         7.17         9.67         4.87        11.28 
TCGA-19-5958 TCGA-19-A6J4 TCGA-26-1439 TCGA-27-2521 TCGA-28-1750 TCGA-28-1757 
        5.39         3.98        13.87        10.39         8.35         0.13 
TCGA-28-2506 TCGA-28-2513 TCGA-28-5220 TCGA-32-1970 TCGA-32-4208 TCGA-32-4211 
        6.74         7.30        10.49        15.39        21.14        12.59 
TCGA-32-4213 TCGA-32-4719 TCGA-41-2572 TCGA-74-6584 TCGA-76-6282 TCGA-OX-A56R 
       19.86        10.85        13.35         7.50        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 
        9.17         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        10.36        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         0.23        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         0.16        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        16.21 
TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 
        2.70         0.26         4.04        47.31         0.10         3.58 
TCGA-06-0129 TCGA-06-0130 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 
       32.52        10.52        14.07        23.08        22.16        10.75 
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        16.70 
TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0155 
        9.80         7.86        19.46        46.59        11.80         8.65 
TCGA-06-0157 TCGA-06-0159 TCGA-06-0160 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 
        3.19         9.44        11.80        56.88        10.65         5.29 
TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 
       19.04         3.12        13.02         2.20         2.73        91.00 
TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 
       53.98        19.00         2.53        40.37        73.84        26.33 
TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 
       28.47        14.93        10.29        18.31         4.67         7.04 
TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 
        2.60         0.39         6.48        11.84         0.20        12.43 
TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 
       22.49         0.36        18.02        11.80        20.42        14.96 
TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0410 TCGA-06-0413 TCGA-06-0414 
       10.32         5.52         0.26         4.70         0.16        35.01 
TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 
       12.33         3.22         4.47         9.67         2.04        23.57 
TCGA-06-0686 TCGA-06-0744 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 
        9.40        19.56         2.70         2.17         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        22.98         5.85         5.42        20.94 
TCGA-06-1084 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1804 TCGA-06-1805 
        7.43         3.58        26.79         8.65        13.61        33.90 
TCGA-06-2558 TCGA-06-2559 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 
        0.76         4.93         2.83        30.64         5.95         6.81 
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        11.24         3.55 
TCGA-06-5411 TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 TCGA-06-5856 
        8.35         8.81         8.98         8.55         6.71         3.75 
TCGA-06-5858 TCGA-06-6388 TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 
        6.15         3.95         7.79         5.39         1.48         0.49 
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-A5U1 TCGA-06-A6S0 TCGA-08-0244 TCGA-08-0245 TCGA-08-0344 TCGA-08-0345 
        1.87         3.12        22.68        34.75       108.82         1.74 
TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 
        4.34        13.78        10.39         7.59         3.42        53.82 
TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0356 TCGA-08-0357 TCGA-08-0359 
        1.28         6.41        15.06        14.70        35.64         0.95 
TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 
       10.85        15.72         3.19        10.59         0.30         0.56 
TCGA-08-0512 TCGA-08-0514 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 
       11.77         8.52         1.28        10.75         4.80         6.54 
TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 
       15.98        17.33         5.52        14.43         1.64        10.39 
TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 
        5.95         7.17        65.92         0.10        38.17        25.97 
TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0769 TCGA-12-0772 
       24.13         6.12         2.63        18.12        12.43        53.10 
TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 
       43.10         5.49         9.11        14.86        14.27        91.76 
TCGA-12-0819 TCGA-12-0820 TCGA-12-0822 TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 
       24.79        18.48        23.51        38.76         8.94        20.58 
TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1092 TCGA-12-1094 TCGA-12-1095 
      127.59         5.82         6.25        21.63        11.38        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         3.42         9.44        25.28 
TCGA-12-1600 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 
       13.61        59.41        43.23        25.78        11.54        10.95 
TCGA-12-3651 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0781 TCGA-14-0783 
       11.77        13.12         3.22         2.04         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-14-1401 TCGA-14-1402 TCGA-14-1450 
       15.95        19.30         0.79         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         6.15 
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-15-1446 TCGA-15-1449 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 
        9.86        19.10         5.52         9.93        26.07        16.31 
TCGA-16-0861 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 
        4.31         9.90        13.35         3.65        18.28        13.97 
TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 TCGA-19-0962 TCGA-19-0964 
        6.41        11.77        21.90         8.61         0.43         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         3.48 
TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 
       12.66         3.25         0.13         1.08         7.53         0.16 
TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 TCGA-19-5951 
        4.08        16.47         7.00         7.04         6.64         8.02 
TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5959 
       18.64         4.73         7.96         1.78         6.51         5.29 
TCGA-19-5960 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 
        5.42        16.57        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         1.22 
TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 
        1.58         7.92         2.33         4.80        16.60         9.86 
TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 
       18.25        33.14        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-28-2502 TCGA-28-2509 TCGA-28-2514 
        1.22         1.55         2.83         0.66         4.77         5.26 
TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 
        3.91         9.04        15.58        14.53        11.77        31.27 
TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-6450 
       14.20         7.79        13.64         4.21        22.68         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-32-1987 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        21.17 
TCGA-32-4210 TCGA-32-5222 TCGA-41-2571 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 
        3.72        10.62         0.85         8.94         9.53         0.99 
TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 TCGA-74-6573 
        4.44        11.84         0.20        11.54         7.76         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-76-4934 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-76-6285 TCGA-76-6286 TCGA-76-6656 
        3.29         2.70        11.38         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 
       17.72        26.30 

  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 
            10.80              9.86 
[1] "0.1 - 100.0 (10.8)" "0.1 - 127.6 (9.9)" 
[1] "hr=" "1.1"
D58V2, continuous
D58V3, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    40  50
  9Q LOSS WILD-TYPE 180 290
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     40   50
  9Q LOSS WILD-TYPE  180  290
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE              40               180
  MALE                50               290
[1] 2 2
[1] FALSE
D58V4, continuous
                   vv
clus                GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  9Q LOSS MUTATED                               5                   5
  9Q LOSS WILD-TYPE                            12                  13
                   vv
clus                UNTREATED PRIMARY (DE NOVO) GBM
  9Q LOSS MUTATED                                80
  9Q LOSS WILD-TYPE                             445
D58V5, multiclass
                                 clus
vv                                9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                 5                12
  TREATED PRIMARY GBM                           5                13
  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"
D58V6, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    62  28
  9Q LOSS WILD-TYPE 320 150
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     62   28
  9Q LOSS WILD-TYPE  320  150
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  NO               62               320
  YES              28               150
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9Q LOSS MUTATED       1                        11    75
  9Q LOSS WILD-TYPE    12                        28   410
D58V7, multiclass
                           clus
vv                          9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  ASIAN                                   1                12
  BLACK OR AFRICAN AMERICAN              11                28
  WHITE                                  75               410
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V8, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED     0  80
  9Q LOSS WILD-TYPE  12 382
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      0   80
  9Q LOSS WILD-TYPE   12  382
                        clus
vv                       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                12
  NOT HISPANIC OR LATINO              80               382
[1] 2 2
[1] FALSE

Clustering(59) Variable = 10P LOSS MUTATION ANALYSIS
D59V1, survival
                    sevent
clus2                  0   1
  10P LOSS MUTATED    75 391
  10P LOSS WILD-TYPE  23  71
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               466                 94 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               391                 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        55.86        77.65 
TCGA-02-0023 TCGA-02-0027 TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 
       20.12        10.36         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         0.23 
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        16.21         2.70         0.26 
TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0130 
        4.04        47.31         0.10         3.58        22.72        10.52 
TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 
       18.74        14.07        23.08        22.16        10.75         0.20 
TCGA-06-0141 TCGA-06-0143 TCGA-06-0145 TCGA-06-0147 TCGA-06-0149 TCGA-06-0150 
        9.21        11.74         2.33        16.70         7.86        19.46 
TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 
       46.59        11.80        12.79         8.65         3.19         5.46 
TCGA-06-0159 TCGA-06-0162 TCGA-06-0164 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 
        9.44         2.56        56.88         5.29        19.04         3.12 
TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0177 TCGA-06-0179 
       13.02         0.23         2.20         2.73         2.01        19.00 
TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 
        2.53        40.37        73.84        26.33        28.47        14.93 
TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 
       10.29        18.31         4.67         7.04         2.60         0.39 
TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0214 
        6.48         5.49         3.91         4.96        11.84        12.43 
TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 TCGA-06-0241 
       22.49         0.36        18.02        10.36        11.80        14.96 
TCGA-06-0394 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 TCGA-06-0414 
       10.32         0.26        70.52         4.70         8.05        35.01 
TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 
       12.33         3.22         4.47         9.67         2.04        23.57 
TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 
        9.40        22.32        19.56         5.39         2.70         2.17 
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        22.98 
TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1087 TCGA-06-1800 
        5.85         5.42        20.94         7.43         3.58        26.79 
TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-2557 TCGA-06-2558 
        8.65         7.89        13.61        33.90         1.08         0.76 
TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 
        9.27         2.83        30.64         5.95         6.81         5.98 
TCGA-06-2567 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 
        4.37        11.24         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         3.95 
TCGA-06-6390 TCGA-06-6693 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 
        5.39         0.49         8.32        12.85         4.77         1.55 
TCGA-06-6700 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-08-0244 TCGA-08-0245 
        4.77         1.87         3.12         2.56        22.68        34.75 
TCGA-08-0246 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 
        3.91         1.74         4.34        13.78        10.39         7.59 
TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 
        1.28         6.41        15.06        22.52        14.70        35.64 
TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 
       19.53         0.95         9.17        10.85        15.72         3.19 
TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 
       10.59         0.30         0.56         3.52        11.77         8.52 
TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0529 TCGA-12-0615 TCGA-12-0616 
        1.28        10.75         4.80        17.33        14.01        14.43 
TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 
        1.64        10.39         5.95         7.17        65.92         0.10 
TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 
       38.17        25.97        24.13         6.12         2.63        18.12 
TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 
       28.41        12.43        53.10         5.49         9.11        14.86 
TCGA-12-0780 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 TCGA-12-0826 
       14.27        24.79        18.48        10.62        23.51        27.78 
TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1091 TCGA-12-1093 
       38.76         8.94        20.58       127.59        30.54        11.97 
TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1598 
       11.38        15.85         9.11        14.53         3.98         9.44 
TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 
       25.28        13.61         6.41        59.41        43.23        25.78 
TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 
       11.54        10.95        11.77        34.52        11.74        13.12 
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-14-1401 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-14-1453 TCGA-14-1454 TCGA-14-1455 
       58.78        23.11         7.10         1.15        30.18         0.92 
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-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-15-1449 
       17.49         7.96         9.86        50.53        19.10         5.52 
TCGA-16-0848 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 
        9.93        29.03         0.82         9.90        13.35         3.65 
TCGA-16-1062 TCGA-16-1063 TCGA-19-0955 TCGA-19-0957 TCGA-19-0962 TCGA-19-0963 
       18.28        13.97        11.77        21.90         0.43        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 
        3.48         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        16.47         7.00 
TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 
        7.04         6.64        11.28         8.02        18.64         4.73 
TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5959 TCGA-19-5960 TCGA-19-A6J4 
        7.96         1.78         6.51         5.29         5.42         3.98 
TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1799 TCGA-26-5132 
       16.57        10.03        13.87         9.73         9.37         9.40 
TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 TCGA-26-6174 
       14.86         5.49         8.88         1.22         1.58         2.33 
TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 
        4.80        16.60         9.86        18.25        33.14        21.30 
TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 
       30.05        14.04        11.51        24.76        10.39        10.39 
TCGA-27-2523 TCGA-27-2524 TCGA-27-2527 TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 
       16.08         7.59        14.40        15.78         0.20         2.53 
TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 TCGA-28-1757 
        9.21         8.35         7.63         8.48         1.22         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         3.91 
TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 
        9.04        15.58        14.53        11.77        31.27        14.20 
TCGA-28-5215 TCGA-28-5216 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 
        7.79        13.64        22.68        10.49         5.42        15.39 
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-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 
       12.69        14.86        12.23        20.78        15.02        15.95 
TCGA-32-2634 TCGA-32-2638 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 
       22.78        21.17         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 
       10.62         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-74-6573 
        4.44        11.84         0.20        11.54         7.76         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-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R 
        1.61        17.72        26.30         5.92 

$`10P LOSS WILD-TYPE`
TCGA-02-0001 TCGA-02-0007 TCGA-02-0010 TCGA-02-0011 TCGA-02-0015 TCGA-02-0024 
        9.17        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         0.16        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        32.52         2.20        20.09 
TCGA-06-0148 TCGA-06-0160 TCGA-06-0165 TCGA-06-0176 TCGA-06-0178 TCGA-06-0213 
        9.80        11.80        10.65        91.00        53.98         0.20 
TCGA-06-0240 TCGA-06-0397 TCGA-06-0413 TCGA-06-1086 TCGA-06-1806 TCGA-06-2559 
       20.42         5.52         0.16         6.35        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-08-0344 TCGA-08-0350 TCGA-08-0351 TCGA-08-0516 
        7.36         4.96       108.82         3.42        53.82        18.44 
TCGA-08-0517 TCGA-08-0524 TCGA-08-0525 TCGA-08-0531 TCGA-12-0773 TCGA-12-0818 
       58.19         6.54        15.98         5.52        43.10        91.76 
TCGA-12-1089 TCGA-12-1090 TCGA-12-1092 TCGA-12-1099 TCGA-14-1396 TCGA-14-1456 
        5.82         6.25        21.63         3.42         1.12        40.96 
TCGA-14-1458 TCGA-14-1459 TCGA-14-1821 TCGA-14-3477 TCGA-14-4157 TCGA-15-1447 
        6.15        12.43        17.79         3.78         3.42        53.19 
TCGA-16-0846 TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 TCGA-16-1460 TCGA-19-0960 
        3.91        26.07        16.31         4.31         6.41         8.61 
TCGA-19-1390 TCGA-19-1787 TCGA-19-5958 TCGA-26-1442 TCGA-26-1443 TCGA-26-6173 
       25.38        12.66         5.39        31.33         7.13         7.92 
TCGA-27-2526 TCGA-28-1755 TCGA-28-1756 TCGA-28-5218 TCGA-32-1973 TCGA-32-1991 
        2.86         1.55         2.83         4.21        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               0.16 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            127.59             108.82 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             9.860             12.545 
[1] "0.1 - 127.6 (9.9)"  "0.2 - 108.8 (12.5)"
[1] "hr=" "1.7"
D59V2, continuous
D59V3, binary
                    cls
clus                   0   1
  10P LOSS MUTATED   178 288
  10P LOSS WILD-TYPE  42  52
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED    178  288
  10P LOSS WILD-TYPE   42   52
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE              178                 42
  MALE                288                 52
[1] 2 2
[1] FALSE
D59V4, continuous
                    vv
clus                 GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  10P LOSS MUTATED                              12                  10
  10P LOSS WILD-TYPE                             5                   8
                    vv
clus                 UNTREATED PRIMARY (DE NOVO) GBM
  10P LOSS MUTATED                               444
  10P LOSS WILD-TYPE                              81
D59V5, multiclass
                                 clus
vv                                10P LOSS MUTATED 10P LOSS WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                 12                  5
  TREATED PRIMARY GBM                           10                  8
  UNTREATED PRIMARY (DE NOVO) GBM              444                 81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V6, binary
                    cls
clus                   0   1
  10P LOSS MUTATED   316 150
  10P LOSS WILD-TYPE  66  28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED    316  150
  10P LOSS WILD-TYPE   66   28
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  NO               316                 66
  YES              150                 28
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10P LOSS MUTATED       8                        33   405
  10P LOSS WILD-TYPE     5                         6    80
D59V7, multiclass
                           clus
vv                          10P LOSS MUTATED 10P LOSS WILD-TYPE
  ASIAN                                    8                  5
  BLACK OR AFRICAN AMERICAN               33                  6
  WHITE                                  405                 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"
D59V8, binary
                    cls
clus                   0   1
  10P LOSS MUTATED     8 383
  10P LOSS WILD-TYPE   4  79
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      8  383
  10P LOSS WILD-TYPE    4   79
                        clus
vv                       10P LOSS MUTATED 10P LOSS WILD-TYPE
  HISPANIC OR LATINO                    8                  4
  NOT HISPANIC OR LATINO              383                 79
[1] 2 2
[1] FALSE

Clustering(60) Variable = 10Q LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                  0   1
  10Q LOSS MUTATED    78 400
  10Q LOSS WILD-TYPE  20  62
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               478                 82 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               400                 62 
$`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 
       55.86        77.65        20.12        24.59        10.36         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         0.23        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 
       16.21         2.70         0.26         4.04        47.31         0.10 
TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 
        3.58        22.72        32.52        10.52        18.74        14.07 
TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0143 
       23.08        22.16        10.75         0.20         9.21        11.74 
TCGA-06-0145 TCGA-06-0147 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 
        2.33        16.70         7.86        19.46        46.59        11.80 
TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0162 
       12.79         8.65         3.19         5.46         9.44         2.56 
TCGA-06-0164 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 
       56.88         5.29        19.04         3.12        13.02         0.23 
TCGA-06-0174 TCGA-06-0175 TCGA-06-0177 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 
        2.20         2.73         2.01        19.00         2.53        40.37 
TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 
       73.84        26.33        28.47        14.93        10.29        18.31 
TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 
        4.67         7.04         2.60         0.39         6.48         5.49 
TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 
        3.91         4.96        11.84        12.43        22.49         0.36 
TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 TCGA-06-0241 TCGA-06-0394 TCGA-06-0402 
       18.02        10.36        11.80        14.96        10.32         0.26 
TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 
       70.52         4.70         8.05        35.01        12.33         3.22 
TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 
        4.47         9.67         2.04        23.57         9.40        22.32 
TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 
       19.56         5.39         2.70         2.17         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        22.98         5.85         5.42 
TCGA-06-0939 TCGA-06-1084 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 
       20.94         7.43         3.58        26.79         8.65         7.89 
TCGA-06-1804 TCGA-06-1805 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 
       13.61        33.90         1.08         0.76         4.93         9.27 
TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 
        2.83        30.64         5.95         6.81         5.98         4.37 
TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 
       11.24         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         3.95         5.39 
TCGA-06-6693 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 
        0.49         8.32        12.85         4.77         1.55         4.77 
TCGA-06-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-08-0244 TCGA-08-0245 TCGA-08-0246 
        1.87         3.12         2.56        22.68        34.75         3.91 
TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0352 
        1.74         4.34        13.78        10.39         7.59         1.28 
TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 
        6.41        15.06        22.52        14.70        35.64        19.53 
TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 
        0.95         9.17        10.85        15.72         3.19        10.59 
TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 TCGA-08-0518 
        0.30         0.56         3.52        11.77         8.52         1.28 
TCGA-08-0520 TCGA-08-0521 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 
       10.75         4.80        15.98        17.33         5.52        14.01 
TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 
       14.43         1.64        10.39         5.95         7.17        65.92 
TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0692 TCGA-12-0703 
        0.10        38.17        25.97        24.13         2.63        18.12 
TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 
       28.41        12.43        53.10         5.49         9.11        14.86 
TCGA-12-0780 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 TCGA-12-0826 
       14.27        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        30.54 
TCGA-12-1092 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1598 
       21.63        11.38        15.85         9.11        14.53         9.44 
TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 
       25.28        13.61         6.41        59.41        43.23        25.78 
TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 
       11.54        10.95        11.77        34.52        11.74        13.12 
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-14-1401 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-14-1453 TCGA-14-1454 TCGA-14-1455 
       58.78        23.11         7.10         1.15        30.18         0.92 
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-14-3477 TCGA-15-0742 TCGA-15-1444 
        7.17        17.49         7.96         3.78         9.86        50.53 
TCGA-15-1446 TCGA-15-1449 TCGA-16-0848 TCGA-16-0850 TCGA-16-1045 TCGA-16-1047 
       19.10         5.52         9.93        16.31        29.03         0.82 
TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-19-0957 
        9.90        13.35         3.65        18.28        13.97        21.90 
TCGA-19-0960 TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 
        8.61         0.43        14.27         3.39        10.75         9.07 
TCGA-19-1387 TCGA-19-1388 TCGA-19-1389 TCGA-19-1392 TCGA-19-1786 TCGA-19-1789 
        5.95        12.95         4.64         3.48         7.17         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        16.47         7.00         7.04         6.64        11.28 
TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5959 
        8.02        18.64         4.73         7.96         1.78         5.29 
TCGA-19-5960 TCGA-19-A6J4 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1443 
        5.42         3.98        10.03        13.87         9.73         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         1.22 
TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 
        1.58         7.92         2.33         4.80        16.60         9.86 
TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 
       18.25        33.14        21.30        30.05        14.04        11.51 
TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 
       24.76        10.39        10.39         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-28-1757 TCGA-28-2502 TCGA-28-2506 
        8.48         1.22         1.55         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         3.91         9.04        15.58 
TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 
       14.53        11.77        31.27        14.20         7.79        13.64 
TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1976 TCGA-32-1977 
       22.68        10.49         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-32-2615 TCGA-32-2634 
       16.93        12.23        20.78        15.02        15.95        22.78 
TCGA-32-2638 TCGA-32-4208 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 
       21.17        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 
       10.62         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-74-6573 
        4.44        11.84         0.20        11.54         7.76         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-81-5910 TCGA-81-5911 TCGA-87-5896 TCGA-OX-A56R 
        1.61        17.72        26.30         5.92 

$`10Q LOSS WILD-TYPE`
TCGA-02-0001 TCGA-02-0011 TCGA-02-0015 TCGA-02-0024 TCGA-02-0025 TCGA-02-0028 
        9.17        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         0.16        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         9.80        11.80        10.65        91.00 
TCGA-06-0178 TCGA-06-0213 TCGA-06-0240 TCGA-06-0397 TCGA-06-0413 TCGA-06-1086 
       53.98         0.20        20.42         5.52         0.16         6.35 
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       108.82         3.42        53.82 
TCGA-08-0516 TCGA-08-0517 TCGA-08-0524 TCGA-12-0691 TCGA-12-0773 TCGA-12-0818 
       18.44        58.19         6.54         6.12        43.10        91.76 
TCGA-12-1090 TCGA-12-1093 TCGA-12-1098 TCGA-12-1099 TCGA-14-1396 TCGA-14-1456 
        6.25        11.97         3.98         3.42         1.12        40.96 
TCGA-14-1458 TCGA-14-1821 TCGA-14-4157 TCGA-15-1447 TCGA-16-0846 TCGA-16-0849 
        6.15        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         6.51 
TCGA-19-5958 TCGA-19-A6J5 TCGA-26-1442 TCGA-27-2523 TCGA-28-1756 TCGA-28-5218 
        5.39        16.57        31.33        16.08         2.83         4.21 
TCGA-32-1973 TCGA-32-2616 TCGA-32-2632 TCGA-76-6664 
       21.07         7.36         8.84         7.79 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              0.10               0.16 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            127.59             108.82 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              9.86              12.18 
[1] "0.1 - 127.6 (9.9)"  "0.2 - 108.8 (12.2)"
[1] "hr=" "1.7"
D60V2, continuous
D60V3, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED   185 293
  10Q LOSS WILD-TYPE  35  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED    185  293
  10Q LOSS WILD-TYPE   35   47
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE              185                 35
  MALE                293                 47
[1] 2 2
[1] FALSE
D60V4, continuous
                    vv
clus                 GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  10Q LOSS MUTATED                              11                  13
  10Q LOSS WILD-TYPE                             6                   5
                    vv
clus                 UNTREATED PRIMARY (DE NOVO) GBM
  10Q LOSS MUTATED                               454
  10Q LOSS WILD-TYPE                              71
D60V5, multiclass
                                 clus
vv                                10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                 11                  6
  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"
D60V6, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED   328 150
  10Q LOSS WILD-TYPE  54  28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED    328  150
  10Q LOSS WILD-TYPE   54   28
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  NO               328                 54
  YES              150                 28
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10Q LOSS MUTATED       8                        33   416
  10Q LOSS WILD-TYPE     5                         6    69
D60V7, multiclass
                           clus
vv                          10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  ASIAN                                    8                  5
  BLACK OR AFRICAN AMERICAN               33                  6
  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"
D60V8, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED     8 394
  10Q LOSS WILD-TYPE   4  68
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      8  394
  10Q LOSS WILD-TYPE    4   68
                        clus
vv                       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    8                  4
  NOT HISPANIC OR LATINO              394                 68
[1] 2 2
[1] FALSE

Clustering(61) Variable = 11P LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                  0   1
  11P LOSS MUTATED    16  81
  11P LOSS WILD-TYPE  82 381
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                97                463 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                81                381 
$`11P LOSS MUTATED`
TCGA-02-0001 TCGA-02-0010 TCGA-02-0024 TCGA-02-0033 TCGA-02-0047 TCGA-02-0048 
        9.17        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 
        0.23         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         5.29 
TCGA-06-0174 TCGA-06-0177 TCGA-06-0184 TCGA-06-0192 TCGA-06-0197 TCGA-06-0216 
        2.20         2.01        40.37        18.31         2.60        22.49 
TCGA-06-0221 TCGA-06-0238 TCGA-06-0409 TCGA-06-0410 TCGA-06-0414 TCGA-06-0649 
       18.02        11.80        70.52         4.70        35.01         2.04 
TCGA-06-0686 TCGA-06-0876 TCGA-06-1086 TCGA-06-1800 TCGA-06-1805 TCGA-06-1806 
        9.40        46.19         6.35        26.79        33.90        15.32 
TCGA-06-2558 TCGA-06-2570 TCGA-06-5856 TCGA-06-6389 TCGA-06-6694 TCGA-08-0245 
        0.76        31.50         3.75         7.79         7.36        34.75 
TCGA-08-0510 TCGA-08-0520 TCGA-12-0616 TCGA-12-0619 TCGA-12-0691 TCGA-12-0772 
        3.52        10.75        14.43        10.39         6.12        53.10 
TCGA-12-0819 TCGA-12-0822 TCGA-12-1099 TCGA-12-1602 TCGA-12-3646 TCGA-12-3653 
       24.79        23.51         3.42         6.41        43.23        11.74 
TCGA-14-0740 TCGA-14-0783 TCGA-14-0817 TCGA-14-0865 TCGA-14-0867 TCGA-14-0871 
       11.97         6.21         5.39        16.50         2.04        28.93 
TCGA-14-1454 TCGA-14-1459 TCGA-14-1794 TCGA-14-1821 TCGA-14-1823 TCGA-14-3477 
       30.18        12.43         0.99        17.79        17.85         3.78 
TCGA-15-1447 TCGA-15-1449 TCGA-16-0846 TCGA-16-0850 TCGA-16-1045 TCGA-19-1387 
       53.19         5.52         3.91        16.31        29.03         5.95 
TCGA-19-1390 TCGA-19-1392 TCGA-19-2623 TCGA-19-5959 TCGA-19-5960 TCGA-26-1439 
       25.38         3.48         7.53         5.29         5.42        13.87 
TCGA-26-5133 TCGA-27-1830 TCGA-28-1756 TCGA-28-2509 TCGA-28-5216 TCGA-32-1976 
       14.86         4.80         2.83         4.77        13.64         0.49 
TCGA-32-2615 TCGA-32-2632 TCGA-32-4210 TCGA-32-4719 TCGA-41-3915 TCGA-74-6584 
       15.95         8.84         3.72        10.85        11.84         7.50 
TCGA-76-4934 
        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        55.86        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 
       10.36        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 
        0.16        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        16.21         2.70         0.26 
TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0129 TCGA-06-0130 
        4.04        47.31         0.10         3.58        32.52        10.52 
TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 
       18.74        14.07        23.08        22.16        10.75         0.20 
TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 TCGA-06-0147 
        9.21         2.20        11.74         2.33        20.09        16.70 
TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 
        9.80         7.86        19.46        46.59        11.80        12.79 
TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 
        8.65         3.19         5.46        11.80         2.56        56.88 
TCGA-06-0165 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0175 
       10.65        19.04         3.12        13.02         0.23         2.73 
TCGA-06-0176 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0185 TCGA-06-0187 
       91.00        53.98        19.00         2.53        73.84        26.33 
TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0194 TCGA-06-0195 TCGA-06-0201 
       28.47        14.93        10.29         4.67         7.04         0.39 
TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 
        6.48         5.49         3.91         4.96        11.84         0.20 
TCGA-06-0214 TCGA-06-0219 TCGA-06-0237 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 
       12.43         0.36        10.36        20.42        14.96        10.32 
TCGA-06-0397 TCGA-06-0402 TCGA-06-0412 TCGA-06-0413 TCGA-06-0644 TCGA-06-0645 
        5.52         0.26         8.05         0.16        12.33         3.22 
TCGA-06-0646 TCGA-06-0648 TCGA-06-0650 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 
        4.47         9.67        23.57        22.32        19.56         5.39 
TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0877 TCGA-06-0878 
        2.70         2.17         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 
       22.98         5.85         5.42        20.94         7.43         3.58 
TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-2557 TCGA-06-2559 TCGA-06-2561 
        8.65         7.89        13.61         1.08         4.93         9.27 
TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 
        2.83        30.64         5.95         6.81         5.98         4.37 
TCGA-06-2569 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 
        0.43        11.24         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 
        3.95         5.39         1.48         0.49         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-08-0244 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 
        2.56        22.68         3.91       108.82         1.74         4.34 
TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 
       13.78        10.39         7.59         3.42        53.82         1.28 
TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 
        6.41        15.06        22.52        14.70        35.64        19.53 
TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 
        0.95         9.17        10.85        15.72         3.19        10.59 
TCGA-08-0392 TCGA-08-0509 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 
        0.30         0.56        11.77         8.52        18.44        58.19 
TCGA-08-0518 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 
        1.28         4.80         6.54        15.98        17.33         5.52 
TCGA-12-0615 TCGA-12-0618 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 
       14.01         1.64         5.95         7.17        65.92         0.10 
TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 
       38.17        25.97        24.13         2.63        18.12        28.41 
TCGA-12-0769 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 
       12.43        43.10         5.49         9.11        14.86        14.27 
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         6.25        30.54        21.63 
TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 
       11.97        11.38        15.85         9.11        14.53         3.98 
TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 TCGA-12-3644 TCGA-12-3648 TCGA-12-3649 
        9.44        25.28        13.61        59.41        25.78        11.54 
TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 
       10.95        11.77        34.52        13.12         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-14-0813 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-14-1455 TCGA-14-1456 TCGA-14-1458 
       23.11         7.10         1.15         0.92        40.96         6.15 
TCGA-14-1795 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 
        1.97         7.63         5.88         7.17        17.49         7.96 
TCGA-14-4157 TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-16-0848 TCGA-16-0849 
        3.42         9.86        50.53        19.10         9.93        26.07 
TCGA-16-0861 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 
        4.31         0.82         9.90        13.35         3.65        18.28 
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         0.43 
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-19-1786 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-19-2624 TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 
        1.08         0.16         4.08        16.47         7.00         7.04 
TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 
        6.64        11.28         8.02        18.64         4.73         7.96 
TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 
        1.78         6.51         5.39         3.98        16.57        10.03 
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-27-1831 
        8.88         1.22         1.58         7.92         2.33        16.60 
TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 
        9.86        18.25        33.14        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-28-1757 
        8.35         7.63         8.48         1.22         1.55         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         3.91         9.04 
TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 
       15.58        14.53        11.77        31.27        14.20         7.79 
TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 
        4.21        22.68        10.49         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-32-2616 
       14.86        16.93        12.23        20.78        15.02         7.36 
TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4211 TCGA-32-4213 TCGA-32-5222 
       22.78        21.17        21.14        12.59        19.86        10.62 
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-74-6573 TCGA-74-6575 TCGA-74-6577 
        0.20        11.54         7.76         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-81-5910 TCGA-81-5911 TCGA-87-5896 
        9.27         7.73         7.79         1.61        17.72        26.30 
TCGA-OX-A56R 
        5.92 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              0.23               0.10 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             99.98             127.59 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             10.75               9.90 
[1] "0.2 - 100.0 (10.8)" "0.1 - 127.6 (9.9)" 
[1] "hr=" "1.2"
D61V2, continuous
D61V3, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    46  51
  11P LOSS WILD-TYPE 174 289
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     46   51
  11P LOSS WILD-TYPE  174  289
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE               46                174
  MALE                 51                289
[1] 2 2
[1] FALSE
D61V4, continuous
                    vv
clus                 GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  11P LOSS MUTATED                               2                   5
  11P LOSS WILD-TYPE                            15                  13
                    vv
clus                 UNTREATED PRIMARY (DE NOVO) GBM
  11P LOSS MUTATED                                90
  11P LOSS WILD-TYPE                             435
D61V5, multiclass
                                 clus
vv                                11P LOSS MUTATED 11P LOSS WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                  2                 15
  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"
D61V6, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    64  33
  11P LOSS WILD-TYPE 318 145
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     64   33
  11P LOSS WILD-TYPE  318  145
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  NO                64                318
  YES               33                145
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11P LOSS MUTATED       1                         8    85
  11P LOSS WILD-TYPE    12                        31   400
D61V7, multiclass
                           clus
vv                          11P LOSS MUTATED 11P LOSS WILD-TYPE
  ASIAN                                    1                 12
  BLACK OR AFRICAN AMERICAN                8                 31
  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"
D61V8, binary
                    cls
clus                   0   1
  11P LOSS MUTATED     1  78
  11P LOSS WILD-TYPE  11 384
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      1   78
  11P LOSS WILD-TYPE   11  384
                        clus
vv                       11P LOSS MUTATED 11P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 11
  NOT HISPANIC OR LATINO               78                384
[1] 2 2
[1] FALSE

Clustering(62) Variable = 11Q LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                  0   1
  11Q LOSS MUTATED    11  81
  11Q LOSS WILD-TYPE  87 381
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                92                468 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                81                381 
$`11Q LOSS MUTATED`
TCGA-02-0001 TCGA-02-0010 TCGA-02-0024 TCGA-02-0033 TCGA-02-0048 TCGA-02-0052 
        9.17        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        10.52         9.44         5.29         2.20         2.01 
TCGA-06-0184 TCGA-06-0188 TCGA-06-0190 TCGA-06-0192 TCGA-06-0195 TCGA-06-0197 
       40.37        28.47        10.29        18.31         7.04         2.60 
TCGA-06-0216 TCGA-06-0221 TCGA-06-0238 TCGA-06-0409 TCGA-06-0410 TCGA-06-0414 
       22.49        18.02        11.80        70.52         4.70        35.01 
TCGA-06-0649 TCGA-06-0686 TCGA-06-0876 TCGA-06-1800 TCGA-06-1806 TCGA-06-5856 
        2.04         9.40        46.19        26.79        15.32         3.75 
TCGA-06-6389 TCGA-08-0245 TCGA-08-0510 TCGA-08-0520 TCGA-12-0616 TCGA-12-0619 
        7.79        34.75         3.52        10.75        14.43        10.39 
TCGA-12-0691 TCGA-12-0772 TCGA-12-0819 TCGA-12-0822 TCGA-12-1099 TCGA-12-1598 
        6.12        53.10        24.79        23.51         3.42         9.44 
TCGA-12-1602 TCGA-12-3646 TCGA-12-3651 TCGA-12-3653 TCGA-14-0783 TCGA-14-0817 
        6.41        43.23        11.77        11.74         6.21         5.39 
TCGA-14-0865 TCGA-14-0867 TCGA-14-0871 TCGA-14-1454 TCGA-14-1459 TCGA-14-1794 
       16.50         2.04        28.93        30.18        12.43         0.99 
TCGA-14-1823 TCGA-14-3477 TCGA-15-1449 TCGA-16-0846 TCGA-16-0850 TCGA-16-1045 
       17.85         3.78         5.52         3.91        16.31        29.03 
TCGA-19-1387 TCGA-19-1390 TCGA-19-1392 TCGA-19-2623 TCGA-19-5959 TCGA-19-5960 
        5.95        25.38         3.48         7.53         5.29         5.42 
TCGA-26-1439 TCGA-27-1830 TCGA-28-2509 TCGA-28-5216 TCGA-32-1976 TCGA-32-1986 
       13.87         4.80         4.77        13.64         0.49        12.69 
TCGA-32-2615 TCGA-32-2632 TCGA-32-4210 TCGA-32-4719 TCGA-41-3915 TCGA-74-6584 
       15.95         8.84         3.72        10.85        11.84         7.50 
TCGA-76-4934 TCGA-81-5910 
        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        55.86        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 
       10.36        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         0.23        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         0.16        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        16.21 
TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 
        2.70         0.26         4.04        47.31         0.10         3.58 
TCGA-06-0128 TCGA-06-0129 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 
       22.72        32.52        18.74        14.07        23.08        22.16 
TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 
       10.75         0.20         9.21         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        16.70         9.80         7.86        19.46        46.59 
TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0160 
       11.80        12.79         8.65         3.19         5.46        11.80 
TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 
        2.56        56.88        10.65        19.04         3.12        13.02 
TCGA-06-0173 TCGA-06-0175 TCGA-06-0176 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 
        0.23         2.73        91.00        53.98        19.00         2.53 
TCGA-06-0185 TCGA-06-0187 TCGA-06-0189 TCGA-06-0194 TCGA-06-0201 TCGA-06-0206 
       73.84        26.33        14.93         4.67         0.39         6.48 
TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 
        5.49         3.91         4.96        11.84         0.20        12.43 
TCGA-06-0219 TCGA-06-0237 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 
        0.36        10.36        20.42        14.96        10.32         5.52 
TCGA-06-0402 TCGA-06-0412 TCGA-06-0413 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 
        0.26         8.05         0.16        12.33         3.22         4.47 
TCGA-06-0648 TCGA-06-0650 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 
        9.67        23.57        22.32        19.56         5.39         2.70 
TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0877 TCGA-06-0878 TCGA-06-0879 
        2.17         0.92        43.46         5.65         7.17        22.98 
TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 
        5.85         5.42        20.94         7.43         6.35         3.58 
TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-2557 TCGA-06-2558 
        8.65         7.89        13.61        33.90         1.08         0.76 
TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 
        4.93         9.27         2.83        30.64         5.95         6.81 
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        11.24         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         3.95         5.39         1.48 
TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 
        0.49         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-08-0244 
        4.77         4.96         1.87         3.12         2.56        22.68 
TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 
        3.91       108.82         1.74         4.34        13.78        10.39 
TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 
        7.59         3.42        53.82         1.28         6.41        15.06 
TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 
       22.52        14.70        35.64        19.53         0.95         9.17 
TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 
       10.85        15.72         3.19        10.59         0.30         0.56 
TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0521 
       11.77         8.52        18.44        58.19         1.28         4.80 
TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0618 
        6.54        15.98        17.33         5.52        14.01         1.64 
TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 
        5.95         7.17        65.92         0.10        38.17        25.97 
TCGA-12-0688 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0773 
       24.13         2.63        18.12        28.41        12.43        43.10 
TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0820 
        5.49         9.11        14.86        14.27        91.76        18.48 
TCGA-12-0821 TCGA-12-0826 TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 
       10.62        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         6.25        30.54        21.63        11.97        11.38 
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        25.28        13.61 
TCGA-12-3644 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3652 TCGA-12-5295 
       59.41        25.78        11.54        10.95        34.52        13.12 
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-14-0866 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-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1795 TCGA-14-1821 TCGA-14-1825 
        0.92        40.96         6.15         1.97        17.79         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         9.86 
TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 TCGA-16-0848 TCGA-16-0849 TCGA-16-0861 
       50.53        19.10        53.19         9.93        26.07         4.31 
TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 
        0.82         9.90        13.35         3.65        18.28        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         0.43        14.27 
TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 TCGA-19-1388 TCGA-19-1389 TCGA-19-1786 
        3.39        10.75         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-19-2624 TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 
        0.16         4.08        16.47         7.00         7.04         6.64 
TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 
       11.28         8.02        18.64         4.73         7.96         1.78 
TCGA-19-5956 TCGA-19-5958 TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1440 
        6.51         5.39         3.98        16.57        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-27-1831 
        8.88         1.22         1.58         7.92         2.33        16.60 
TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 
        9.86        18.25        33.14        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-28-2513 TCGA-28-2514 TCGA-28-5204 
        0.13         0.66         6.74         7.30         5.26         3.91 
TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 
        9.04        15.58        14.53        11.77        31.27        14.20 
TCGA-28-5215 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 
        7.79         4.21        22.68        10.49         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-32-1987 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-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4211 TCGA-32-4213 TCGA-32-5222 
       22.78        21.17        21.14        12.59        19.86        10.62 
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-74-6573 TCGA-74-6575 TCGA-74-6577 
        0.20        11.54         7.76         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 

  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 
            10.340              9.915 
[1] "0.5 - 92.7 (10.3)" "0.1 - 127.6 (9.9)"
[1] "hr=" "1"  
D62V2, continuous
D62V3, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    40  52
  11Q LOSS WILD-TYPE 180 288
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     40   52
  11Q LOSS WILD-TYPE  180  288
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE               40                180
  MALE                 52                288
[1] 2 2
[1] FALSE
D62V4, continuous
                    vv
clus                 GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  11Q LOSS MUTATED                               2                   3
  11Q LOSS WILD-TYPE                            15                  15
                    vv
clus                 UNTREATED PRIMARY (DE NOVO) GBM
  11Q LOSS MUTATED                                87
  11Q LOSS WILD-TYPE                             438
D62V5, multiclass
                                 clus
vv                                11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                  2                 15
  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"
D62V6, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    58  34
  11Q LOSS WILD-TYPE 324 144
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     58   34
  11Q LOSS WILD-TYPE  324  144
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  NO                58                324
  YES               34                144
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11Q LOSS MUTATED       2                         6    81
  11Q LOSS WILD-TYPE    11                        33   404
D62V7, multiclass
                           clus
vv                          11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  ASIAN                                    2                 11
  BLACK OR AFRICAN AMERICAN                6                 33
  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"
D62V8, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED     0  76
  11Q LOSS WILD-TYPE  12 386
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      0   76
  11Q LOSS WILD-TYPE   12  386
                        clus
vv                       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 12
  NOT HISPANIC OR LATINO               76                386
[1] 2 2
[1] FALSE

Clustering(63) Variable = 12P LOSS MUTATION ANALYSIS
D63V1, survival
                    sevent
clus2                  0   1
  12P LOSS MUTATED     9  50
  12P LOSS WILD-TYPE  89 412
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                59                501 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                50                412 
$`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        16.70         7.86         9.44         2.01         2.53 
TCGA-06-0190 TCGA-06-0195 TCGA-06-0197 TCGA-06-0221 TCGA-06-0237 TCGA-06-0414 
       10.29         7.04         2.60        18.02        10.36        35.01 
TCGA-06-0648 TCGA-06-0686 TCGA-06-5856 TCGA-06-6390 TCGA-08-0245 TCGA-08-0349 
        9.67         9.40         3.75         5.39        34.75         7.59 
TCGA-08-0386 TCGA-08-0510 TCGA-08-0514 TCGA-12-0619 TCGA-12-0670 TCGA-12-1600 
       15.72         3.52         8.52        10.39        25.97        13.61 
TCGA-12-1602 TCGA-12-3646 TCGA-14-0783 TCGA-14-0817 TCGA-14-0867 TCGA-14-0871 
        6.41        43.23         6.21         5.39         2.04        28.93 
TCGA-14-1451 TCGA-14-1794 TCGA-14-3477 TCGA-16-0849 TCGA-16-0850 TCGA-16-1055 
       23.11         0.99         3.78        26.07        16.31         9.90 
TCGA-19-0960 TCGA-19-1385 TCGA-19-1388 TCGA-19-1390 TCGA-19-2623 TCGA-19-2624 
        8.61        10.75        12.95        25.38         7.53         0.16 
TCGA-19-4065 TCGA-19-5960 TCGA-26-1438 TCGA-26-5132 TCGA-26-5136 TCGA-27-1836 
        7.04         5.42        10.03         9.40         1.22        30.05 
TCGA-28-5204 TCGA-32-1978 TCGA-32-2494 TCGA-32-4210 TCGA-76-6193 
        3.91        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 
        9.17         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        55.86        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        10.36        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         0.23        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         0.16 
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        16.21 
TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 
        2.70         0.26         4.04        47.31         0.10         3.58 
TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 
       22.72        32.52        10.52        18.74        14.07        23.08 
TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 
       22.16        10.75         0.20         9.21         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         9.80        19.46        46.59        11.80 
TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0160 TCGA-06-0162 
       12.79         8.65         3.19         5.46        11.80         2.56 
TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 
       56.88        10.65         5.29        19.04         3.12        13.02 
TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0178 TCGA-06-0179 
        0.23         2.20         2.73        91.00        53.98        19.00 
TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0192 
       40.37        73.84        26.33        28.47        14.93        18.31 
TCGA-06-0194 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 
        4.67         0.39         6.48         5.49         3.91         4.96 
TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0238 
       11.84         0.20        12.43        22.49         0.36        11.80 
TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 
       20.42        14.96        10.32         5.52         0.26        70.52 
TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 
        4.70         8.05         0.16        12.33         3.22         4.47 
TCGA-06-0649 TCGA-06-0650 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 
        2.04        23.57        22.32        19.56         5.39         2.70 
TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 
        2.17         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 
       22.98         5.85         5.42        20.94         7.43         6.35 
TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 
        3.58        26.79         8.65         7.89        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         0.76         4.93         9.27         2.83 
TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 
       30.64         5.95         6.81         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        11.24         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-06-6389 TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 
        3.95         7.79         1.48         0.49         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-08-0244 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 
        3.12         2.56        22.68         3.91       108.82         1.74 
TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 
        4.34        13.78        10.39         3.42        53.82         1.28 
TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 
        6.41        15.06        22.52        14.70        35.64        19.53 
TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 
        0.95         9.17        10.85         3.19        10.59         0.30 
TCGA-08-0509 TCGA-08-0512 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 
        0.56        11.77        18.44        58.19         1.28        10.75 
TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 
        4.80         6.54        15.98        17.33         5.52        14.01 
TCGA-12-0616 TCGA-12-0618 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 
       14.43         1.64         5.95         7.17        65.92         0.10 
TCGA-12-0662 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 
       38.17        24.13         6.12         2.63        18.12        28.41 
TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 
       12.43        53.10        43.10         5.49         9.11        14.86 
TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 
       14.27        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 
        6.25        30.54        21.63        11.97        11.38        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         3.42         9.44        25.28 
TCGA-12-3644 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 
       59.41        25.78        11.54        10.95        11.77        34.52 
TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 
       11.74        13.12         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-14-0865 TCGA-14-0866 TCGA-14-1034 TCGA-14-1037 
        1.35         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         6.15 
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         9.86        50.53 
TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 TCGA-16-0861 
       19.10        53.19         5.52         3.91         9.93         4.31 
TCGA-16-1045 TCGA-16-1047 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 
       29.03         0.82        13.35         3.65        18.28        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         0.43        14.27         3.39 
TCGA-19-1386 TCGA-19-1387 TCGA-19-1389 TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 
        9.07         5.95         4.64         3.48         7.17        12.66 
TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2625 
        3.25         0.13         9.67         4.87         1.08         4.08 
TCGA-19-2629 TCGA-19-2631 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 
       16.47         7.00         6.64        11.28         8.02        18.64 
TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 
        4.73         7.96         1.78         6.51         5.39         5.29 
TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 
        3.98        16.57        13.87         9.73        31.33         7.13 
TCGA-26-1799 TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 TCGA-26-5139 TCGA-26-6173 
        9.37        14.86         5.49         8.88         1.58         7.92 
TCGA-26-6174 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 
        2.33         4.80        16.60         9.86        18.25        33.14 
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         9.04        15.58        14.53        11.77 
TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 
       31.27        14.20         7.79        13.64         4.21        22.68 
TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 
       10.49         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 
       21.17        21.14        12.59        19.86        10.85        10.62 
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-74-6573 TCGA-74-6575 
       11.84         0.20        11.54         7.76         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-76-6280 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 
        3.29        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 
       17.72        26.30         5.92 

  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 
              9.67              10.36 
[1] "0.2 - 92.7 (9.7)"   "0.1 - 127.6 (10.4)"
[1] "hr=" "1"  
D63V2, continuous
D63V3, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    20  39
  12P LOSS WILD-TYPE 200 301
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     20   39
  12P LOSS WILD-TYPE  200  301
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE               20                200
  MALE                 39                301
[1] 2 2
[1] FALSE
D63V4, continuous
                    vv
clus                 GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  12P LOSS MUTATED                               1                   2
  12P LOSS WILD-TYPE                            16                  16
                    vv
clus                 UNTREATED PRIMARY (DE NOVO) GBM
  12P LOSS MUTATED                                56
  12P LOSS WILD-TYPE                             469
D63V5, multiclass
                                 clus
vv                                12P LOSS MUTATED 12P LOSS WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                  1                 16
  TREATED PRIMARY GBM                            2                 16
  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"
D63V6, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    42  17
  12P LOSS WILD-TYPE 340 161
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     42   17
  12P LOSS WILD-TYPE  340  161
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  NO                42                340
  YES               17                161
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12P LOSS MUTATED       0                         2    54
  12P LOSS WILD-TYPE    13                        37   431
D63V7, multiclass
                           clus
vv                          12P LOSS MUTATED 12P LOSS WILD-TYPE
  ASIAN                                    0                 13
  BLACK OR AFRICAN AMERICAN                2                 37
  WHITE                                   54                431
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V8, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     1  50
  12P LOSS WILD-TYPE  11 412
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      1   50
  12P LOSS WILD-TYPE   11  412
                        clus
vv                       12P LOSS MUTATED 12P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 11
  NOT HISPANIC OR LATINO               50                412
[1] 2 2
[1] FALSE

Clustering(64) Variable = 12Q LOSS MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                  0   1
  12Q LOSS MUTATED    10  48
  12Q LOSS WILD-TYPE  88 414
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                58                502 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                48                414 
$`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         0.23        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        16.70         7.86         9.44         2.01 
TCGA-06-0182 TCGA-06-0184 TCGA-06-0190 TCGA-06-0197 TCGA-06-0221 TCGA-06-0237 
        2.53        40.37        10.29         2.60        18.02        10.36 
TCGA-06-0414 TCGA-06-0648 TCGA-06-0686 TCGA-06-5856 TCGA-06-6389 TCGA-06-6390 
       35.01         9.67         9.40         3.75         7.79         5.39 
TCGA-08-0245 TCGA-08-0349 TCGA-08-0386 TCGA-08-0510 TCGA-08-0514 TCGA-12-0619 
       34.75         7.59        15.72         3.52         8.52        10.39 
TCGA-12-0670 TCGA-12-1600 TCGA-12-1602 TCGA-12-3646 TCGA-14-0740 TCGA-14-0783 
       25.97        13.61         6.41        43.23        11.97         6.21 
TCGA-14-0813 TCGA-14-0817 TCGA-14-0867 TCGA-14-0871 TCGA-14-1451 TCGA-14-1794 
        1.35         5.39         2.04        28.93        23.11         0.99 
TCGA-14-3477 TCGA-15-1447 TCGA-16-0849 TCGA-16-0850 TCGA-19-1388 TCGA-19-1390 
        3.78        53.19        26.07        16.31        12.95        25.38 
TCGA-19-2623 TCGA-19-2624 TCGA-19-4065 TCGA-19-5960 TCGA-26-1438 TCGA-26-5132 
        7.53         0.16         7.04         5.42        10.03         9.40 
TCGA-26-5136 TCGA-32-1978 TCGA-32-4210 TCGA-76-6193 
        1.22        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 
        9.17         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        55.86        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        10.36        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 
        0.16        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        16.21 
TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 
        2.70         0.26         4.04        47.31         0.10         3.58 
TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 
       22.72        32.52        10.52        18.74        14.07        23.08 
TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 
       22.16        10.75         0.20         9.21         2.20        11.74 
TCGA-06-0145 TCGA-06-0148 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 
        2.33         9.80        19.46        46.59        11.80        12.79 
TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 
        8.65         3.19         5.46        11.80         2.56        56.88 
TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 
       10.65         5.29        19.04         3.12        13.02         0.23 
TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0178 TCGA-06-0179 TCGA-06-0185 
        2.20         2.73        91.00        53.98        19.00        73.84 
TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 
       26.33        28.47        14.93        18.31         4.67         7.04 
TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 
        0.39         6.48         5.49         3.91         4.96        11.84 
TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0238 TCGA-06-0240 
        0.20        12.43        22.49         0.36        11.80        20.42 
TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 
       14.96        10.32         5.52         0.26        70.52         4.70 
TCGA-06-0412 TCGA-06-0413 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0649 
        8.05         0.16        12.33         3.22         4.47         2.04 
TCGA-06-0650 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 
       23.57        22.32        19.56         5.39         2.70         2.17 
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        22.98 
TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 
        5.85         5.42        20.94         7.43         6.35         3.58 
TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 
       26.79         8.65         7.89        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         0.76         4.93         9.27         2.83        30.64 
TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 
        5.95         6.81         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 
       11.24         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         3.95 
TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 
        1.48         0.49         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-08-0244 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 
       22.68         3.91       108.82         1.74         4.34        13.78 
TCGA-08-0348 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 
       10.39         3.42        53.82         1.28         6.41        15.06 
TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 
       22.52        14.70        35.64        19.53         0.95         9.17 
TCGA-08-0380 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0512 
       10.85         3.19        10.59         0.30         0.56        11.77 
TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 
       18.44        58.19         1.28        10.75         4.80         6.54 
TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 
       15.98        17.33         5.52        14.01        14.43         1.64 
TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0688 
        5.95         7.17        65.92         0.10        38.17        24.13 
TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 
        6.12         2.63        18.12        28.41        12.43        53.10 
TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 
       43.10         5.49         9.11        14.86        14.27        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         6.25        30.54 
TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 
       21.63        11.97        11.38        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         3.42         9.44        25.28        59.41        25.78 
TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 
       11.54        10.95        11.77        34.52        11.74        13.12 
TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0781 TCGA-14-0786 TCGA-14-0787 
        3.22         2.04        15.12         0.95        23.05         2.24 
TCGA-14-0789 TCGA-14-0790 TCGA-14-0812 TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 
       11.24        13.78         3.25         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-14-1452 TCGA-14-1453 TCGA-14-1454 TCGA-14-1455 
       32.05        58.78         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         6.15        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-15-1449 TCGA-16-0846 TCGA-16-0848 
        9.86        50.53        19.10         5.52         3.91         9.93 
TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 
        4.31        29.03         0.82         9.90        13.35         3.65 
TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 
       18.28        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 
        0.43        14.27         3.39        10.75         9.07         5.95 
TCGA-19-1389 TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 
        4.64         3.48         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        16.47         7.00 
TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 
        6.64        11.28         8.02        18.64         4.73         7.96 
TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-A6J4 TCGA-19-A6J5 
        1.78         6.51         5.39         5.29         3.98        16.57 
TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 TCGA-26-5133 
       13.87         9.73        31.33         7.13         9.37        14.86 
TCGA-26-5134 TCGA-26-5135 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-27-1830 
        5.49         8.88         1.58         7.92         2.33         4.80 
TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 
       16.60         9.86        18.25        33.14        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         3.91         9.04        15.58        14.53        11.77 
TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 
       31.27        14.20         7.79        13.64         4.21        22.68 
TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 
       10.49         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        21.17        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 
       10.62         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-74-6573 
        4.44        11.84         0.20        11.54         7.76         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-76-6656 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 
        1.61        17.72        26.30         5.92 

  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 
             9.555             10.340 
[1] "0.2 - 92.7 (9.6)"   "0.1 - 127.6 (10.3)"
[1] "hr=" "1"  
D64V2, continuous
D64V3, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    20  38
  12Q LOSS WILD-TYPE 200 302
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     20   38
  12Q LOSS WILD-TYPE  200  302
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FEMALE               20                200
  MALE                 38                302
[1] 2 2
[1] FALSE
D64V4, continuous
                    vv
clus                 GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  12Q LOSS MUTATED                               1                   3
  12Q LOSS WILD-TYPE                            16                  15
                    vv
clus                 UNTREATED PRIMARY (DE NOVO) GBM
  12Q LOSS MUTATED                                54
  12Q LOSS WILD-TYPE                             471
D64V5, multiclass
                                 clus
vv                                12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                  1                 16
  TREATED PRIMARY GBM                            3                 15
  UNTREATED PRIMARY (DE NOVO) GBM               54                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"
D64V6, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    39  19
  12Q LOSS WILD-TYPE 343 159
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     39   19
  12Q LOSS WILD-TYPE  343  159
     clus
vv    12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  NO                39                343
  YES               19                159
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12Q LOSS MUTATED       0                         2    53
  12Q LOSS WILD-TYPE    13                        37   432
D64V7, multiclass
                           clus
vv                          12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  ASIAN                                    0                 13
  BLACK OR AFRICAN AMERICAN                2                 37
  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
  12Q LOSS MUTATED     2  46
  12Q LOSS WILD-TYPE  10 416
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      2   46
  12Q LOSS WILD-TYPE   10  416
                        clus
vv                       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                 10
  NOT HISPANIC OR LATINO               46                416
[1] 2 2
[1] FALSE

Clustering(65) Variable = 13Q LOSS MUTATION ANALYSIS
D65V1, survival
                    sevent
clus2                  0   1
  13Q LOSS MUTATED    32 149
  13Q LOSS WILD-TYPE  66 313
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               181                379 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               149                313 
$`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         0.26        22.72 
TCGA-06-0130 TCGA-06-0138 TCGA-06-0140 TCGA-06-0147 TCGA-06-0149 TCGA-06-0152 
       10.52        22.16         0.20        16.70         7.86        11.80 
TCGA-06-0158 TCGA-06-0159 TCGA-06-0162 TCGA-06-0164 TCGA-06-0166 TCGA-06-0168 
        5.46         9.44         2.56        56.88         5.29        19.04 
TCGA-06-0177 TCGA-06-0182 TCGA-06-0184 TCGA-06-0188 TCGA-06-0192 TCGA-06-0195 
        2.01         2.53        40.37        28.47        18.31         7.04 
TCGA-06-0197 TCGA-06-0206 TCGA-06-0209 TCGA-06-0214 TCGA-06-0219 TCGA-06-0402 
        2.60         6.48         3.91        12.43         0.36         0.26 
TCGA-06-0410 TCGA-06-0414 TCGA-06-0648 TCGA-06-0649 TCGA-06-0745 TCGA-06-0875 
        4.70        35.01         9.67         2.04         5.39        43.46 
TCGA-06-0881 TCGA-06-1087 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 
        5.85         3.58         7.89        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         0.76         4.37        11.24         4.54         8.98 
TCGA-06-5416 TCGA-06-5856 TCGA-06-5859 TCGA-06-6389 TCGA-06-6694 TCGA-08-0245 
        6.71         3.75         4.57         7.79         7.36        34.75 
TCGA-08-0246 TCGA-08-0347 TCGA-08-0349 TCGA-08-0354 TCGA-08-0359 TCGA-08-0389 
        3.91        13.78         7.59        15.06         0.95         3.19 
TCGA-08-0392 TCGA-08-0510 TCGA-08-0512 TCGA-08-0516 TCGA-08-0517 TCGA-08-0520 
        0.30         3.52        11.77        18.44        58.19        10.75 
TCGA-12-0615 TCGA-12-0662 TCGA-12-0691 TCGA-12-0769 TCGA-12-0772 TCGA-12-0776 
       14.01        38.17         6.12        12.43        53.10         9.11 
TCGA-12-0819 TCGA-12-0826 TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 
       24.79        27.78        38.76         8.94        20.58       127.59 
TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1096 TCGA-12-1097 
       30.54        21.63        11.97        11.38         9.11        14.53 
TCGA-12-1099 TCGA-12-1598 TCGA-12-3644 TCGA-12-3646 TCGA-12-3653 TCGA-12-5295 
        3.42         9.44        59.41        43.23        11.74        13.12 
TCGA-14-0736 TCGA-14-0740 TCGA-14-0783 TCGA-14-0787 TCGA-14-0812 TCGA-14-0862 
       15.12        11.97         6.21         2.24         3.25         2.89 
TCGA-14-0865 TCGA-14-1034 TCGA-14-1396 TCGA-14-1451 TCGA-14-1453 TCGA-14-1454 
       16.50        15.95         1.12        23.11         1.15        30.18 
TCGA-14-1456 TCGA-14-1458 TCGA-14-1823 TCGA-14-1825 TCGA-14-3477 TCGA-15-0742 
       40.96         6.15        17.85         7.63         3.78         9.86 
TCGA-15-1444 TCGA-15-1447 TCGA-15-1449 TCGA-16-0846 TCGA-16-0849 TCGA-16-0850 
       50.53        53.19         5.52         3.91        26.07        16.31 
TCGA-16-1045 TCGA-19-1385 TCGA-19-1387 TCGA-19-1392 TCGA-19-2621 TCGA-19-2625 
       29.03        10.75         5.95         3.48         1.08         4.08 
TCGA-19-2629 TCGA-19-4065 TCGA-19-5947 TCGA-26-1439 TCGA-26-5133 TCGA-26-6173 
       16.47         7.04         6.64        13.87        14.86         7.92 
TCGA-27-1830 TCGA-27-1834 TCGA-27-2519 TCGA-27-2521 TCGA-28-1746 TCGA-28-1750 
        4.80        33.14        10.39        10.39         0.20         8.35 
TCGA-28-1752 TCGA-28-2502 TCGA-28-2509 TCGA-28-5215 TCGA-28-5216 TCGA-28-5219 
        8.48         0.66         4.77         7.79        13.64        22.68 
TCGA-32-1976 TCGA-32-1987 TCGA-32-2616 TCGA-32-2634 TCGA-32-4210 TCGA-32-4719 
        0.49        14.86         7.36        22.78         3.72        10.85 
TCGA-41-2573 TCGA-41-3392 TCGA-41-3915 TCGA-41-4097 TCGA-74-6584 TCGA-76-4929 
        8.94         0.99        11.84         0.20         7.50         3.65 
TCGA-76-4934 TCGA-76-4935 TCGA-76-6193 TCGA-76-6285 TCGA-76-6286 TCGA-76-6661 
        2.53        10.78         2.70         8.35        20.98         0.23 
TCGA-81-5911 
       17.72 

$`13Q LOSS WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0009 TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 
        9.17         4.73        10.59        82.59        20.61        55.86 
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        10.36 
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         0.23        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         0.16        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        16.21         2.70         4.04        47.31 
TCGA-06-0126 TCGA-06-0127 TCGA-06-0129 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 
        0.10         3.58        32.52        18.74        14.07        23.08 
TCGA-06-0139 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 
       10.75         9.21         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 
        9.80        19.46        46.59        12.79         8.65         3.19 
TCGA-06-0160 TCGA-06-0165 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 
       11.80        10.65         3.12        13.02         0.23         2.20 
TCGA-06-0175 TCGA-06-0176 TCGA-06-0178 TCGA-06-0179 TCGA-06-0185 TCGA-06-0187 
        2.73        91.00        53.98        19.00        73.84        26.33 
TCGA-06-0189 TCGA-06-0190 TCGA-06-0194 TCGA-06-0201 TCGA-06-0208 TCGA-06-0210 
       14.93        10.29         4.67         0.39         5.49         4.96 
TCGA-06-0211 TCGA-06-0213 TCGA-06-0216 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 
       11.84         0.20        22.49        18.02        10.36        11.80 
TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0409 TCGA-06-0412 
       20.42        14.96        10.32         5.52        70.52         8.05 
TCGA-06-0413 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0650 TCGA-06-0686 
        0.16        12.33         3.22         4.47        23.57         9.40 
TCGA-06-0743 TCGA-06-0744 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0876 
       22.32        19.56         2.70         2.17         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        22.98         5.42        20.94         7.43 
TCGA-06-1086 TCGA-06-1800 TCGA-06-1801 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 
        6.35        26.79         8.65         4.93         9.27         2.83 
TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2569 TCGA-06-2570 
       30.64         5.95         6.81         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 
        3.95         5.39         1.48         0.49         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-08-0244 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0348 
        2.56        22.68       108.82         1.74         4.34        10.39 
TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0355 TCGA-08-0356 
        3.42        53.82         1.28         6.41        22.52        14.70 
TCGA-08-0357 TCGA-08-0358 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0390 
       35.64        19.53         9.17        10.85        15.72        10.59 
TCGA-08-0509 TCGA-08-0514 TCGA-08-0518 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 
        0.56         8.52         1.28         4.80         6.54        15.98 
TCGA-08-0529 TCGA-08-0531 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 
       17.33         5.52        14.43         1.64        10.39         5.95 
TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0670 TCGA-12-0688 TCGA-12-0692 
        7.17        65.92         0.10        25.97        24.13         2.63 
TCGA-12-0703 TCGA-12-0707 TCGA-12-0773 TCGA-12-0775 TCGA-12-0778 TCGA-12-0780 
       18.12        28.41        43.10         5.49        14.86        14.27 
TCGA-12-0818 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 TCGA-12-1089 TCGA-12-1090 
       91.76        18.48        10.62        23.51         5.82         6.25 
TCGA-12-1095 TCGA-12-1098 TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 TCGA-12-3648 
       15.85         3.98        25.28        13.61         6.41        25.78 
TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-5299 TCGA-12-5301 
       11.54        10.95        11.77        34.52         3.22         2.04 
TCGA-14-0781 TCGA-14-0786 TCGA-14-0789 TCGA-14-0790 TCGA-14-0813 TCGA-14-0817 
        0.95        23.05        11.24        13.78         1.35         5.39 
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-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1452 TCGA-14-1455 TCGA-14-1459 
        3.75        32.05        58.78         7.10         0.92        12.43 
TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 
        0.99         1.97        17.79         5.88         7.17        17.49 
TCGA-14-2555 TCGA-14-4157 TCGA-15-1446 TCGA-16-0848 TCGA-16-0861 TCGA-16-1047 
        7.96         3.42        19.10         9.93         4.31         0.82 
TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 
        9.90        13.35         3.65        18.28        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         0.43        14.27         3.39 
TCGA-19-1386 TCGA-19-1388 TCGA-19-1389 TCGA-19-1390 TCGA-19-1786 TCGA-19-1787 
        9.07        12.95         4.64        25.38         7.17        12.66 
TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 TCGA-19-2623 TCGA-19-2624 
        3.25         0.13         9.67         4.87         7.53         0.16 
TCGA-19-2631 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 
        7.00        11.28         8.02        18.64         4.73         7.96 
TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A6J4 
        1.78         6.51         5.39         5.29         5.42         3.98 
TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 
       16.57        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-26-6174 
        9.40         5.49         8.88         1.22         1.58         2.33 
TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 
       16.60         9.86        18.25        21.30        30.05        14.04 
TCGA-27-1838 TCGA-27-2518 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 
       11.51        24.76        16.08         7.59         2.86        14.40 
TCGA-27-2528 TCGA-28-1747 TCGA-28-1749 TCGA-28-1751 TCGA-28-1753 TCGA-28-1755 
       15.78         2.53         9.21         7.63         1.22         1.55 
TCGA-28-1756 TCGA-28-1757 TCGA-28-2506 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 
        2.83         0.13         6.74         7.30         5.26         3.91 
TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 
        9.04        15.58        14.53        11.77        31.27        14.20 
TCGA-28-5218 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 TCGA-32-1977 
        4.21        10.49         5.42        15.39        21.07         0.10 
TCGA-32-1978 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1991 
       15.85        19.50         1.18         4.67        12.69        16.93 
TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 TCGA-32-2632 TCGA-32-2638 
       12.23        20.78        15.02        15.95         8.84        21.17 
TCGA-32-4208 TCGA-32-4211 TCGA-32-4213 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 
       21.14        12.59        19.86        10.62         0.85        13.35 
TCGA-41-2575 TCGA-41-3393 TCGA-41-5651 TCGA-41-6646 TCGA-74-6573 TCGA-74-6575 
        9.53         4.44        11.54         7.76         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-76-4931 TCGA-76-6191 TCGA-76-6192 TCGA-76-6280 TCGA-76-6282 TCGA-76-6656 
        9.17        16.70         3.29        11.38        17.06         4.83 
TCGA-76-6657 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-87-5896 
        5.03         9.27         7.73         7.79         1.61        26.30 
TCGA-OX-A56R 
        5.92 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               0.2                0.1 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            127.59             108.82 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             10.39               9.93 
[1] "0.2 - 127.6 (10.4)" "0.1 - 108.8 (9.9)" 
[1] "hr=" "1"  
D65V2, continuous
D65V3, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    72 109
  13Q LOSS WILD-TYPE 148 231
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     72  109
  13Q LOSS WILD-TYPE  148  231
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE               72                148
  MALE                109                231
[1] 2 2
[1] FALSE
D65V4, continuous
                    vv
clus                 GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  13Q LOSS MUTATED                               4                   4
  13Q LOSS WILD-TYPE                            13                  14
                    vv
clus                 UNTREATED PRIMARY (DE NOVO) GBM
  13Q LOSS MUTATED                               173
  13Q LOSS WILD-TYPE                             352
D65V5, multiclass
                                 clus
vv                                13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                  4                 13
  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"
D65V6, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED   121  60
  13Q LOSS WILD-TYPE 261 118
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED    121   60
  13Q LOSS WILD-TYPE  261  118
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  NO               121                261
  YES               60                118
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  13Q LOSS MUTATED       5                         9   161
  13Q LOSS WILD-TYPE     8                        30   324
D65V7, multiclass
                           clus
vv                          13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  ASIAN                                    5                  8
  BLACK OR AFRICAN AMERICAN                9                 30
  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"
D65V8, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED     3 150
  13Q LOSS WILD-TYPE   9 312
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      3  150
  13Q LOSS WILD-TYPE    9  312
                        clus
vv                       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  9
  NOT HISPANIC OR LATINO              150                312
[1] 2 2
[1] FALSE

Clustering(66) Variable = 14Q LOSS MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                  0   1
  14Q LOSS MUTATED    29 116
  14Q LOSS WILD-TYPE  69 346
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               145                415 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               116                346 
$`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        55.86        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        32.52        10.52 
TCGA-06-0138 TCGA-06-0141 TCGA-06-0143 TCGA-06-0146 TCGA-06-0162 TCGA-06-0166 
       22.16         9.21        11.74        20.09         2.56         5.29 
TCGA-06-0171 TCGA-06-0188 TCGA-06-0194 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 
       13.02        28.47         4.67        22.49         0.36        18.02 
TCGA-06-0241 TCGA-06-0409 TCGA-06-0410 TCGA-06-0644 TCGA-06-0646 TCGA-06-0649 
       14.96        70.52         4.70        12.33         4.47         2.04 
TCGA-06-0745 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0878 
        5.39         2.17         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 
        7.43         9.27         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-08-0245 TCGA-08-0380 TCGA-08-0390 TCGA-08-0392 TCGA-08-0512 TCGA-08-0520 
       34.75        10.85        10.59         0.30        11.77        10.75 
TCGA-12-0615 TCGA-12-0616 TCGA-12-0654 TCGA-12-0662 TCGA-12-0692 TCGA-12-0821 
       14.01        14.43         7.17        38.17         2.63        10.62 
TCGA-12-0827 TCGA-12-1088 TCGA-12-1089 TCGA-12-1091 TCGA-12-1092 TCGA-12-1096 
       38.76       127.59         5.82        30.54        21.63         9.11 
TCGA-12-1598 TCGA-12-1602 TCGA-12-3653 TCGA-12-5295 TCGA-14-0736 TCGA-14-0783 
        9.44         6.41        11.74        13.12        15.12         6.21 
TCGA-14-0813 TCGA-14-0817 TCGA-14-0862 TCGA-14-0865 TCGA-14-1396 TCGA-14-1455 
        1.35         5.39         2.89        16.50         1.12         0.92 
TCGA-14-1823 TCGA-14-1825 TCGA-14-1829 TCGA-14-3477 TCGA-15-1447 TCGA-16-0861 
       17.85         7.63         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        16.47 
TCGA-19-5947 TCGA-19-5956 TCGA-19-5960 TCGA-19-A6J4 TCGA-26-1439 TCGA-26-1440 
        6.64         6.51         5.42         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        33.14        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         9.04 
TCGA-28-5213 TCGA-28-5215 TCGA-28-5216 TCGA-28-5220 TCGA-32-1976 TCGA-32-1980 
       31.27         7.79        13.64        10.49         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 
        9.17         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        10.36        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 
        0.23        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         0.16         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        16.21         2.70         0.26 
TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0132 TCGA-06-0133 
        4.04        47.31         0.10         3.58        18.74        14.07 
TCGA-06-0137 TCGA-06-0139 TCGA-06-0140 TCGA-06-0142 TCGA-06-0145 TCGA-06-0147 
       23.08        10.75         0.20         2.20         2.33        16.70 
TCGA-06-0148 TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 
        9.80         7.86        19.46        46.59        11.80        12.79 
TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0164 
        8.65         3.19         5.46         9.44        11.80        56.88 
TCGA-06-0165 TCGA-06-0168 TCGA-06-0169 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 
       10.65        19.04         3.12         0.23         2.20         2.73 
TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 
       91.00         2.01        53.98        19.00         2.53        40.37 
TCGA-06-0185 TCGA-06-0187 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0195 
       73.84        26.33        14.93        10.29        18.31         7.04 
TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 
        2.60         0.39         6.48         5.49         3.91         4.96 
TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 
       11.84         0.20        12.43        10.36        11.80        20.42 
TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 
       10.32         5.52         0.26         8.05         0.16        35.01 
TCGA-06-0645 TCGA-06-0648 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 
        3.22         9.67        23.57         9.40        22.32        19.56 
TCGA-06-0747 TCGA-06-0877 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 
        2.70         5.65        22.98         5.85         5.42        20.94 
TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 
        6.35         3.58        26.79         8.65         7.89        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         0.76         4.93         2.83 
TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 
       30.64         5.95         6.81         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        11.24         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         3.95         1.48         0.49 
TCGA-06-6694 TCGA-06-6695 TCGA-06-6698 TCGA-06-6700 TCGA-06-6701 TCGA-06-A6S0 
        7.36         8.32         4.77         4.77         4.96         3.12 
TCGA-08-0244 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 
       22.68         3.91       108.82         1.74         4.34        13.78 
TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 
       10.39         7.59         3.42        53.82         1.28         6.41 
TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 
       15.06        22.52        14.70        35.64        19.53         0.95 
TCGA-08-0375 TCGA-08-0386 TCGA-08-0389 TCGA-08-0509 TCGA-08-0510 TCGA-08-0514 
        9.17        15.72         3.19         0.56         3.52         8.52 
TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 
       18.44        58.19         1.28         4.80         6.54        15.98 
TCGA-08-0529 TCGA-08-0531 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0656 
       17.33         5.52         1.64        10.39         5.95        65.92 
TCGA-12-0657 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0703 TCGA-12-0707 
        0.10        25.97        24.13         6.12        18.12        28.41 
TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 
       12.43        53.10        43.10         5.49         9.11        14.86 
TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0822 TCGA-12-0826 
       14.27        91.76        24.79        18.48        23.51        27.78 
TCGA-12-0828 TCGA-12-0829 TCGA-12-1090 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 
        8.94        20.58         6.25        11.97        11.38        15.85 
TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 TCGA-12-1599 TCGA-12-1600 TCGA-12-3644 
       14.53         3.98         3.42        25.28        13.61        59.41 
TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 
       43.23        25.78        11.54        10.95        11.77        34.52 
TCGA-12-5299 TCGA-12-5301 TCGA-14-0740 TCGA-14-0781 TCGA-14-0786 TCGA-14-0787 
        3.22         2.04        11.97         0.95        23.05         2.24 
TCGA-14-0789 TCGA-14-0790 TCGA-14-0812 TCGA-14-0866 TCGA-14-0867 TCGA-14-0871 
       11.24        13.78         3.25        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-14-1453 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-14-1827 
        6.15        12.43         0.99         1.97        17.79         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         9.86        50.53        19.10 
TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 TCGA-16-1047 
        5.52         3.91         9.93        26.07        16.31         0.82 
TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 
        9.90        13.35         3.65        18.28        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         0.43        14.27         3.39 
TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 TCGA-19-1388 TCGA-19-1392 TCGA-19-1786 
       10.75         9.07         5.95        12.95         3.48         7.17 
TCGA-19-1787 TCGA-19-1789 TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2624 
       12.66         3.25         9.67         4.87         1.08         0.16 
TCGA-19-2625 TCGA-19-2631 TCGA-19-4065 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 
        4.08         7.00         7.04        11.28         8.02        18.64 
TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5958 TCGA-19-5959 TCGA-19-A6J5 
        4.73         7.96         1.78         5.39         5.29        16.57 
TCGA-26-1438 TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 TCGA-26-5135 
       10.03        31.33         7.13         9.37         9.40         8.88 
TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-27-1830 TCGA-27-1831 
        1.22         1.58         7.92         2.33         4.80        16.60 
TCGA-27-1833 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 
       18.25        21.30        30.05        14.04        11.51        24.76 
TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2528 TCGA-28-1746 
       10.39        16.08         7.59         2.86        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-28-1757 TCGA-28-2502 TCGA-28-2513 TCGA-28-5204 TCGA-28-5208 TCGA-28-5209 
        0.13         0.66         7.30         3.91        15.58        14.53 
TCGA-28-5211 TCGA-28-5214 TCGA-28-5218 TCGA-28-5219 TCGA-28-6450 TCGA-32-1970 
       11.77        14.20         4.21        22.68         5.42        15.39 
TCGA-32-1973 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 TCGA-32-1982 TCGA-32-1986 
       21.07         0.10        15.85        19.50         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-32-2638 TCGA-32-4208 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 
        8.84        21.17        21.14         3.72        12.59        19.86 
TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-3393 TCGA-41-3915 
       10.85        10.62         0.85        13.35         4.44        11.84 
TCGA-41-5651 TCGA-41-6646 TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 
       11.54         7.76         3.45        20.91         4.34        14.33 
TCGA-74-6581 TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 TCGA-76-4931 TCGA-76-4935 
        8.22         7.50         4.80         4.54         9.17        10.78 
TCGA-76-6191 TCGA-76-6192 TCGA-76-6280 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 
       16.70         3.29        11.38        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 
       26.30 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              0.13               0.10 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            127.59             108.82 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              9.27              10.39 
[1] "0.1 - 127.6 (9.3)"  "0.1 - 108.8 (10.4)"
[1] "hr=" "1"  
D66V2, continuous
D66V3, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    61  84
  14Q LOSS WILD-TYPE 159 256
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     61   84
  14Q LOSS WILD-TYPE  159  256
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE               61                159
  MALE                 84                256
[1] 2 2
[1] FALSE
D66V4, continuous
                    vv
clus                 GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  14Q LOSS MUTATED                               4                   6
  14Q LOSS WILD-TYPE                            13                  12
                    vv
clus                 UNTREATED PRIMARY (DE NOVO) GBM
  14Q LOSS MUTATED                               135
  14Q LOSS WILD-TYPE                             390
D66V5, multiclass
                                 clus
vv                                14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                  4                 13
  TREATED PRIMARY GBM                            6                 12
  UNTREATED PRIMARY (DE NOVO) GBM              135                390
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V6, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED   100  45
  14Q LOSS WILD-TYPE 282 133
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED    100   45
  14Q LOSS WILD-TYPE  282  133
     clus
vv    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  NO               100                282
  YES               45                133
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  14Q LOSS MUTATED       4                        16   121
  14Q LOSS WILD-TYPE     9                        23   364
D66V7, multiclass
                           clus
vv                          14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  ASIAN                                    4                  9
  BLACK OR AFRICAN AMERICAN               16                 23
  WHITE                                  121                364
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V8, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED     1 121
  14Q LOSS WILD-TYPE  11 341
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      1  121
  14Q LOSS WILD-TYPE   11  341
                        clus
vv                       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 11
  NOT HISPANIC OR LATINO              121                341
[1] 2 2
[1] FALSE

Clustering(67) Variable = 15Q LOSS MUTATION ANALYSIS
D67V1, survival
                    sevent
clus2                  0   1
  15Q LOSS MUTATED    17  84
  15Q LOSS WILD-TYPE  81 378
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               101                459 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                84                378 
$`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         0.23        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         4.04 
TCGA-06-0128 TCGA-06-0129 TCGA-06-0174 TCGA-06-0188 TCGA-06-0192 TCGA-06-0209 
       22.72        32.52         2.20        28.47        18.31         3.91 
TCGA-06-0213 TCGA-06-0216 TCGA-06-0237 TCGA-06-0402 TCGA-06-0410 TCGA-06-0645 
        0.20        22.49        10.36         0.26         4.70         3.22 
TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0875 TCGA-06-1801 TCGA-06-2558 
        4.47         9.67         2.04        43.46         8.65         0.76 
TCGA-06-5416 TCGA-06-5856 TCGA-06-6694 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-08-0246 
        6.71         3.75         7.36         1.87         3.12         3.91 
TCGA-08-0344 TCGA-08-0348 TCGA-08-0359 TCGA-08-0386 TCGA-08-0510 TCGA-12-0618 
      108.82        10.39         0.95        15.72         3.52         1.64 
TCGA-12-0619 TCGA-12-1088 TCGA-12-1096 TCGA-12-1099 TCGA-12-1600 TCGA-12-1602 
       10.39       127.59         9.11         3.42        13.61         6.41 
TCGA-12-3646 TCGA-14-0783 TCGA-14-0817 TCGA-14-0867 TCGA-14-1794 TCGA-15-1447 
       43.23         6.21         5.39         2.04         0.99        53.19 
TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 TCGA-16-1045 
        5.52         3.91         9.93        26.07        16.31        29.03 
TCGA-19-1385 TCGA-19-1387 TCGA-19-1390 TCGA-19-1392 TCGA-19-2629 TCGA-19-5955 
       10.75         5.95        25.38         3.48        16.47         1.78 
TCGA-19-5956 TCGA-26-1438 TCGA-26-1439 TCGA-26-6174 TCGA-27-1830 TCGA-27-1834 
        6.51        10.03        13.87         2.33         4.80        33.14 
TCGA-27-2519 TCGA-27-2524 TCGA-28-1746 TCGA-28-1750 TCGA-28-1756 TCGA-28-5215 
       10.39         7.59         0.20         8.35         2.83         7.79 
TCGA-28-5219 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-2616 TCGA-32-2634 
       22.68        15.39        21.07         0.49         7.36        22.78 
TCGA-32-4210 TCGA-32-4211 TCGA-32-4719 TCGA-41-2573 TCGA-41-3915 TCGA-41-5651 
        3.72        12.59        10.85         8.94        11.84        11.54 
TCGA-76-4929 TCGA-76-4935 TCGA-76-6191 TCGA-76-6285 TCGA-76-6286 
        3.65        10.78        16.70         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 
        9.17        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        55.86        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        10.36        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         0.16        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        16.21         2.70         0.26        47.31         0.10 
TCGA-06-0127 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 
        3.58        10.52        18.74        14.07        23.08        22.16 
TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 
       10.75         0.20         9.21         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        16.70         9.80         7.86        19.46        46.59 
TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 
       11.80        12.79         8.65         3.19         5.46         9.44 
TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 
       11.80         2.56        56.88        10.65         5.29        19.04 
TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 
        3.12        13.02         0.23         2.73        91.00         2.01 
TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 
       53.98        19.00         2.53        40.37        73.84        26.33 
TCGA-06-0189 TCGA-06-0190 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 
       14.93        10.29         4.67         7.04         2.60         0.39 
TCGA-06-0206 TCGA-06-0208 TCGA-06-0210 TCGA-06-0211 TCGA-06-0214 TCGA-06-0219 
        6.48         5.49         4.96        11.84        12.43         0.36 
TCGA-06-0221 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 
       18.02        11.80        20.42        14.96        10.32         5.52 
TCGA-06-0409 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0650 
       70.52         8.05         0.16        35.01        12.33        23.57 
TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 
        9.40        22.32        19.56         5.39         2.70         2.17 
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        22.98         5.85 
TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 
        5.42        20.94         7.43         6.35         3.58        26.79 
TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 TCGA-06-2557 TCGA-06-2559 
        7.89        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 
        9.27         2.83        30.64         5.95         6.81         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        11.24         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         3.95         7.79         5.39         1.48         0.49 
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-A6S1 TCGA-08-0244 TCGA-08-0245 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 
        2.56        22.68        34.75         1.74         4.34        13.78 
TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 
        7.59         3.42        53.82         1.28         6.41        15.06 
TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0375 TCGA-08-0380 
       22.52        14.70        35.64        19.53         9.17        10.85 
TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0512 TCGA-08-0514 
        3.19        10.59         0.30         0.56        11.77         8.52 
TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 
       18.44        58.19         1.28        10.75         4.80         6.54 
TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0620 
       15.98        17.33         5.52        14.01        14.43         5.95 
TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 
        7.17        65.92         0.10        38.17        25.97        24.13 
TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 
        6.12         2.63        18.12        28.41        12.43        53.10 
TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 
       43.10         5.49         9.11        14.86        14.27        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-12-1089 TCGA-12-1090 TCGA-12-1091 TCGA-12-1092 
        8.94        20.58         5.82         6.25        30.54        21.63 
TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1097 TCGA-12-1098 TCGA-12-1598 
       11.97        11.38        15.85        14.53         3.98         9.44 
TCGA-12-1599 TCGA-12-3644 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 
       25.28        59.41        25.78        11.54        10.95        11.77 
TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 
       34.52        11.74        13.12         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-14-0813 TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 TCGA-14-0871 
        3.25         1.35         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         6.15        12.43         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-16-0861 
        3.78         3.42         9.86        50.53        19.10         4.31 
TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 
        0.82         9.90        13.35         3.65        18.28        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         0.43        14.27 
TCGA-19-0964 TCGA-19-1386 TCGA-19-1388 TCGA-19-1389 TCGA-19-1786 TCGA-19-1787 
        3.39         9.07        12.95         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-19-2625 TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 
        0.16         4.08         7.00         7.04         6.64        11.28 
TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5958 TCGA-19-5959 
        8.02        18.64         4.73         7.96         5.39         5.29 
TCGA-19-5960 TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 
        5.42         3.98        16.57         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         1.22 
TCGA-26-5139 TCGA-26-6173 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1835 
        1.58         7.92        16.60         9.86        18.25        21.30 
TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2521 TCGA-27-2523 
       30.05        14.04        11.51        24.76        10.39        16.08 
TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1747 TCGA-28-1749 TCGA-28-1751 
        2.86        14.40        15.78         2.53         9.21         7.63 
TCGA-28-1752 TCGA-28-1753 TCGA-28-1755 TCGA-28-1757 TCGA-28-2502 TCGA-28-2506 
        8.48         1.22         1.55         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         3.91         9.04        15.58 
TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5216 TCGA-28-5218 
       14.53        11.77        31.27        14.20        13.64         4.21 
TCGA-28-5220 TCGA-28-6450 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 TCGA-32-1980 
       10.49         5.42         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-32-2632 TCGA-32-2638 TCGA-32-4208 TCGA-32-4213 
       15.02        15.95         8.84        21.17        21.14        19.86 
TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 
       10.62         0.85        13.35         9.53         0.99         4.44 
TCGA-41-4097 TCGA-41-6646 TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 
        0.20         7.76         3.45        20.91         4.34        14.33 
TCGA-74-6581 TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4931 
        8.22         7.50         4.80         4.54         3.09         9.17 
TCGA-76-4934 TCGA-76-6192 TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 TCGA-76-6656 
        2.53         3.29         2.70        11.38        17.06         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 
       17.72        26.30         5.92 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               0.2                0.1 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            127.59              99.98 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              8.94              10.49 
[1] "0.2 - 127.6 (8.9)"  "0.1 - 100.0 (10.5)"
[1] "hr=" "1"  
D67V2, continuous
D67V3, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED    43  58
  15Q LOSS WILD-TYPE 177 282
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     43   58
  15Q LOSS WILD-TYPE  177  282
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE               43                177
  MALE                 58                282
[1] 2 2
[1] FALSE
D67V4, continuous
                    vv
clus                 GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  15Q LOSS MUTATED                               2                   2
  15Q LOSS WILD-TYPE                            15                  16
                    vv
clus                 UNTREATED PRIMARY (DE NOVO) GBM
  15Q LOSS MUTATED                                97
  15Q LOSS WILD-TYPE                             428
D67V5, multiclass
                                 clus
vv                                15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                  2                 15
  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"
D67V6, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED    61  40
  15Q LOSS WILD-TYPE 321 138
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     61   40
  15Q LOSS WILD-TYPE  321  138
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  NO                61                321
  YES               40                138
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  15Q LOSS MUTATED       2                         4    91
  15Q LOSS WILD-TYPE    11                        35   394
D67V7, multiclass
                           clus
vv                          15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  ASIAN                                    2                 11
  BLACK OR AFRICAN AMERICAN                4                 35
  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"
D67V8, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     4  84
  15Q LOSS WILD-TYPE   8 378
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      4   84
  15Q LOSS WILD-TYPE    8  378
                        clus
vv                       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  8
  NOT HISPANIC OR LATINO               84                378
[1] 2 2
[1] FALSE

Clustering(68) Variable = 16P LOSS MUTATION ANALYSIS
D68V1, survival
                    sevent
clus2                  0   1
  16P LOSS MUTATED     8  55
  16P LOSS WILD-TYPE  90 407
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                63                497 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                55                407 
$`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        16.21        18.74        56.88 
TCGA-06-0168 TCGA-06-0171 TCGA-06-0177 TCGA-06-0214 TCGA-06-0216 TCGA-06-0221 
       19.04        13.02         2.01        12.43        22.49        18.02 
TCGA-06-0394 TCGA-06-0414 TCGA-06-0645 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 
       10.32        35.01         3.22         9.40        22.32        19.56 
TCGA-06-0879 TCGA-06-1087 TCGA-06-2557 TCGA-06-2569 TCGA-06-5859 TCGA-06-6389 
       22.98         3.58         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         6.41         0.30         0.56 
TCGA-08-0514 TCGA-12-0619 TCGA-12-0776 TCGA-12-0826 TCGA-12-1099 TCGA-12-1600 
        8.52        10.39         9.11        27.78         3.42        13.61 
TCGA-12-3653 TCGA-14-0812 TCGA-14-0813 TCGA-14-0871 TCGA-14-1823 TCGA-19-1392 
       11.74         3.25         1.35        28.93        17.85         3.48 
TCGA-19-5953 TCGA-19-5955 TCGA-19-5956 TCGA-27-1835 TCGA-27-2521 TCGA-27-2524 
        4.73         1.78         6.51        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         3.91        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 
        9.17         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        55.86        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        10.36        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         0.23        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         0.16        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         0.26         4.04 
TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 
       47.31         0.10         3.58        22.72        32.52        10.52 
TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 
       14.07        23.08        22.16        10.75         0.20         9.21 
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        16.70         9.80 
TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 
        7.86        19.46        46.59        11.80        12.79         8.65 
TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 TCGA-06-0165 
        3.19         5.46         9.44        11.80         2.56        10.65 
TCGA-06-0166 TCGA-06-0169 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 
        5.29         3.12         0.23         2.20         2.73        91.00 
TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 
       53.98        19.00         2.53        40.37        73.84        26.33 
TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 
       28.47        14.93        10.29        18.31         4.67         7.04 
TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 
        2.60         0.39         6.48         5.49         3.91         4.96 
TCGA-06-0211 TCGA-06-0213 TCGA-06-0219 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 
       11.84         0.20         0.36        10.36        11.80        20.42 
TCGA-06-0241 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 
       14.96         5.52         0.26        70.52         4.70         8.05 
TCGA-06-0413 TCGA-06-0644 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 
        0.16        12.33         4.47         9.67         2.04        23.57 
TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 
        5.39         2.70         2.17         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         5.85         5.42        20.94         7.43 
TCGA-06-1086 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 
        6.35        26.79         8.65         7.89        13.61        33.90 
TCGA-06-1806 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 
       15.32         0.76         4.93         9.27         2.83        30.64 
TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2570 TCGA-06-5408 
        5.95         6.81         5.98         4.37        31.50        11.24 
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         3.95         5.39 
TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 TCGA-06-6699 
        1.48         0.49         7.36         8.32        12.85         1.55 
TCGA-06-6701 TCGA-06-A5U1 TCGA-06-A6S1 TCGA-08-0244 TCGA-08-0245 TCGA-08-0246 
        4.96         1.87         2.56        22.68        34.75         3.91 
TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 
      108.82         1.74         4.34        13.78        10.39         7.59 
TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 
        3.42        53.82         1.28        15.06        22.52        14.70 
TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 
       35.64        19.53         0.95         9.17        10.85        15.72 
TCGA-08-0389 TCGA-08-0390 TCGA-08-0510 TCGA-08-0512 TCGA-08-0516 TCGA-08-0517 
        3.19        10.59         3.52        11.77        18.44        58.19 
TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 
        1.28        10.75         4.80         6.54        15.98        17.33 
TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0620 TCGA-12-0654 
        5.52        14.01        14.43         1.64         5.95         7.17 
TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 
       65.92         0.10        38.17        25.97        24.13         6.12 
TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 
        2.63        18.12        28.41        12.43        53.10        43.10 
TCGA-12-0775 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 
        5.49        14.86        14.27        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         6.25        30.54        21.63        11.97        11.38 
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         9.44        25.28 
TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 
        6.41        59.41        43.23        25.78        11.54        10.95 
TCGA-12-3651 TCGA-12-3652 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 
       11.77        34.52        13.12         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-14-0817 TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 TCGA-14-0867 
       13.78         5.39         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-14-1453 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         6.15        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         9.86        50.53        19.10        53.19 
TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 
        5.52         3.91         9.93        26.07        16.31         4.31 
TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 
       29.03         0.82         9.90        13.35         3.65        18.28 
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         0.43 
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-19-4065 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 
       16.47         7.00         7.04         6.64        11.28         8.02 
TCGA-19-5952 TCGA-19-5954 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A6J4 
       18.64         7.96         5.39         5.29         5.42         3.98 
TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 
       16.57        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         1.22 
TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 
        1.58         7.92         2.33         4.80        16.60         9.86 
TCGA-27-1833 TCGA-27-1834 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 
       18.25        33.14        30.05        14.04        11.51        24.76 
TCGA-27-2519 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-28-2502 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         9.04        15.58        14.53        11.77        31.27 
TCGA-28-5214 TCGA-28-5215 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 
       14.20         7.79         4.21        22.68        10.49         5.42 
TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 TCGA-32-1979 TCGA-32-1982 
       15.39        21.07         0.49         0.10        19.50         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        21.17        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        10.62         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        11.54 
TCGA-41-6646 TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 
        7.76         3.45        20.91         4.34        14.33         8.22 
TCGA-74-6584 TCGA-76-4926 TCGA-76-4929 TCGA-76-4931 TCGA-76-4934 TCGA-76-4935 
        7.50         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 
        7.79         1.61        17.72        26.30         5.92 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
               0.3                0.1 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             56.88             127.59 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              9.11              10.36 
[1] "0.3 - 56.9 (9.1)"   "0.1 - 127.6 (10.4)"
[1] "hr=" "1.3"
D68V2, continuous
D68V3, binary
                    cls
clus                   0   1
  16P LOSS MUTATED    23  40
  16P LOSS WILD-TYPE 197 300
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     23   40
  16P LOSS WILD-TYPE  197  300
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE               23                197
  MALE                 40                300
[1] 2 2
[1] FALSE
D68V4, continuous
                    vv
clus                 GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  16P LOSS MUTATED                               1                   0
  16P LOSS WILD-TYPE                            16                  18
                    vv
clus                 UNTREATED PRIMARY (DE NOVO) GBM
  16P LOSS MUTATED                                62
  16P LOSS WILD-TYPE                             463
D68V5, multiclass
                                 clus
vv                                16P LOSS MUTATED 16P LOSS WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                  1                 16
  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"
D68V6, binary
                    cls
clus                   0   1
  16P LOSS MUTATED    36  27
  16P LOSS WILD-TYPE 346 151
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     36   27
  16P LOSS WILD-TYPE  346  151
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  NO                36                346
  YES               27                151
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16P LOSS MUTATED       1                         5    56
  16P LOSS WILD-TYPE    12                        34   429
D68V7, multiclass
                           clus
vv                          16P LOSS MUTATED 16P LOSS WILD-TYPE
  ASIAN                                    1                 12
  BLACK OR AFRICAN AMERICAN                5                 34
  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"
D68V8, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     1  55
  16P LOSS WILD-TYPE  11 407
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      1   55
  16P LOSS WILD-TYPE   11  407
                        clus
vv                       16P LOSS MUTATED 16P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 11
  NOT HISPANIC OR LATINO               55                407
[1] 2 2
[1] FALSE

Clustering(69) Variable = 16Q LOSS MUTATION ANALYSIS
D69V1, survival
                    sevent
clus2                  0   1
  16Q LOSS MUTATED     9  73
  16Q LOSS WILD-TYPE  89 389
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                82                478 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                73                389 
$`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        16.21 
TCGA-06-0132 TCGA-06-0164 TCGA-06-0168 TCGA-06-0171 TCGA-06-0177 TCGA-06-0214 
       18.74        56.88        19.04        13.02         2.01        12.43 
TCGA-06-0216 TCGA-06-0221 TCGA-06-0394 TCGA-06-0414 TCGA-06-0645 TCGA-06-0686 
       22.49        18.02        10.32        35.01         3.22         9.40 
TCGA-06-0743 TCGA-06-0744 TCGA-06-0749 TCGA-06-0879 TCGA-06-0882 TCGA-06-1087 
       22.32        19.56         2.17        22.98         5.42         3.58 
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         0.49 
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         6.41         0.30 
TCGA-08-0509 TCGA-08-0520 TCGA-08-0525 TCGA-12-0618 TCGA-12-0619 TCGA-12-0654 
        0.56        10.75        15.98         1.64        10.39         7.17 
TCGA-12-0692 TCGA-12-0826 TCGA-12-1099 TCGA-12-1600 TCGA-12-3653 TCGA-12-5295 
        2.63        27.78         3.42        13.61        11.74        13.12 
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         6.51 
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         3.91 
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 
        9.17         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        55.86        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        10.36        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         0.23        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         0.16        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         0.26         4.04        47.31         0.10 
TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 TCGA-06-0133 TCGA-06-0137 
        3.58        22.72        32.52        10.52        14.07        23.08 
TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 
       22.16        10.75         0.20         9.21         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        16.70         9.80         7.86        19.46 
TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 
       46.59        11.80        12.79         8.65         3.19         5.46 
TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 TCGA-06-0165 TCGA-06-0166 TCGA-06-0169 
        9.44        11.80         2.56        10.65         5.29         3.12 
TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0178 TCGA-06-0179 
        0.23         2.20         2.73        91.00        53.98        19.00 
TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 
        2.53        40.37        73.84        26.33        28.47        14.93 
TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 
       10.29        18.31         4.67         7.04         2.60         0.39 
TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 
        6.48         5.49         3.91         4.96        11.84         0.20 
TCGA-06-0219 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0397 
        0.36        10.36        11.80        20.42        14.96         5.52 
TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0644 
        0.26        70.52         4.70         8.05         0.16        12.33 
TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0745 TCGA-06-0747 
        4.47         9.67         2.04        23.57         5.39         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         5.85 
TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 
       20.94         7.43         6.35        26.79         8.65         7.89 
TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 
       13.61        33.90        15.32         0.76         4.93         9.27 
TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 
        2.83        30.64         5.95         6.81         5.98         4.37 
TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 
       31.50        11.24         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         3.95 
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-A5U1 TCGA-08-0244 TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 
        4.96         1.87        22.68        34.75         3.91       108.82 
TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 
        1.74         4.34        13.78        10.39         7.59         3.42 
TCGA-08-0351 TCGA-08-0352 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 
       53.82         1.28        15.06        22.52        14.70        35.64 
TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 
       19.53         0.95         9.17        10.85        15.72         3.19 
TCGA-08-0390 TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 
       10.59         3.52        11.77         8.52        18.44        58.19 
TCGA-08-0518 TCGA-08-0521 TCGA-08-0524 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 
        1.28         4.80         6.54        17.33         5.52        14.01 
TCGA-12-0616 TCGA-12-0620 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 
       14.43         5.95        65.92         0.10        38.17        25.97 
TCGA-12-0688 TCGA-12-0691 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 
       24.13         6.12        18.12        28.41        12.43        53.10 
TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 
       43.10         5.49         9.11        14.86        14.27        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         6.25        30.54        21.63 
TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 
       11.97        11.38        15.85         9.11        14.53         3.98 
TCGA-12-1598 TCGA-12-1599 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 
        9.44        25.28         6.41        59.41        43.23        25.78 
TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-5299 TCGA-14-0740 
       11.54        10.95        11.77        34.52         3.22        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-14-0817 TCGA-14-0865 TCGA-14-0866 TCGA-14-0867 TCGA-14-1034 TCGA-14-1037 
        5.39        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-14-1825 
        6.15        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 
        9.86        50.53        19.10        53.19         5.52         3.91 
TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 TCGA-16-1047 TCGA-16-1055 
        9.93        26.07        16.31         4.31         0.82         9.90 
TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 
       13.35         3.65        18.28        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         0.43        14.27         3.39        10.75 
TCGA-19-1386 TCGA-19-1387 TCGA-19-1388 TCGA-19-1390 TCGA-19-1392 TCGA-19-1786 
        9.07         5.95        12.95        25.38         3.48         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        16.47         7.00         7.04 
TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5954 TCGA-19-5958 
        6.64        11.28         8.02        18.64         7.96         5.39 
TCGA-19-5959 TCGA-19-5960 TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 
        5.29         5.42         3.98        16.57        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         1.22         1.58         7.92         2.33 
TCGA-27-1830 TCGA-27-1831 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 
        4.80        16.60        18.25        33.14        21.30        30.05 
TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2523 TCGA-27-2526 
       14.04        11.51        24.76        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-28-1756 TCGA-28-1757 TCGA-28-2502 TCGA-28-2506 
        8.48         1.22         2.83         0.13         0.66         6.74 
TCGA-28-2509 TCGA-28-2513 TCGA-28-2514 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 
        4.77         7.30         5.26         9.04        15.58        14.53 
TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5218 TCGA-28-5219 
       11.77        31.27        14.20         7.79         4.21        22.68 
TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1976 TCGA-32-1977 TCGA-32-1979 
       10.49         5.42        15.39         0.49         0.10        19.50 
TCGA-32-1982 TCGA-32-1986 TCGA-32-1991 TCGA-32-2491 TCGA-32-2495 TCGA-32-2615 
        4.67        12.69        16.93        12.23        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        21.17        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        10.62         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        11.54         7.76 
TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6581 TCGA-74-6584 TCGA-76-4925 
        3.45        20.91         4.34         8.22         7.50         4.80 
TCGA-76-4926 TCGA-76-4929 TCGA-76-4931 TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 
        4.54         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 
        1.61        17.72        26.30         5.92 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               0.3                0.1 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             99.98             127.59 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              9.63              10.36 
[1] "0.3 - 100.0 (9.6)"  "0.1 - 127.6 (10.4)"
[1] "hr=" "1.4"
D69V2, continuous
D69V3, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED    32  50
  16Q LOSS WILD-TYPE 188 290
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     32   50
  16Q LOSS WILD-TYPE  188  290
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE               32                188
  MALE                 50                290
[1] 2 2
[1] FALSE
D69V4, continuous
                    vv
clus                 GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  16Q LOSS MUTATED                               2                   1
  16Q LOSS WILD-TYPE                            15                  17
                    vv
clus                 UNTREATED PRIMARY (DE NOVO) GBM
  16Q LOSS MUTATED                                79
  16Q LOSS WILD-TYPE                             446
D69V5, multiclass
                                 clus
vv                                16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                  2                 15
  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"
D69V6, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED    47  35
  16Q LOSS WILD-TYPE 335 143
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     47   35
  16Q LOSS WILD-TYPE  335  143
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  NO                47                335
  YES               35                143
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16Q LOSS MUTATED       1                         9    69
  16Q LOSS WILD-TYPE    12                        30   416
D69V7, multiclass
                           clus
vv                          16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  ASIAN                                    1                 12
  BLACK OR AFRICAN AMERICAN                9                 30
  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"
D69V8, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED     2  70
  16Q LOSS WILD-TYPE  10 392
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      2   70
  16Q LOSS WILD-TYPE   10  392
                        clus
vv                       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                 10
  NOT HISPANIC OR LATINO               70                392
[1] 2 2
[1] FALSE

Clustering(70) Variable = 17P LOSS MUTATION ANALYSIS
D70V1, survival
                    sevent
clus2                  0   1
  17P LOSS MUTATED    11  50
  17P LOSS WILD-TYPE  87 412
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                61                499 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                50                412 
$`17P LOSS MUTATED`
TCGA-02-0001 TCGA-02-0033 TCGA-02-0051 TCGA-02-0055 TCGA-02-0059 TCGA-02-0069 
        9.17         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        10.52        16.70         7.86        11.80         9.44 
TCGA-06-0177 TCGA-06-0184 TCGA-06-0187 TCGA-06-0189 TCGA-06-0190 TCGA-06-0197 
        2.01        40.37        26.33        14.93        10.29         2.60 
TCGA-06-0410 TCGA-06-0644 TCGA-06-2561 TCGA-06-5408 TCGA-08-0245 TCGA-08-0353 
        4.70        12.33         9.27        11.24        34.75         6.41 
TCGA-08-0386 TCGA-08-0390 TCGA-12-0619 TCGA-12-0772 TCGA-12-0826 TCGA-12-1098 
       15.72        10.59        10.39        53.10        27.78         3.98 
TCGA-12-3653 TCGA-14-0871 TCGA-14-1396 TCGA-14-1453 TCGA-15-1447 TCGA-15-1449 
       11.74        28.93         1.12         1.15        53.19         5.52 
TCGA-16-0846 TCGA-19-0960 TCGA-19-2623 TCGA-19-4065 TCGA-26-1442 TCGA-26-5133 
        3.91         8.61         7.53         7.04        31.33        14.86 
TCGA-27-1835 TCGA-28-2509 TCGA-28-5215 TCGA-32-1976 TCGA-32-2491 TCGA-41-2573 
       21.30         4.77         7.79         0.49        12.23         8.94 
TCGA-41-3392 TCGA-41-3915 TCGA-41-5651 TCGA-76-4925 TCGA-76-4934 TCGA-76-6285 
        0.99        11.84        11.54         4.80         2.53         8.35 
TCGA-76-6662 
        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        55.86        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        10.36        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         0.23        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         0.16 
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        16.21 
TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 
        2.70         0.26         4.04        47.31         0.10         3.58 
TCGA-06-0128 TCGA-06-0129 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 
       22.72        32.52        18.74        14.07        23.08        22.16 
TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 
       10.75         0.20         9.21         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         9.80        19.46        46.59        12.79         8.65 
TCGA-06-0157 TCGA-06-0158 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 
        3.19         5.46        11.80         2.56        56.88        10.65 
TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 
        5.29        19.04         3.12        13.02         0.23         2.20 
TCGA-06-0175 TCGA-06-0176 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0185 
        2.73        91.00        53.98        19.00         2.53        73.84 
TCGA-06-0188 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0201 TCGA-06-0206 
       28.47        18.31         4.67         7.04         0.39         6.48 
TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 
        5.49         3.91         4.96        11.84         0.20        12.43 
TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 
       22.49         0.36        18.02        10.36        11.80        20.42 
TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0412 
       14.96        10.32         5.52         0.26        70.52         8.05 
TCGA-06-0413 TCGA-06-0414 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 
        0.16        35.01         3.22         4.47         9.67         2.04 
TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 
       23.57         9.40        22.32        19.56         5.39         2.70 
TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 
        2.17         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 
       22.98         5.85         5.42        20.94         7.43         6.35 
TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 
        3.58        26.79         8.65         7.89        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         0.76         4.93         2.83        30.64 
TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 
        5.95         6.81         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         3.95 
TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 
        7.79         5.39         1.48         0.49         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-08-0244 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 
        3.12         2.56        22.68         3.91       108.82         1.74 
TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 
        4.34        13.78        10.39         7.59         3.42        53.82 
TCGA-08-0352 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 
        1.28        15.06        22.52        14.70        35.64        19.53 
TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0389 TCGA-08-0392 TCGA-08-0509 
        0.95         9.17        10.85         3.19         0.30         0.56 
TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 
        3.52        11.77         8.52        18.44        58.19         1.28 
TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 
       10.75         4.80         6.54        15.98        17.33         5.52 
TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 
       14.01        14.43         1.64         5.95         7.17        65.92 
TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 
        0.10        38.17        25.97        24.13         6.12         2.63 
TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 
       18.12        28.41        12.43        43.10         5.49         9.11 
TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 
       14.86        14.27        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 
        6.25        30.54        21.63        11.97        11.38        15.85 
TCGA-12-1096 TCGA-12-1097 TCGA-12-1099 TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 
        9.11        14.53         3.42         9.44        25.28        13.61 
TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 
        6.41        59.41        43.23        25.78        11.54        10.95 
TCGA-12-3651 TCGA-12-3652 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 
       11.77        34.52        13.12         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-14-1034 TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 
       26.33         2.04        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         6.15        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         9.86        50.53        19.10 
TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 
        9.93        26.07        16.31         4.31        29.03         0.82 
TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 
        9.90        13.35         3.65        18.28        13.97         6.41 
TCGA-19-0955 TCGA-19-0957 TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 
       11.77        21.90         0.43        14.27         3.39        10.75 
TCGA-19-1386 TCGA-19-1387 TCGA-19-1388 TCGA-19-1389 TCGA-19-1390 TCGA-19-1392 
        9.07         5.95        12.95         4.64        25.38         3.48 
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-19-2624 TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-5947 
        1.08         0.16         4.08        16.47         7.00         6.64 
TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 
       11.28         8.02        18.64         4.73         7.96         1.78 
TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A6J4 TCGA-19-A6J5 
        6.51         5.39         5.29         5.42         3.98        16.57 
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-26-5134 TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 
        5.49         8.88         1.22         1.58         7.92         2.33 
TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1836 
        4.80        16.60         9.86        18.25        33.14        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 
        3.91         9.04        15.58        14.53        11.77        31.27 
TCGA-28-5214 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 
       14.20        13.64         4.21        22.68        10.49         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-32-1987 TCGA-32-1991 TCGA-32-2494 TCGA-32-2495 
        4.67        12.69        14.86        16.93        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        21.17        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        10.62         0.85 
TCGA-41-2572 TCGA-41-2575 TCGA-41-3393 TCGA-41-4097 TCGA-41-6646 TCGA-74-6573 
       13.35         9.53         4.44         0.20         7.76         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-76-6286 TCGA-76-6656 TCGA-76-6657 
        2.70        11.38        17.06        20.98         4.83         5.03 
TCGA-76-6661 TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
        0.23         7.73         7.79         1.61        17.72        26.30 
TCGA-OX-A56R 
        5.92 

  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 
             10.39               9.93 
[1] "0.5 - 92.7 (10.4)" "0.1 - 127.6 (9.9)"
[1] "hr=" "1"  
D70V2, continuous
D70V3, binary
                    cls
clus                   0   1
  17P LOSS MUTATED    28  33
  17P LOSS WILD-TYPE 192 307
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     28   33
  17P LOSS WILD-TYPE  192  307
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE               28                192
  MALE                 33                307
[1] 2 2
[1] FALSE
D70V4, continuous
                    vv
clus                 GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  17P LOSS MUTATED                               1                   1
  17P LOSS WILD-TYPE                            16                  17
                    vv
clus                 UNTREATED PRIMARY (DE NOVO) GBM
  17P LOSS MUTATED                                59
  17P LOSS WILD-TYPE                             466
D70V5, multiclass
                                 clus
vv                                17P LOSS MUTATED 17P LOSS WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                  1                 16
  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"
D70V6, binary
                    cls
clus                   0   1
  17P LOSS MUTATED    37  24
  17P LOSS WILD-TYPE 345 154
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     37   24
  17P LOSS WILD-TYPE  345  154
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  NO                37                345
  YES               24                154
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17P LOSS MUTATED       1                         3    57
  17P LOSS WILD-TYPE    12                        36   428
D70V7, multiclass
                           clus
vv                          17P LOSS MUTATED 17P LOSS WILD-TYPE
  ASIAN                                    1                 12
  BLACK OR AFRICAN AMERICAN                3                 36
  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"
D70V8, binary
                    cls
clus                   0   1
  17P LOSS MUTATED     1  51
  17P LOSS WILD-TYPE  11 411
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      1   51
  17P LOSS WILD-TYPE   11  411
                        clus
vv                       17P LOSS MUTATED 17P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 11
  NOT HISPANIC OR LATINO               51                411
[1] 2 2
[1] FALSE

Clustering(71) Variable = 17Q LOSS MUTATION ANALYSIS
D71V1, survival
                    sevent
clus2                  0   1
  17Q LOSS MUTATED     5  35
  17Q LOSS WILD-TYPE  93 427
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                40                520 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                35                427 
$`17Q LOSS MUTATED`
TCGA-02-0001 TCGA-02-0033 TCGA-02-0051 TCGA-02-0055 TCGA-02-0059 TCGA-02-0079 
        9.17         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        10.52        16.70 
TCGA-06-0149 TCGA-06-0152 TCGA-06-0159 TCGA-06-0177 TCGA-06-0184 TCGA-06-0187 
        7.86        11.80         9.44         2.01        40.37        26.33 
TCGA-06-0189 TCGA-06-0190 TCGA-06-0197 TCGA-06-0644 TCGA-06-5408 TCGA-08-0353 
       14.93        10.29         2.60        12.33        11.24         6.41 
TCGA-08-0386 TCGA-12-0772 TCGA-12-0826 TCGA-12-1098 TCGA-12-3653 TCGA-14-0871 
       15.72        53.10        27.78         3.98        11.74        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        11.54         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        55.86        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        10.36        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         0.23        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         0.16        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        16.21         2.70         0.26         4.04 
TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0132 
       47.31         0.10         3.58        22.72        32.52        18.74 
TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 
       14.07        23.08        22.16        10.75         0.20         9.21 
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         9.80        19.46 
TCGA-06-0151 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0160 
       46.59        12.79         8.65         3.19         5.46        11.80 
TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 
        2.56        56.88        10.65         5.29        19.04         3.12 
TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0178 
       13.02         0.23         2.20         2.73        91.00        53.98 
TCGA-06-0179 TCGA-06-0182 TCGA-06-0185 TCGA-06-0188 TCGA-06-0192 TCGA-06-0194 
       19.00         2.53        73.84        28.47        18.31         4.67 
TCGA-06-0195 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 
        7.04         0.39         6.48         5.49         3.91         4.96 
TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 
       11.84         0.20        12.43        22.49         0.36        18.02 
TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 
       10.36        11.80        20.42        14.96        10.32         5.52 
TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 
        0.26        70.52         4.70         8.05         0.16        35.01 
TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 
        3.22         4.47         9.67         2.04        23.57         9.40 
TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 
       22.32        19.56         5.39         2.70         2.17         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        22.98         5.85 
TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 
        5.42        20.94         7.43         6.35         3.58        26.79 
TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 TCGA-06-2557 
        8.65         7.89        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 
        0.76         4.93         9.27         2.83        30.64         5.95 
TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-5410 
        6.81         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         3.95         7.79 
TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 
        5.39         1.48         0.49         7.36         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-08-0244 TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 
        2.56        22.68        34.75         3.91       108.82         1.74 
TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 
        4.34        13.78        10.39         7.59         3.42        53.82 
TCGA-08-0352 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 
        1.28        15.06        22.52        14.70        35.64        19.53 
TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 
        0.95         9.17        10.85         3.19        10.59         0.30 
TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 
        0.56         3.52        11.77         8.52        18.44        58.19 
TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 
        1.28        10.75         4.80         6.54        15.98        17.33 
TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 
        5.52        14.01        14.43         1.64        10.39         5.95 
TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 
        7.17        65.92         0.10        38.17        25.97        24.13 
TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0773 
        6.12         2.63        18.12        28.41        12.43        43.10 
TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 
        5.49         9.11        14.86        14.27        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         6.25        30.54        21.63        11.97 
TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1099 TCGA-12-1598 
       11.38        15.85         9.11        14.53         3.42         9.44 
TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 
       25.28        13.61         6.41        59.41        43.23        25.78 
TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-5295 TCGA-12-5299 
       11.54        10.95        11.77        34.52        13.12         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-14-1034 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-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 
       23.11         7.10        30.18         0.92        40.96         6.15 
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-15-1449 TCGA-16-0846 TCGA-16-0848 
        9.86        50.53        19.10         5.52         3.91         9.93 
TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 
       26.07        16.31         4.31        29.03         0.82         9.90 
TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 
       13.35         3.65        18.28        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         0.43        14.27         3.39        10.75 
TCGA-19-1386 TCGA-19-1387 TCGA-19-1388 TCGA-19-1389 TCGA-19-1390 TCGA-19-1392 
        9.07         5.95        12.95         4.64        25.38         3.48 
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-19-2624 TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-5947 
        1.08         0.16         4.08        16.47         7.00         6.64 
TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 
       11.28         8.02        18.64         4.73         7.96         1.78 
TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A6J4 TCGA-19-A6J5 
        6.51         5.39         5.29         5.42         3.98        16.57 
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         1.22         1.58 
TCGA-26-6173 TCGA-26-6174 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 
        7.92         2.33         4.80        16.60         9.86        18.25 
TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 
       33.14        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         3.91         9.04        15.58 
TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 
       14.53        11.77        31.27        14.20         7.79        13.64 
TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 
        4.21        22.68        10.49         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-32-2494 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-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4210 
        7.36         8.84        22.78        21.17        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        10.62         0.85        13.35 
TCGA-41-2573 TCGA-41-2575 TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-41-6646 
        8.94         9.53         4.44        11.84         0.20         7.76 
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-76-6286 
       16.70         3.29         2.70        11.38        17.06        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 
        1.61        17.72        26.30         5.92 

  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 
            10.995              9.900 
[1] "1.0 - 92.7 (11.0)" "0.1 - 127.6 (9.9)"
[1] "hr=" "1"  
D71V2, continuous
D71V3, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    18  22
  17Q LOSS WILD-TYPE 202 318
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     18   22
  17Q LOSS WILD-TYPE  202  318
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE               18                202
  MALE                 22                318
[1] 2 2
[1] FALSE
D71V4, continuous
                    vv
clus                 GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  17Q LOSS MUTATED                               1                   1
  17Q LOSS WILD-TYPE                            16                  17
                    vv
clus                 UNTREATED PRIMARY (DE NOVO) GBM
  17Q LOSS MUTATED                                38
  17Q LOSS WILD-TYPE                             487
D71V5, multiclass
                                 clus
vv                                17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                  1                 16
  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"
D71V6, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    21  19
  17Q LOSS WILD-TYPE 361 159
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     21   19
  17Q LOSS WILD-TYPE  361  159
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  NO                21                361
  YES               19                159
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17Q LOSS MUTATED       0                         2    38
  17Q LOSS WILD-TYPE    13                        37   447
D71V7, multiclass
                           clus
vv                          17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  ASIAN                                    0                 13
  BLACK OR AFRICAN AMERICAN                2                 37
  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"
D71V8, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     1  33
  17Q LOSS WILD-TYPE  11 429
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      1   33
  17Q LOSS WILD-TYPE   11  429
                        clus
vv                       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 11
  NOT HISPANIC OR LATINO               33                429
[1] 2 2
[1] FALSE

Clustering(72) Variable = 18P LOSS MUTATION ANALYSIS
D72V1, survival
                    sevent
clus2                  0   1
  18P LOSS MUTATED    15  53
  18P LOSS WILD-TYPE  83 409
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                68                492 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                53                409 
$`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        32.52 
TCGA-06-0151 TCGA-06-0171 TCGA-06-0173 TCGA-06-0206 TCGA-06-0213 TCGA-06-0237 
       46.59        13.02         0.23         6.48         0.20        10.36 
TCGA-06-0648 TCGA-06-0649 TCGA-06-0876 TCGA-06-1086 TCGA-06-1800 TCGA-06-1806 
        9.67         2.04        46.19         6.35        26.79        15.32 
TCGA-06-5408 TCGA-06-5859 TCGA-06-6694 TCGA-06-6695 TCGA-08-0245 TCGA-08-0350 
       11.24         4.57         7.36         8.32        34.75         3.42 
TCGA-08-0510 TCGA-08-0525 TCGA-12-0776 TCGA-12-0826 TCGA-12-1088 TCGA-12-1096 
        3.52        15.98         9.11        27.78       127.59         9.11 
TCGA-14-0812 TCGA-14-0817 TCGA-14-1453 TCGA-14-4157 TCGA-16-0846 TCGA-16-0850 
        3.25         5.39         1.15         3.42         3.91        16.31 
TCGA-19-1390 TCGA-19-4065 TCGA-19-5960 TCGA-26-1438 TCGA-26-1439 TCGA-26-5133 
       25.38         7.04         5.42        10.03        13.87        14.86 
TCGA-27-1830 TCGA-27-1834 TCGA-27-1838 TCGA-28-1750 TCGA-28-2514 TCGA-28-5207 
        4.80        33.14        11.51         8.35         5.26         9.04 
TCGA-28-5213 TCGA-28-5216 TCGA-32-1976 TCGA-32-2491 TCGA-32-2634 TCGA-32-4210 
       31.27        13.64         0.49        12.23        22.78         3.72 
TCGA-41-3392 TCGA-74-6575 TCGA-76-4925 TCGA-76-4929 TCGA-76-6191 TCGA-76-6285 
        0.99        20.91         4.80         3.65        16.70         8.35 
TCGA-76-6286 TCGA-81-5911 
       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 
        9.17         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 
       55.86        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 
       10.36        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         0.23        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         0.16        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        16.21         2.70         0.26         4.04        47.31 
TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 
        0.10         3.58        22.72        10.52        18.74        14.07 
TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 
       23.08        22.16        10.75         0.20         9.21         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        16.70         9.80         7.86 
TCGA-06-0150 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 
       19.46        11.80        12.79         8.65         3.19         5.46 
TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 
        9.44        11.80         2.56        56.88        10.65         5.29 
TCGA-06-0168 TCGA-06-0169 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 
       19.04         3.12         2.20         2.73        91.00         2.01 
TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 
       53.98        19.00         2.53        40.37        73.84        26.33 
TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 
       28.47        14.93        10.29        18.31         4.67         7.04 
TCGA-06-0197 TCGA-06-0201 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 
        2.60         0.39         5.49         3.91         4.96        11.84 
TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0238 TCGA-06-0240 
       12.43        22.49         0.36        18.02        11.80        20.42 
TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 
       14.96        10.32         5.52         0.26        70.52         4.70 
TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 
        8.05         0.16        35.01        12.33         3.22         4.47 
TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 
       23.57         9.40        22.32        19.56         5.39         2.70 
TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0877 TCGA-06-0878 TCGA-06-0879 
        2.17         0.92        43.46         5.65         7.17        22.98 
TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1087 TCGA-06-1801 
        5.85         5.42        20.94         7.43         3.58         8.65 
TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 
        7.89        13.61        33.90         1.08         0.76         4.93 
TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 
        9.27         2.83        30.64         5.95         6.81         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         3.95         7.79         5.39         1.48         0.49 
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-08-0244 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 
        3.12         2.56        22.68         3.91       108.82         1.74 
TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0351 TCGA-08-0352 
        4.34        13.78        10.39         7.59        53.82         1.28 
TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 
        6.41        15.06        22.52        14.70        35.64        19.53 
TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 
        0.95         9.17        10.85        15.72         3.19        10.59 
TCGA-08-0392 TCGA-08-0509 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 
        0.30         0.56        11.77         8.52        18.44        58.19 
TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0529 TCGA-08-0531 
        1.28        10.75         4.80         6.54        17.33         5.52 
TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 
       14.01        14.43         1.64        10.39         5.95         7.17 
TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 
       65.92         0.10        38.17        25.97        24.13         6.12 
TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 
        2.63        18.12        28.41        12.43        53.10        43.10 
TCGA-12-0775 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 
        5.49        14.86        14.27        91.76        24.79        18.48 
TCGA-12-0821 TCGA-12-0822 TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 TCGA-12-1089 
       10.62        23.51        38.76         8.94        20.58         5.82 
TCGA-12-1090 TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 
        6.25        30.54        21.63        11.97        11.38        15.85 
TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 
       14.53         3.98         3.42         9.44        25.28        13.61 
TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 
        6.41        59.41        43.23        25.78        11.54        10.95 
TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 
       11.77        34.52        11.74        13.12         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-14-0862 TCGA-14-0865 TCGA-14-0866 
       11.24        13.78         1.35         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-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 TCGA-14-1794 
       30.18         0.92        40.96         6.15        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-15-0742 TCGA-15-1444 TCGA-15-1446 
       17.49         7.96         3.78         9.86        50.53        19.10 
TCGA-15-1447 TCGA-15-1449 TCGA-16-0848 TCGA-16-0849 TCGA-16-0861 TCGA-16-1045 
       53.19         5.52         9.93        26.07         4.31        29.03 
TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 
        0.82         9.90        13.35         3.65        18.28        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         0.43        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-19-1787 TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 
        3.48         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        16.47 
TCGA-19-2631 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 
        7.00         6.64        11.28         8.02        18.64         4.73 
TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-A6J4 
        7.96         1.78         6.51         5.39         5.29         3.98 
TCGA-19-A6J5 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 
       16.57         9.73        31.33         7.13         9.37         9.40 
TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 
        5.49         8.88         1.22         1.58         7.92         2.33 
TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 
       16.60         9.86        18.25        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-28-1751 
       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-28-5204 TCGA-28-5208 TCGA-28-5209 
        6.74         4.77         7.30         3.91        15.58        14.53 
TCGA-28-5211 TCGA-28-5214 TCGA-28-5215 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 
       11.77        14.20         7.79         4.21        22.68        10.49 
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-32-2494 
        1.18         4.67        12.69        14.86        16.93        20.78 
TCGA-32-2495 TCGA-32-2615 TCGA-32-2616 TCGA-32-2632 TCGA-32-2638 TCGA-32-4208 
       15.02        15.95         7.36         8.84        21.17        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        10.62         0.85        13.35 
TCGA-41-2573 TCGA-41-2575 TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 
        8.94         9.53         4.44        11.84         0.20        11.54 
TCGA-41-6646 TCGA-74-6573 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 
        7.76         3.45         4.34        14.33         8.22         7.50 
TCGA-76-4926 TCGA-76-4928 TCGA-76-4931 TCGA-76-4934 TCGA-76-4935 TCGA-76-6192 
        4.54         3.09         9.17         2.53        10.78         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-87-5896 TCGA-OX-A56R 
        9.27         7.73         7.79         1.61        26.30         5.92 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               0.2                0.1 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            127.59             108.82 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            11.375              9.900 
[1] "0.2 - 127.6 (11.4)" "0.1 - 108.8 (9.9)" 
[1] "hr=" "1.3"
D72V2, continuous
D72V3, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    24  44
  18P LOSS WILD-TYPE 196 296
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     24   44
  18P LOSS WILD-TYPE  196  296
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE               24                196
  MALE                 44                296
[1] 2 2
[1] FALSE
D72V4, continuous
                    vv
clus                 GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  18P LOSS MUTATED                               2                   3
  18P LOSS WILD-TYPE                            15                  15
                    vv
clus                 UNTREATED PRIMARY (DE NOVO) GBM
  18P LOSS MUTATED                                63
  18P LOSS WILD-TYPE                             462
D72V5, multiclass
                                 clus
vv                                18P LOSS MUTATED 18P LOSS WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                  2                 15
  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"
D72V6, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    47  21
  18P LOSS WILD-TYPE 335 157
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     47   21
  18P LOSS WILD-TYPE  335  157
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  NO                47                335
  YES               21                157
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18P LOSS MUTATED       3                         5    57
  18P LOSS WILD-TYPE    10                        34   428
D72V7, multiclass
                           clus
vv                          18P LOSS MUTATED 18P LOSS WILD-TYPE
  ASIAN                                    3                 10
  BLACK OR AFRICAN AMERICAN                5                 34
  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"
D72V8, binary
                    cls
clus                   0   1
  18P LOSS MUTATED     2  55
  18P LOSS WILD-TYPE  10 407
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      2   55
  18P LOSS WILD-TYPE   10  407
                        clus
vv                       18P LOSS MUTATED 18P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                 10
  NOT HISPANIC OR LATINO               55                407
[1] 2 2
[1] FALSE

Clustering(73) Variable = 18Q LOSS MUTATION ANALYSIS
D73V1, survival
                    sevent
clus2                  0   1
  18Q LOSS MUTATED    12  48
  18Q LOSS WILD-TYPE  86 414
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                60                500 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                48                414 
$`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        32.52        46.59         0.23         6.48 
TCGA-06-0213 TCGA-06-0237 TCGA-06-0648 TCGA-06-0649 TCGA-06-0749 TCGA-06-1086 
        0.20        10.36         9.67         2.04         2.17         6.35 
TCGA-06-1800 TCGA-06-1806 TCGA-06-2559 TCGA-06-5859 TCGA-06-6694 TCGA-08-0245 
       26.79        15.32         4.93         4.57         7.36        34.75 
TCGA-08-0359 TCGA-08-0510 TCGA-08-0525 TCGA-12-0776 TCGA-12-0826 TCGA-12-1088 
        0.95         3.52        15.98         9.11        27.78       127.59 
TCGA-12-1096 TCGA-14-0812 TCGA-14-0817 TCGA-16-0846 TCGA-19-0962 TCGA-19-1390 
        9.11         3.25         5.39         3.91         0.43        25.38 
TCGA-19-2619 TCGA-19-4065 TCGA-19-5960 TCGA-26-1438 TCGA-26-1439 TCGA-26-5133 
        9.67         7.04         5.42        10.03        13.87        14.86 
TCGA-27-1834 TCGA-27-1838 TCGA-28-1750 TCGA-28-2514 TCGA-28-5207 TCGA-28-5213 
       33.14        11.51         8.35         5.26         9.04        31.27 
TCGA-28-5216 TCGA-32-1973 TCGA-32-1976 TCGA-32-1987 TCGA-32-2491 TCGA-32-2634 
       13.64        21.07         0.49        14.86        12.23        22.78 
TCGA-32-4210 TCGA-41-3392 TCGA-76-4925 TCGA-76-6285 TCGA-76-6286 TCGA-81-5911 
        3.72         0.99         4.80         8.35        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 
        9.17         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        55.86        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        10.36        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         0.23        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         0.16        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        16.21         2.70 
TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 
        0.26         4.04        47.31         0.10         3.58        22.72 
TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 
       10.52        18.74        14.07        23.08        22.16        10.75 
TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 
        0.20         9.21         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 
       16.70         9.80         7.86        19.46        11.80        12.79 
TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 
        8.65         3.19         5.46         9.44        11.80         2.56 
TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 
       56.88        10.65         5.29        19.04         3.12        13.02 
TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 
        2.20         2.73        91.00         2.01        53.98        19.00 
TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 
        2.53        40.37        73.84        26.33        28.47        14.93 
TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 
       10.29        18.31         4.67         7.04         2.60         0.39 
TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0214 TCGA-06-0216 
        5.49         3.91         4.96        11.84        12.43        22.49 
TCGA-06-0219 TCGA-06-0221 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 
        0.36        18.02        11.80        20.42        14.96        10.32 
TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 
        5.52         0.26        70.52         4.70         8.05         0.16 
TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0650 TCGA-06-0686 
       35.01        12.33         3.22         4.47        23.57         9.40 
TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0750 TCGA-06-0875 
       22.32        19.56         5.39         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        22.98         5.85         5.42 
TCGA-06-0939 TCGA-06-1084 TCGA-06-1087 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 
       20.94         7.43         3.58         8.65         7.89        13.61 
TCGA-06-1805 TCGA-06-2557 TCGA-06-2558 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 
       33.90         1.08         0.76         9.27         2.83        30.64 
TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 
        5.95         6.81         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 
       11.24         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         3.95 
TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6695 TCGA-06-6697 
        7.79         5.39         1.48         0.49         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-08-0244 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 
        2.56        22.68         3.91       108.82         1.74         4.34 
TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 
       13.78        10.39         7.59         3.42        53.82         1.28 
TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 
        6.41        15.06        22.52        14.70        35.64        19.53 
TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 
        9.17        10.85        15.72         3.19        10.59         0.30 
TCGA-08-0509 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 
        0.56        11.77         8.52        18.44        58.19         1.28 
TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 
       10.75         4.80         6.54        17.33         5.52        14.01 
TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 
       14.43         1.64        10.39         5.95         7.17        65.92 
TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 
        0.10        38.17        25.97        24.13         6.12         2.63 
TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 
       18.12        28.41        12.43        53.10        43.10         5.49 
TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 
       14.86        14.27        91.76        24.79        18.48        10.62 
TCGA-12-0822 TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 TCGA-12-1089 TCGA-12-1090 
       23.51        38.76         8.94        20.58         5.82         6.25 
TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1097 
       30.54        21.63        11.97        11.38        15.85        14.53 
TCGA-12-1098 TCGA-12-1099 TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 
        3.98         3.42         9.44        25.28        13.61         6.41 
TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 
       59.41        43.23        25.78        11.54        10.95        11.77 
TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 
       34.52        11.74        13.12         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-14-0862 TCGA-14-0865 TCGA-14-0866 TCGA-14-0867 
       13.78         1.35         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         6.15        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         9.86        50.53 
TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 
       19.10        53.19         5.52         9.93        26.07        16.31 
TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 
        4.31        29.03         0.82         9.90        13.35         3.65 
TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 
       18.28        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-19-1392 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 
        4.64         3.48         7.17        12.66         3.25         0.13 
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        16.47 
TCGA-19-2631 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 
        7.00         6.64        11.28         8.02        18.64         4.73 
TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-A6J4 
        7.96         1.78         6.51         5.39         5.29         3.98 
TCGA-19-A6J5 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 
       16.57         9.73        31.33         7.13         9.37         9.40 
TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 
        5.49         8.88         1.22         1.58         7.92         2.33 
TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1835 TCGA-27-1836 
        4.80        16.60         9.86        18.25        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-28-1751 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         3.91        15.58 
TCGA-28-5209 TCGA-28-5211 TCGA-28-5214 TCGA-28-5215 TCGA-28-5218 TCGA-28-5219 
       14.53        11.77        14.20         7.79         4.21        22.68 
TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 
       10.49         5.42        15.39         0.10        15.85        19.50 
TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1991 TCGA-32-2494 TCGA-32-2495 
        1.18         4.67        12.69        16.93        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        21.17        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        10.62         0.85        13.35         8.94 
TCGA-41-2575 TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 
        9.53         4.44        11.84         0.20        11.54         7.76 
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-76-4934 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-76-6656 
       16.70         3.29         2.70        11.38        17.06         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-87-5896 TCGA-OX-A56R 
       26.30         5.92 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               0.2                0.1 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            127.59             108.82 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              9.85              10.24 
[1] "0.2 - 127.6 (9.8)"  "0.1 - 108.8 (10.2)"
[1] "hr=" "1.2"
D73V2, continuous
D73V3, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED    22  38
  18Q LOSS WILD-TYPE 198 302
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     22   38
  18Q LOSS WILD-TYPE  198  302
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE               22                198
  MALE                 38                302
[1] 2 2
[1] FALSE
D73V4, continuous
                    vv
clus                 GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  18Q LOSS MUTATED                               2                   1
  18Q LOSS WILD-TYPE                            15                  17
                    vv
clus                 UNTREATED PRIMARY (DE NOVO) GBM
  18Q LOSS MUTATED                                57
  18Q LOSS WILD-TYPE                             468
D73V5, multiclass
                                 clus
vv                                18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                  2                 15
  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"
D73V6, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED    37  23
  18Q LOSS WILD-TYPE 345 155
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     37   23
  18Q LOSS WILD-TYPE  345  155
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  NO                37                345
  YES               23                155
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18Q LOSS MUTATED       3                         5    50
  18Q LOSS WILD-TYPE    10                        34   435
D73V7, multiclass
                           clus
vv                          18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  ASIAN                                    3                 10
  BLACK OR AFRICAN AMERICAN                5                 34
  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"
D73V8, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED     3  50
  18Q LOSS WILD-TYPE   9 412
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      3   50
  18Q LOSS WILD-TYPE    9  412
                        clus
vv                       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  9
  NOT HISPANIC OR LATINO               50                412
[1] 2 2
[1] FALSE

Clustering(74) Variable = 19P LOSS MUTATION ANALYSIS
D74V1, survival
                    sevent
clus2                  0   1
  19P LOSS MUTATED     6  19
  19P LOSS WILD-TYPE  92 443
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                25                535 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                19                443 
$`19P LOSS MUTATED`
TCGA-02-0026 TCGA-02-0055 TCGA-02-0456 TCGA-06-0875 TCGA-06-2569 TCGA-06-5411 
       24.59         2.50         3.35        43.46         0.43         8.35 
TCGA-06-6389 TCGA-08-0344 TCGA-08-0349 TCGA-08-0358 TCGA-12-0619 TCGA-12-1095 
        7.79       108.82         7.59        19.53        10.39        15.85 
TCGA-14-0740 TCGA-14-0865 TCGA-14-1458 TCGA-14-3477 TCGA-15-1444 TCGA-16-0850 
       11.97        16.50         6.15         3.78        50.53        16.31 
TCGA-26-5136 TCGA-27-1834 TCGA-27-2519 TCGA-32-1976 TCGA-32-4210 TCGA-76-4929 
        1.22        33.14        10.39         0.49         3.72         3.65 
TCGA-76-4931 
        9.17 

$`19P LOSS WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 
        9.17         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        55.86        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        10.36        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 
        0.23        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         0.16        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-02-2486 TCGA-06-0119 TCGA-06-0122 
       12.92        15.32        15.45        16.21         2.70         0.26 
TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 
        4.04        47.31         0.10         3.58        22.72        32.52 
TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 
       10.52        18.74        14.07        23.08        22.16        10.75 
TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 
        0.20         9.21         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 
       16.70         9.80         7.86        19.46        46.59        11.80 
TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 
       12.79         8.65         3.19         5.46         9.44        11.80 
TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 
        2.56        56.88        10.65         5.29        19.04         3.12 
TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 
       13.02         0.23         2.20         2.73        91.00         2.01 
TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 
       53.98        19.00         2.53        40.37        73.84        26.33 
TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 
       28.47        14.93        10.29        18.31         4.67         7.04 
TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 
        2.60         0.39         6.48         5.49         3.91         4.96 
TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 
       11.84         0.20        12.43        22.49         0.36        18.02 
TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 
       10.36        11.80        20.42        14.96        10.32         5.52 
TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 
        0.26        70.52         4.70         8.05         0.16        35.01 
TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 
       12.33         3.22         4.47         9.67         2.04        23.57 
TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 
        9.40        22.32        19.56         5.39         2.70         2.17 
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        22.98         5.85 
TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 
        5.42        20.94         7.43         6.35         3.58        26.79 
TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 TCGA-06-2557 
        8.65         7.89        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 
        0.76         4.93         9.27         2.83        30.64         5.95 
TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 
        6.81         5.98         4.37        31.50        11.24         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-06-6390 TCGA-06-6391 
        3.75         6.15         4.57         3.95         5.39         1.48 
TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 
        0.49         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-08-0244 
        4.77         4.96         1.87         3.12         2.56        22.68 
TCGA-08-0245 TCGA-08-0246 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 
       34.75         3.91         1.74         4.34        13.78        10.39 
TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 
        3.42        53.82         1.28         6.41        15.06        22.52 
TCGA-08-0356 TCGA-08-0357 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 
       14.70        35.64         0.95         9.17        10.85        15.72 
TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 
        3.19        10.59         0.30         0.56         3.52        11.77 
TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 
        8.52        18.44        58.19         1.28        10.75         4.80 
TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 
        6.54        15.98        17.33         5.52        14.01        14.43 
TCGA-12-0618 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 
        1.64         5.95         7.17        65.92         0.10        38.17 
TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 
       25.97        24.13         6.12         2.63        18.12        28.41 
TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 
       12.43        53.10        43.10         5.49         9.11        14.86 
TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 
       14.27        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-12-1096 
        6.25        30.54        21.63        11.97        11.38         9.11 
TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 TCGA-12-1598 TCGA-12-1599 TCGA-12-1600 
       14.53         3.98         3.42         9.44        25.28        13.61 
TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 
        6.41        59.41        43.23        25.78        11.54        10.95 
TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 
       11.77        34.52        11.74        13.12         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-14-0812 TCGA-14-0813 TCGA-14-0817 TCGA-14-0862 TCGA-14-0866 
       13.78         3.25         1.35         5.39         2.89        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-14-1459 TCGA-14-1794 
        1.15        30.18         0.92        40.96        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-15-1446 TCGA-15-1447 
       17.49         7.96         3.42         9.86        19.10        53.19 
TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 TCGA-16-0861 TCGA-16-1045 
        5.52         3.91         9.93        26.07         4.31        29.03 
TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 
        0.82         9.90        13.35         3.65        18.28        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         0.43        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         3.48         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 
       16.47         7.00         7.04         6.64        11.28         8.02 
TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 
       18.64         4.73         7.96         1.78         6.51         5.39 
TCGA-19-5959 TCGA-19-5960 TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 
        5.29         5.42         3.98        16.57        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-27-1830 
        5.49         8.88         1.58         7.92         2.33         4.80 
TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 
       16.60         9.86        18.25        21.30        30.05        14.04 
TCGA-27-1838 TCGA-27-2518 TCGA-27-2521 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         3.91 
TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 
        9.04        15.58        14.53        11.77        31.27        14.20 
TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 
        7.79        13.64         4.21        22.68        10.49         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-32-1987 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        21.17 
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        10.62         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-74-6573 TCGA-74-6575 TCGA-74-6577 
        0.20        11.54         7.76         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-76-4934 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 
        5.92 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              0.43               0.10 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
            108.82             127.59 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              9.17              10.19 
[1] "0.4 - 108.8 (9.2)"  "0.1 - 127.6 (10.2)"
[1] "hr=" "1.2"
D74V2, continuous
D74V3, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    11  14
  19P LOSS WILD-TYPE 209 326
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     11   14
  19P LOSS WILD-TYPE  209  326
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE               11                209
  MALE                 14                326
[1] 2 2
[1] FALSE
D74V4, continuous
                    vv
clus                 GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  19P LOSS MUTATED                               1                   0
  19P LOSS WILD-TYPE                            16                  18
                    vv
clus                 UNTREATED PRIMARY (DE NOVO) GBM
  19P LOSS MUTATED                                24
  19P LOSS WILD-TYPE                             501
D74V5, multiclass
                                 clus
vv                                19P LOSS MUTATED 19P LOSS WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                  1                 16
  TREATED PRIMARY GBM                            0                 18
  UNTREATED PRIMARY (DE NOVO) GBM               24                501
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V6, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    17   8
  19P LOSS WILD-TYPE 365 170
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     17    8
  19P LOSS WILD-TYPE  365  170
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  NO                17                365
  YES                8                170
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19P LOSS MUTATED       0                         2    22
  19P LOSS WILD-TYPE    13                        37   463
D74V7, multiclass
                           clus
vv                          19P LOSS MUTATED 19P LOSS WILD-TYPE
  ASIAN                                    0                 13
  BLACK OR AFRICAN AMERICAN                2                 37
  WHITE                                   22                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"
D74V8, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     0  21
  19P LOSS WILD-TYPE  12 441
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      0   21
  19P LOSS WILD-TYPE   12  441
                        clus
vv                       19P LOSS MUTATED 19P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 12
  NOT HISPANIC OR LATINO               21                441
[1] 2 2
[1] FALSE

Clustering(75) Variable = 19Q LOSS MUTATION ANALYSIS
D75V1, survival
                    sevent
clus2                  0   1
  19Q LOSS MUTATED     4  29
  19Q LOSS WILD-TYPE  94 433
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                33                527 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                29                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         9.27         0.43         8.35 
TCGA-06-A6S1 TCGA-08-0344 TCGA-08-0349 TCGA-08-0358 TCGA-12-0619 TCGA-12-1095 
        2.56       108.82         7.59        19.53        10.39        15.85 
TCGA-12-1598 TCGA-14-0740 TCGA-14-0862 TCGA-14-0865 TCGA-14-1458 TCGA-15-1444 
        9.44        11.97         2.89        16.50         6.15        50.53 
TCGA-16-0850 TCGA-26-5136 TCGA-27-1834 TCGA-27-2519 TCGA-32-1976 TCGA-32-2491 
       16.31         1.22        33.14        10.39         0.49        12.23 
TCGA-32-4210 TCGA-76-4929 TCGA-76-4931 
        3.72         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 
        9.17         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        55.86        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        10.36         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         0.23        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         0.16        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        16.21         2.70 
TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 
        0.26         4.04        47.31         0.10         3.58        22.72 
TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 
       32.52        10.52        18.74        14.07        23.08        22.16 
TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 
       10.75         0.20         9.21         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        16.70         9.80         7.86        19.46        46.59 
TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 
       11.80        12.79         8.65         3.19         5.46         9.44 
TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 
       11.80         2.56        56.88        10.65         5.29        19.04 
TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 
        3.12        13.02         0.23         2.20         2.73        91.00 
TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 
        2.01        53.98        19.00         2.53        40.37        73.84 
TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 
       26.33        28.47        14.93        10.29        18.31         4.67 
TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 
        7.04         2.60         0.39         6.48         5.49         3.91 
TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 
        4.96        11.84         0.20        12.43        22.49         0.36 
TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 
       18.02        10.36        11.80        20.42        14.96        10.32 
TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 
        5.52         0.26        70.52         4.70         8.05         0.16 
TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 
       35.01        12.33         3.22         4.47         9.67         2.04 
TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 
       23.57         9.40        22.32        19.56         5.39         2.70 
TCGA-06-0749 TCGA-06-0750 TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 TCGA-06-0879 
        2.17         0.92        46.19         5.65         7.17        22.98 
TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 
        5.85         5.42        20.94         7.43         6.35         3.58 
TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 
       26.79         8.65         7.89        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         0.76         4.93         2.83        30.64         5.95 
TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 
        6.81         5.98         4.37        31.50        11.24         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         3.95         7.79         5.39 
TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 
        1.48         0.49         7.36         8.32        12.85         4.77 
TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-06-A5U1 TCGA-06-A6S0 TCGA-08-0244 
        1.55         4.77         4.96         1.87         3.12        22.68 
TCGA-08-0245 TCGA-08-0246 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 
       34.75         3.91         1.74         4.34        13.78        10.39 
TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 
        3.42        53.82         1.28         6.41        15.06        22.52 
TCGA-08-0356 TCGA-08-0357 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 
       14.70        35.64         0.95         9.17        10.85        15.72 
TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 
        3.19        10.59         0.30         0.56         3.52        11.77 
TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 
        8.52        18.44        58.19         1.28        10.75         4.80 
TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 
        6.54        15.98        17.33         5.52        14.01        14.43 
TCGA-12-0618 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 
        1.64         5.95         7.17        65.92         0.10        38.17 
TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 
       25.97        24.13         6.12         2.63        18.12        28.41 
TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 
       12.43        53.10        43.10         5.49         9.11        14.86 
TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 
       14.27        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-12-1096 
        6.25        30.54        21.63        11.97        11.38         9.11 
TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 
       14.53         3.98         3.42        25.28        13.61         6.41 
TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 
       59.41        43.23        25.78        11.54        10.95        11.77 
TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 
       34.52        11.74        13.12         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-14-0817 TCGA-14-0866 TCGA-14-0867 TCGA-14-0871 
        3.25         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-14-1402 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-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 
        0.92        40.96        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-15-1446 TCGA-15-1447 TCGA-15-1449 
        3.78         3.42         9.86        19.10        53.19         5.52 
TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 
        3.91         9.93        26.07         4.31        29.03         0.82 
TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 
        9.90        13.35         3.65        18.28        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         0.43        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 
        3.48         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        16.47 
TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 
        7.00         7.04         6.64        11.28         8.02        18.64 
TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 
        4.73         7.96         1.78         6.51         5.39         5.29 
TCGA-19-5960 TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 
        5.42         3.98        16.57        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-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-27-1830 TCGA-27-1831 
        8.88         1.58         7.92         2.33         4.80        16.60 
TCGA-27-1832 TCGA-27-1833 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 
        9.86        18.25        21.30        30.05        14.04        11.51 
TCGA-27-2518 TCGA-27-2521 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         3.91         9.04 
TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 
       15.58        14.53        11.77        31.27        14.20         7.79 
TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 
       13.64         4.21        22.68        10.49         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-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4211 
        7.36         8.84        22.78        21.17        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        10.62         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        11.54 
TCGA-41-6646 TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 
        7.76         3.45        20.91         4.34        14.33         8.22 
TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4934 TCGA-76-4935 
        7.50         4.80         4.54         3.09         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 
        7.79         1.61        17.72        26.30         5.92 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              0.43               0.10 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
            108.82             127.59 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             10.39              10.03 
[1] "0.4 - 108.8 (10.4)" "0.1 - 127.6 (10.0)"
[1] "hr=" "1.1"
D75V2, continuous
D75V3, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    14  19
  19Q LOSS WILD-TYPE 206 321
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     14   19
  19Q LOSS WILD-TYPE  206  321
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE               14                206
  MALE                 19                321
[1] 2 2
[1] FALSE
D75V4, continuous
                    vv
clus                 GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  19Q LOSS MUTATED                               2                   2
  19Q LOSS WILD-TYPE                            15                  16
                    vv
clus                 UNTREATED PRIMARY (DE NOVO) GBM
  19Q LOSS MUTATED                                29
  19Q LOSS WILD-TYPE                             496
D75V5, multiclass
                                 clus
vv                                19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                  2                 15
  TREATED PRIMARY GBM                            2                 16
  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"
D75V6, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    22  11
  19Q LOSS WILD-TYPE 360 167
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     22   11
  19Q LOSS WILD-TYPE  360  167
     clus
vv    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  NO                22                360
  YES               11                167
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19Q LOSS MUTATED       1                         2    29
  19Q LOSS WILD-TYPE    12                        37   456
D75V7, multiclass
                           clus
vv                          19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  ASIAN                                    1                 12
  BLACK OR AFRICAN AMERICAN                2                 37
  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"
D75V8, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED     0  28
  19Q LOSS WILD-TYPE  12 434
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      0   28
  19Q LOSS WILD-TYPE   12  434
                        clus
vv                       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 12
  NOT HISPANIC OR LATINO               28                434
[1] 2 2
[1] FALSE

Clustering(76) Variable = 20P LOSS MUTATION ANALYSIS
D76V1, survival
                    sevent
clus2                  0   1
  20P LOSS MUTATED     3  15
  20P LOSS WILD-TYPE  95 447
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                18                542 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                15                447 
$`20P LOSS MUTATED`
TCGA-02-0001 TCGA-02-0011 TCGA-02-0051 TCGA-02-0060 TCGA-02-0281 TCGA-06-0188 
        9.17        20.71        15.09         6.02         3.98        28.47 
TCGA-06-0414 TCGA-06-0686 TCGA-08-0245 TCGA-12-1099 TCGA-14-0867 TCGA-14-3477 
       35.01         9.40        34.75         3.42         2.04         3.78 
TCGA-19-1390 TCGA-19-2629 TCGA-27-2521 TCGA-28-1750 TCGA-76-4934 TCGA-76-6286 
       25.38        16.47        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        55.86        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        10.36        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         0.23        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         0.16        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        16.21         2.70         0.26         4.04        47.31 
TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 
        0.10         3.58        22.72        32.52        10.52        18.74 
TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 
       14.07        23.08        22.16        10.75         0.20         9.21 
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        16.70         9.80 
TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 
        7.86        19.46        46.59        11.80        12.79         8.65 
TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 
        3.19         5.46         9.44        11.80         2.56        56.88 
TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 
       10.65         5.29        19.04         3.12        13.02         0.23 
TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 
        2.20         2.73        91.00         2.01        53.98        19.00 
TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0189 TCGA-06-0190 
        2.53        40.37        73.84        26.33        14.93        10.29 
TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 
       18.31         4.67         7.04         2.60         0.39         6.48 
TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 
        5.49         3.91         4.96        11.84         0.20        12.43 
TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 
       22.49         0.36        18.02        10.36        11.80        20.42 
TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 
       14.96        10.32         5.52         0.26        70.52         4.70 
TCGA-06-0412 TCGA-06-0413 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 
        8.05         0.16        12.33         3.22         4.47         9.67 
TCGA-06-0649 TCGA-06-0650 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 
        2.04        23.57        22.32        19.56         5.39         2.70 
TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 
        2.17         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 
       22.98         5.85         5.42        20.94         7.43         6.35 
TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 
        3.58        26.79         8.65         7.89        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         0.76         4.93         9.27         2.83 
TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 
       30.64         5.95         6.81         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        11.24         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         3.95         7.79         5.39         1.48         0.49 
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-A5U1 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-08-0244 TCGA-08-0246 
        4.96         1.87         3.12         2.56        22.68         3.91 
TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 
      108.82         1.74         4.34        13.78        10.39         7.59 
TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 
        3.42        53.82         1.28         6.41        15.06        22.52 
TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 
       14.70        35.64        19.53         0.95         9.17        10.85 
TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 
       15.72         3.19        10.59         0.30         0.56         3.52 
TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 
       11.77         8.52        18.44        58.19         1.28        10.75 
TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 
        4.80         6.54        15.98        17.33         5.52        14.01 
TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 
       14.43         1.64        10.39         5.95         7.17        65.92 
TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 
        0.10        38.17        25.97        24.13         6.12         2.63 
TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 
       18.12        28.41        12.43        53.10        43.10         5.49 
TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 
        9.11        14.86        14.27        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         6.25        30.54        21.63        11.97 
TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1598 
       11.38        15.85         9.11        14.53         3.98         9.44 
TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 
       25.28        13.61         6.41        59.41        43.23        25.78 
TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 
       11.54        10.95        11.77        34.52        11.74        13.12 
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-14-1454 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         6.15        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-14-4157 TCGA-15-0742 TCGA-15-1444 TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 
        3.42         9.86        50.53        19.10        53.19         5.52 
TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 
        3.91         9.93        26.07        16.31         4.31        29.03 
TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 
        0.82         9.90        13.35         3.65        18.28        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         0.43        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-19-1787 TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 
        3.48         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        11.28         8.02        18.64         4.73 
TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 
        7.96         1.78         6.51         5.39         5.29         5.42 
TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 
        3.98        16.57        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-27-1830 TCGA-27-1831 
        1.22         1.58         7.92         2.33         4.80        16.60 
TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 
        9.86        18.25        33.14        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-28-1751 
       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-28-2514 TCGA-28-5204 TCGA-28-5207 
        6.74         4.77         7.30         5.26         3.91         9.04 
TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 
       15.58        14.53        11.77        31.27        14.20         7.79 
TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 
       13.64         4.21        22.68        10.49         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        21.17 
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        10.62 
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-74-6573 TCGA-74-6575 
       11.84         0.20        11.54         7.76         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-76-6656 TCGA-76-6657 
        2.70        11.38        17.06         8.35         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 
       26.30         5.92 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
              2.04               0.10 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             35.01             127.59 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             9.895             10.110 
[1] "2.0 - 35.0 (9.9)"   "0.1 - 127.6 (10.1)"
[1] "hr=" "1.1"
D76V2, continuous
D76V3, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    10   8
  20P LOSS WILD-TYPE 210 332
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     10    8
  20P LOSS WILD-TYPE  210  332
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  FEMALE               10                210
  MALE                  8                332
[1] 2 2
[1] FALSE
D76V4, continuous
                    vv
clus                 GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  20P LOSS MUTATED                               0                   0
  20P LOSS WILD-TYPE                            17                  18
                    vv
clus                 UNTREATED PRIMARY (DE NOVO) GBM
  20P LOSS MUTATED                                18
  20P LOSS WILD-TYPE                             507
D76V5, multiclass
                                 clus
vv                                20P LOSS MUTATED 20P LOSS WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                  0                 17
  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"
D76V6, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    12   6
  20P LOSS WILD-TYPE 370 172
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     12    6
  20P LOSS WILD-TYPE  370  172
     clus
vv    20P LOSS MUTATED 20P LOSS WILD-TYPE
  NO                12                370
  YES                6                172
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20P LOSS MUTATED       1                         2    15
  20P LOSS WILD-TYPE    12                        37   470
D76V7, multiclass
                           clus
vv                          20P LOSS MUTATED 20P LOSS WILD-TYPE
  ASIAN                                    1                 12
  BLACK OR AFRICAN AMERICAN                2                 37
  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"
D76V8, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     1  15
  20P LOSS WILD-TYPE  11 447
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      1   15
  20P LOSS WILD-TYPE   11  447
                        clus
vv                       20P LOSS MUTATED 20P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 11
  NOT HISPANIC OR LATINO               15                447
[1] 2 2
[1] FALSE

Clustering(77) Variable = 20Q LOSS MUTATION ANALYSIS
D77V1, survival
                    sevent
clus2                  0   1
  20Q LOSS MUTATED     2  14
  20Q LOSS WILD-TYPE  96 448
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                16                544 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                14                448 
$`20Q LOSS MUTATED`
TCGA-02-0001 TCGA-02-0051 TCGA-02-0281 TCGA-06-0188 TCGA-06-0414 TCGA-06-0686 
        9.17        15.09         3.98        28.47        35.01         9.40 
TCGA-08-0245 TCGA-12-1099 TCGA-14-0867 TCGA-14-3477 TCGA-19-1390 TCGA-19-2629 
       34.75         3.42         2.04         3.78        25.38        16.47 
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        55.86        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        10.36        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 
        0.23        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         0.16        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        16.21         2.70         0.26 
TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 
        4.04        47.31         0.10         3.58        22.72        32.52 
TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 
       10.52        18.74        14.07        23.08        22.16        10.75 
TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 
        0.20         9.21         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 
       16.70         9.80         7.86        19.46        46.59        11.80 
TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 
       12.79         8.65         3.19         5.46         9.44        11.80 
TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 
        2.56        56.88        10.65         5.29        19.04         3.12 
TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 TCGA-06-0177 
       13.02         0.23         2.20         2.73        91.00         2.01 
TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 
       53.98        19.00         2.53        40.37        73.84        26.33 
TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 
       14.93        10.29        18.31         4.67         7.04         2.60 
TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 
        0.39         6.48         5.49         3.91         4.96        11.84 
TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 
        0.20        12.43        22.49         0.36        18.02        10.36 
TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 
       11.80        20.42        14.96        10.32         5.52         0.26 
TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0644 TCGA-06-0645 
       70.52         4.70         8.05         0.16        12.33         3.22 
TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0743 TCGA-06-0744 
        4.47         9.67         2.04        23.57        22.32        19.56 
TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 
        5.39         2.70         2.17         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        22.98         5.85         5.42        20.94 
TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 
        7.43         6.35         3.58        26.79         8.65         7.89 
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         0.76         4.93 
TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 
        9.27         2.83        30.64         5.95         6.81         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        11.24         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         3.95         7.79         5.39 
TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 
        1.48         0.49         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-08-0244 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 
       22.68         3.91       108.82         1.74         4.34        13.78 
TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 
       10.39         7.59         3.42        53.82         1.28         6.41 
TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 
       15.06        22.52        14.70        35.64        19.53         0.95 
TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 
        9.17        10.85        15.72         3.19        10.59         0.30 
TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 
        0.56         3.52        11.77         8.52        18.44        58.19 
TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 
        1.28        10.75         4.80         6.54        15.98        17.33 
TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 
        5.52        14.01        14.43         1.64        10.39         5.95 
TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 
        7.17        65.92         0.10        38.17        25.97        24.13 
TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 
        6.12         2.63        18.12        28.41        12.43        53.10 
TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 
       43.10         5.49         9.11        14.86        14.27        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         6.25        30.54 
TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 
       21.63        11.97        11.38        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         9.44        25.28        13.61         6.41        59.41 
TCGA-12-3646 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 
       43.23        25.78        11.54        10.95        11.77        34.52 
TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0740 
       11.74        13.12         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         6.15        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         9.86        50.53        19.10 
TCGA-15-1447 TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 
       53.19         5.52         3.91         9.93        26.07        16.31 
TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 
        4.31        29.03         0.82         9.90        13.35         3.65 
TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 
       18.28        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 
        0.43        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         3.48         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-19-2631 TCGA-19-4065 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 
        4.08         7.00         7.04         6.64        11.28         8.02 
TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 
       18.64         4.73         7.96         1.78         6.51         5.39 
TCGA-19-5959 TCGA-19-5960 TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 
        5.29         5.42         3.98        16.57        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         1.22         1.58         7.92         2.33 
TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 
        4.80        16.60         9.86        18.25        33.14        21.30 
TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 
       30.05        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-28-1751 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-28-2502 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         3.91         9.04        15.58        14.53        11.77 
TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 
       31.27        14.20         7.79        13.64         4.21        22.68 
TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 TCGA-32-1977 
       10.49         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-32-2495 TCGA-32-2615 TCGA-32-2616 TCGA-32-2632 
       16.93        12.23        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        21.17        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        10.62         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        11.54         7.76 
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-76-6656 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 
        1.61        17.72        26.30         5.92 

  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
              2.04               0.10 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             35.01             127.59 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
            12.245             10.110 
[1] "2.0 - 35.0 (12.2)"  "0.1 - 127.6 (10.1)"
[1] "hr=" "1.1"
D77V2, continuous
D77V3, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     9   7
  20Q LOSS WILD-TYPE 211 333
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      9    7
  20Q LOSS WILD-TYPE  211  333
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  FEMALE                9                211
  MALE                  7                333
[1] 2 2
[1] FALSE
D77V4, continuous
                    vv
clus                 GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  20Q LOSS MUTATED                               0                   0
  20Q LOSS WILD-TYPE                            17                  18
                    vv
clus                 UNTREATED PRIMARY (DE NOVO) GBM
  20Q LOSS MUTATED                                16
  20Q LOSS WILD-TYPE                             509
D77V5, multiclass
                                 clus
vv                                20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                  0                 17
  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"
D77V6, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED    10   6
  20Q LOSS WILD-TYPE 372 172
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED     10    6
  20Q LOSS WILD-TYPE  372  172
     clus
vv    20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  NO                10                372
  YES                6                172
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20Q LOSS MUTATED       0                         2    14
  20Q LOSS WILD-TYPE    13                        37   471
D77V7, multiclass
                           clus
vv                          20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  ASIAN                                    0                 13
  BLACK OR AFRICAN AMERICAN                2                 37
  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"
D77V8, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     0  14
  20Q LOSS WILD-TYPE  12 448
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      0   14
  20Q LOSS WILD-TYPE   12  448
                        clus
vv                       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 12
  NOT HISPANIC OR LATINO               14                448
[1] 2 2
[1] FALSE

Clustering(78) Variable = 21Q LOSS MUTATION ANALYSIS
D78V1, survival
                    sevent
clus2                  0   1
  21Q LOSS MUTATED     6  34
  21Q LOSS WILD-TYPE  92 428
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                40                520 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                34                428 
$`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-06-0209 TCGA-06-0221 TCGA-06-0402 TCGA-06-0414 
        3.98        12.39         3.91        18.02         0.26        35.01 
TCGA-06-0648 TCGA-06-0875 TCGA-06-6389 TCGA-06-6693 TCGA-06-6694 TCGA-08-0516 
        9.67        43.46         7.79         0.49         7.36        18.44 
TCGA-12-0826 TCGA-12-0827 TCGA-12-1099 TCGA-12-1600 TCGA-12-3653 TCGA-12-5295 
       27.78        38.76         3.42        13.61        11.74        13.12 
TCGA-14-0740 TCGA-14-0817 TCGA-14-1823 TCGA-14-3477 TCGA-15-0742 TCGA-16-0848 
       11.97         5.39        17.85         3.78         9.86         9.93 
TCGA-16-0850 TCGA-19-0960 TCGA-19-2629 TCGA-27-2521 TCGA-28-2514 TCGA-32-1978 
       16.31         8.61        16.47        10.39         5.26        15.85 
TCGA-32-4210 TCGA-41-3392 TCGA-76-4925 TCGA-76-4934 
        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 
        9.17         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        55.86        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        10.36        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         0.23 
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         0.16 
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        16.21         2.70 
TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 
        0.26         4.04        47.31         0.10         3.58        22.72 
TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 
       32.52        10.52        18.74        14.07        23.08        22.16 
TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0143 TCGA-06-0145 
       10.75         0.20         9.21         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        16.70         9.80         7.86        19.46        46.59 
TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0159 
       11.80        12.79         8.65         3.19         5.46         9.44 
TCGA-06-0160 TCGA-06-0162 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 TCGA-06-0168 
       11.80         2.56        56.88        10.65         5.29        19.04 
TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 
        3.12        13.02         0.23         2.20         2.73        91.00 
TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 
        2.01        53.98        19.00         2.53        40.37        73.84 
TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 
       26.33        28.47        14.93        10.29        18.31         4.67 
TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0210 
        7.04         2.60         0.39         6.48         5.49         4.96 
TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0237 
       11.84         0.20        12.43        22.49         0.36        10.36 
TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0409 
       11.80        20.42        14.96        10.32         5.52        70.52 
TCGA-06-0410 TCGA-06-0412 TCGA-06-0413 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 
        4.70         8.05         0.16        12.33         3.22         4.47 
TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 
        2.04        23.57         9.40        22.32        19.56         5.39 
TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 
        2.70         2.17         0.92        46.19         5.65         7.17 
TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 
       22.98         5.85         5.42        20.94         7.43         6.35 
TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 
        3.58        26.79         8.65         7.89        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         0.76         4.93         9.27         2.83 
TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 
       30.64         5.95         6.81         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        11.24         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-06-6390 TCGA-06-6391 TCGA-06-6695 TCGA-06-6697 
        4.57         3.95         5.39         1.48         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-08-0244 TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 
        2.56        22.68        34.75         3.91       108.82         1.74 
TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 
        4.34        13.78        10.39         7.59         3.42        53.82 
TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 
        1.28         6.41        15.06        22.52        14.70        35.64 
TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 
       19.53         0.95         9.17        10.85        15.72         3.19 
TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 TCGA-08-0514 
       10.59         0.30         0.56         3.52        11.77         8.52 
TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 TCGA-08-0521 TCGA-08-0524 TCGA-08-0525 
       58.19         1.28        10.75         4.80         6.54        15.98 
TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 
       17.33         5.52        14.01        14.43         1.64        10.39 
TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 
        5.95         7.17        65.92         0.10        38.17        25.97 
TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 
       24.13         6.12         2.63        18.12        28.41        12.43 
TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 
       53.10        43.10         5.49         9.11        14.86        14.27 
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-12-1090 TCGA-12-1091 TCGA-12-1092 
       20.58       127.59         5.82         6.25        30.54        21.63 
TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 
       11.97        11.38        15.85         9.11        14.53         3.98 
TCGA-12-1598 TCGA-12-1599 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 
        9.44        25.28         6.41        59.41        43.23        25.78 
TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-5299 TCGA-12-5301 
       11.54        10.95        11.77        34.52         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-14-0812 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-14-0867 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         6.15        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-15-1444 TCGA-15-1446 TCGA-15-1447 
       17.49         7.96         3.42        50.53        19.10        53.19 
TCGA-15-1449 TCGA-16-0846 TCGA-16-0849 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 
        5.52         3.91        26.07         4.31        29.03         0.82 
TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 
        9.90        13.35         3.65        18.28        13.97         6.41 
TCGA-19-0955 TCGA-19-0957 TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 
       11.77        21.90         0.43        14.27         3.39        10.75 
TCGA-19-1386 TCGA-19-1387 TCGA-19-1388 TCGA-19-1389 TCGA-19-1390 TCGA-19-1392 
        9.07         5.95        12.95         4.64        25.38         3.48 
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        11.28         8.02        18.64         4.73         7.96 
TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A6J4 
        1.78         6.51         5.39         5.29         5.42         3.98 
TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1442 TCGA-26-1443 
       16.57        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         1.22 
TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 
        1.58         7.92         2.33         4.80        16.60         9.86 
TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 
       18.25        33.14        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-28-5204 TCGA-28-5207 TCGA-28-5208 
        6.74         4.77         7.30         3.91         9.04        15.58 
TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 
       14.53        11.77        31.27        14.20         7.79        13.64 
TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1970 TCGA-32-1973 
        4.21        22.68        10.49         5.42        15.39        21.07 
TCGA-32-1976 TCGA-32-1977 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 
        0.49         0.10        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        21.17        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        10.62         0.85        13.35         8.94 
TCGA-41-2575 TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 
        9.53         4.44        11.84         0.20        11.54         7.76 
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-76-6285 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 
        1.61        17.72        26.30         5.92 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              0.26               0.10 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             99.98             127.59 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            11.705              9.900 
[1] "0.3 - 100.0 (11.7)" "0.1 - 127.6 (9.9)" 
[1] "hr=" "1"  
D78V2, continuous
D78V3, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    18  22
  21Q LOSS WILD-TYPE 202 318
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     18   22
  21Q LOSS WILD-TYPE  202  318
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE               18                202
  MALE                 22                318
[1] 2 2
[1] FALSE
D78V4, continuous
                    vv
clus                 GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  21Q LOSS MUTATED                               0                   1
  21Q LOSS WILD-TYPE                            17                  17
                    vv
clus                 UNTREATED PRIMARY (DE NOVO) GBM
  21Q LOSS MUTATED                                39
  21Q LOSS WILD-TYPE                             486
D78V5, multiclass
                                 clus
vv                                21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                  0                 17
  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"
D78V6, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    25  15
  21Q LOSS WILD-TYPE 357 163
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     25   15
  21Q LOSS WILD-TYPE  357  163
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  NO                25                357
  YES               15                163
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  21Q LOSS MUTATED       1                         2    36
  21Q LOSS WILD-TYPE    12                        37   449
D78V7, multiclass
                           clus
vv                          21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  ASIAN                                    1                 12
  BLACK OR AFRICAN AMERICAN                2                 37
  WHITE                                   36                449
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V8, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED     2  34
  21Q LOSS WILD-TYPE  10 428
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      2   34
  21Q LOSS WILD-TYPE   10  428
                        clus
vv                       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                 10
  NOT HISPANIC OR LATINO               34                428
[1] 2 2
[1] FALSE

Clustering(79) Variable = 22Q LOSS MUTATION ANALYSIS
D79V1, survival
                    sevent
clus2                  0   1
  22Q LOSS MUTATED    27 151
  22Q LOSS WILD-TYPE  71 311
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               178                382 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               151                311 
$`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        55.86        10.36        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         0.16         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        16.21        32.52         0.20         9.21        16.70 
TCGA-06-0152 TCGA-06-0158 TCGA-06-0159 TCGA-06-0162 TCGA-06-0164 TCGA-06-0166 
       11.80         5.46         9.44         2.56        56.88         5.29 
TCGA-06-0168 TCGA-06-0175 TCGA-06-0182 TCGA-06-0185 TCGA-06-0188 TCGA-06-0189 
       19.04         2.73         2.53        73.84        28.47        14.93 
TCGA-06-0194 TCGA-06-0197 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 
        4.67         2.60        22.49         0.36        18.02        10.36 
TCGA-06-0241 TCGA-06-0397 TCGA-06-0402 TCGA-06-0410 TCGA-06-0744 TCGA-06-0745 
       14.96         5.52         0.26         4.70        19.56         5.39 
TCGA-06-0747 TCGA-06-0875 TCGA-06-0878 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 
        2.70        43.46         7.17         5.42        20.94         7.43 
TCGA-06-1804 TCGA-06-1806 TCGA-06-2558 TCGA-06-2562 TCGA-06-2567 TCGA-06-5408 
       13.61        15.32         0.76         2.83         4.37        11.24 
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 
        0.49        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 
       34.75         3.91         7.59         3.42        15.06        15.72 
TCGA-08-0389 TCGA-08-0392 TCGA-08-0512 TCGA-08-0516 TCGA-08-0520 TCGA-12-0619 
        3.19         0.30        11.77        18.44        10.75        10.39 
TCGA-12-0620 TCGA-12-0656 TCGA-12-0662 TCGA-12-0670 TCGA-12-0821 TCGA-12-0826 
        5.95        65.92        38.17        25.97        10.62        27.78 
TCGA-12-1088 TCGA-12-1091 TCGA-12-1096 TCGA-12-1097 TCGA-12-1598 TCGA-12-1600 
      127.59        30.54         9.11        14.53         9.44        13.61 
TCGA-12-3646 TCGA-12-3651 TCGA-12-3653 TCGA-12-5295 TCGA-14-0736 TCGA-14-0783 
       43.23        11.77        11.74        13.12        15.12         6.21 
TCGA-14-0862 TCGA-14-0865 TCGA-14-0867 TCGA-14-1034 TCGA-14-1402 TCGA-14-1450 
        2.89        16.50         2.04        15.95        32.05        58.78 
TCGA-14-1454 TCGA-14-1794 TCGA-14-1821 TCGA-14-3477 TCGA-15-0742 TCGA-15-1444 
       30.18         0.99        17.79         3.78         9.86        50.53 
TCGA-15-1447 TCGA-16-1056 TCGA-19-0962 TCGA-19-0964 TCGA-19-1385 TCGA-19-1389 
       53.19        13.35         0.43         3.39        10.75         4.64 
TCGA-19-1392 TCGA-19-1791 TCGA-19-2620 TCGA-19-2623 TCGA-19-2625 TCGA-19-2629 
        3.48         0.13         4.87         7.53         4.08        16.47 
TCGA-19-2631 TCGA-19-5947 TCGA-19-5956 TCGA-19-5958 TCGA-19-5960 TCGA-19-A6J4 
        7.00         6.64         6.51         5.39         5.42         3.98 
TCGA-26-5132 TCGA-26-5136 TCGA-26-6173 TCGA-27-1830 TCGA-27-1832 TCGA-27-1834 
        9.40         1.22         7.92         4.80         9.86        33.14 
TCGA-27-1835 TCGA-27-2519 TCGA-27-2523 TCGA-27-2527 TCGA-28-1752 TCGA-28-2506 
       21.30        10.39        16.08        14.40         8.48         6.74 
TCGA-28-2509 TCGA-28-5207 TCGA-28-5208 TCGA-28-5213 TCGA-32-1970 TCGA-32-1973 
        4.77         9.04        15.58        31.27        15.39        21.07 
TCGA-32-1976 TCGA-32-1978 TCGA-32-1980 TCGA-32-1986 TCGA-32-2491 TCGA-32-2615 
        0.49        15.85         1.18        12.69        12.23        15.95 
TCGA-32-2632 TCGA-32-2634 TCGA-41-2573 TCGA-41-2575 TCGA-41-3915 TCGA-41-4097 
        8.84        22.78         8.94         9.53        11.84         0.20 
TCGA-41-6646 TCGA-74-6581 TCGA-76-4925 TCGA-76-4926 TCGA-76-4929 TCGA-76-4934 
        7.76         8.22         4.80         4.54         3.65         2.53 
TCGA-76-6280 TCGA-76-6657 TCGA-87-5896 TCGA-OX-A56R 
       11.38         5.03        26.30         5.92 

$`22Q LOSS WILD-TYPE`
TCGA-02-0001 TCGA-02-0003 TCGA-02-0006 TCGA-02-0009 TCGA-02-0011 TCGA-02-0014 
        9.17         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         0.23        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 
        0.26         4.04        47.31         0.10         3.58        22.72 
TCGA-06-0130 TCGA-06-0132 TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 
       10.52        18.74        14.07        23.08        22.16        10.75 
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         9.80         7.86 
TCGA-06-0150 TCGA-06-0151 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0160 
       19.46        46.59        12.79         8.65         3.19        11.80 
TCGA-06-0165 TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0176 
       10.65         3.12        13.02         0.23         2.20        91.00 
TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0184 TCGA-06-0187 TCGA-06-0190 
        2.01        53.98        19.00        40.37        26.33        10.29 
TCGA-06-0192 TCGA-06-0195 TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 
       18.31         7.04         0.39         6.48         5.49         3.91 
TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0238 TCGA-06-0240 
        4.96        11.84         0.20        12.43        11.80        20.42 
TCGA-06-0394 TCGA-06-0409 TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 
       10.32        70.52         8.05         0.16        35.01        12.33 
TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 
        3.22         4.47         9.67         2.04        23.57         9.40 
TCGA-06-0743 TCGA-06-0749 TCGA-06-0750 TCGA-06-0876 TCGA-06-0877 TCGA-06-0879 
       22.32         2.17         0.92        46.19         5.65        22.98 
TCGA-06-0881 TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 
        5.85         6.35         3.58        26.79         8.65         7.89 
TCGA-06-1805 TCGA-06-2557 TCGA-06-2559 TCGA-06-2561 TCGA-06-2563 TCGA-06-2564 
       33.90         1.08         4.93         9.27        30.64         5.95 
TCGA-06-2565 TCGA-06-2566 TCGA-06-2569 TCGA-06-2570 TCGA-06-5410 TCGA-06-5412 
        6.81         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         3.95 
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-A6S0 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 
        3.12       108.82         1.74         4.34        13.78        10.39 
TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 
       53.82         1.28         6.41        22.52        14.70        35.64 
TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 TCGA-08-0390 TCGA-08-0509 
       19.53         0.95         9.17        10.85        10.59         0.56 
TCGA-08-0510 TCGA-08-0514 TCGA-08-0517 TCGA-08-0518 TCGA-08-0521 TCGA-08-0524 
        3.52         8.52        58.19         1.28         4.80         6.54 
TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 
       15.98        17.33         5.52        14.01        14.43         1.64 
TCGA-12-0654 TCGA-12-0657 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 
        7.17         0.10        24.13         6.12         2.63        18.12 
TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 
       28.41        12.43        53.10        43.10         5.49         9.11 
TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 TCGA-12-0820 TCGA-12-0822 
       14.86        14.27        91.76        24.79        18.48        23.51 
TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 TCGA-12-1089 TCGA-12-1090 TCGA-12-1092 
       38.76         8.94        20.58         5.82         6.25        21.63 
TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1098 TCGA-12-1099 TCGA-12-1599 
       11.97        11.38        15.85         3.98         3.42        25.28 
TCGA-12-1602 TCGA-12-3644 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3652 
        6.41        59.41        25.78        11.54        10.95        34.52 
TCGA-12-5299 TCGA-12-5301 TCGA-14-0740 TCGA-14-0781 TCGA-14-0786 TCGA-14-0787 
        3.22         2.04        11.97         0.95        23.05         2.24 
TCGA-14-0789 TCGA-14-0790 TCGA-14-0812 TCGA-14-0813 TCGA-14-0817 TCGA-14-0866 
       11.24        13.78         3.25         1.35         5.39        26.33 
TCGA-14-0871 TCGA-14-1037 TCGA-14-1043 TCGA-14-1395 TCGA-14-1396 TCGA-14-1401 
       28.93        19.30         0.79         1.38         1.12         3.75 
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         6.15 
TCGA-14-1459 TCGA-14-1795 TCGA-14-1823 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 
       12.43         1.97        17.85         7.63         5.88         7.17 
TCGA-14-2554 TCGA-14-2555 TCGA-14-4157 TCGA-15-1446 TCGA-15-1449 TCGA-16-0846 
       17.49         7.96         3.42        19.10         5.52         3.91 
TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 
        9.93        26.07        16.31         4.31        29.03         0.82 
TCGA-16-1055 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 
        9.90         3.65        18.28        13.97         6.41        11.77 
TCGA-19-0957 TCGA-19-0960 TCGA-19-0963 TCGA-19-1386 TCGA-19-1387 TCGA-19-1388 
       21.90         8.61        14.27         9.07         5.95        12.95 
TCGA-19-1390 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 TCGA-19-2619 TCGA-19-2621 
       25.38         7.17        12.66         3.25         9.67         1.08 
TCGA-19-2624 TCGA-19-4065 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 
        0.16         7.04        11.28         8.02        18.64         4.73 
TCGA-19-5954 TCGA-19-5955 TCGA-19-5959 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1439 
        7.96         1.78         5.29        16.57        10.03        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-26-6174 TCGA-27-1831 TCGA-27-1833 TCGA-27-1836 
        8.88         1.58         2.33        16.60        18.25        30.05 
TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2521 TCGA-27-2524 TCGA-27-2526 
       14.04        11.51        24.76        10.39         7.59         2.86 
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-28-1753 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-28-5209 TCGA-28-5211 TCGA-28-5214 TCGA-28-5215 
        5.26         3.91        14.53        11.77        14.20         7.79 
TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-1977 
       13.64         4.21        22.68        10.49         5.42         0.10 
TCGA-32-1979 TCGA-32-1982 TCGA-32-1987 TCGA-32-1991 TCGA-32-2494 TCGA-32-2495 
       19.50         4.67        14.86        16.93        20.78        15.02 
TCGA-32-2616 TCGA-32-2638 TCGA-32-4208 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 
        7.36        21.17        21.14         3.72        12.59        19.86 
TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-3392 TCGA-41-3393 
       10.85        10.62         0.85        13.35         0.99         4.44 
TCGA-41-5651 TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6584 
       11.54         3.45        20.91         4.34        14.33         7.50 
TCGA-76-4928 TCGA-76-4931 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 
        3.09         9.17        10.78        16.70         3.29         2.70 
TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6661 TCGA-76-6662 
       17.06         8.35        20.98         4.83         0.23         9.27 
TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 TCGA-81-5911 
        7.73         7.79         1.61        17.72 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              0.13               0.10 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            127.59             108.82 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             9.715             10.355 
[1] "0.1 - 127.6 (9.7)"  "0.1 - 108.8 (10.4)"
[1] "hr=" "1.1"
D79V2, continuous
D79V3, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    70 108
  22Q LOSS WILD-TYPE 150 232
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     70  108
  22Q LOSS WILD-TYPE  150  232
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE               70                150
  MALE                108                232
[1] 2 2
[1] FALSE
D79V4, continuous
                    vv
clus                 GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  22Q LOSS MUTATED                               8                   6
  22Q LOSS WILD-TYPE                             9                  12
                    vv
clus                 UNTREATED PRIMARY (DE NOVO) GBM
  22Q LOSS MUTATED                               164
  22Q LOSS WILD-TYPE                             361
D79V5, multiclass
                                 clus
vv                                22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                  8                  9
  TREATED PRIMARY GBM                            6                 12
  UNTREATED PRIMARY (DE NOVO) GBM              164                361
[1] 3 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
  22Q LOSS MUTATED   119  59
  22Q LOSS WILD-TYPE 263 119
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED    119   59
  22Q LOSS WILD-TYPE  263  119
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  NO               119                263
  YES               59                119
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  22Q LOSS MUTATED       4                        11   157
  22Q LOSS WILD-TYPE     9                        28   328
D79V7, multiclass
                           clus
vv                          22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  ASIAN                                    4                  9
  BLACK OR AFRICAN AMERICAN               11                 28
  WHITE                                  157                328
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V8, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED     4 155
  22Q LOSS WILD-TYPE   8 307
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      4  155
  22Q LOSS WILD-TYPE    8  307
                        clus
vv                       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  8
  NOT HISPANIC OR LATINO              155                307
[1] 2 2
[1] FALSE

Clustering(80) Variable = XQ LOSS MUTATION ANALYSIS
D80V1, survival
                   sevent
clus2                 0   1
  XQ LOSS MUTATED    23  81
  XQ LOSS WILD-TYPE  75 381
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
              104               456 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               81               381 
$`XQ LOSS MUTATED`
TCGA-02-0007 TCGA-02-0011 TCGA-02-0026 TCGA-02-0039 TCGA-02-0048 TCGA-02-0068 
       23.18        20.71        24.59        10.52         3.22        26.43 
TCGA-02-0099 TCGA-02-0330 TCGA-02-0339 TCGA-02-2466 TCGA-06-0129 TCGA-06-0152 
        3.48        15.91        12.39        16.80        32.52        11.80 
TCGA-06-0162 TCGA-06-0171 TCGA-06-0184 TCGA-06-0185 TCGA-06-0214 TCGA-06-0219 
        2.56        13.02        40.37        73.84        12.43         0.36 
TCGA-06-0221 TCGA-06-0875 TCGA-06-1800 TCGA-06-2558 TCGA-06-2564 TCGA-06-2569 
       18.02        43.46        26.79         0.76         5.95         0.43 
TCGA-06-2570 TCGA-06-5408 TCGA-06-5416 TCGA-06-5418 TCGA-06-5856 TCGA-06-5859 
       31.50        11.24         6.71         2.73         3.75         4.57 
TCGA-06-6693 TCGA-06-A5U1 TCGA-06-A6S1 TCGA-08-0245 TCGA-08-0348 TCGA-08-0354 
        0.49         1.87         2.56        34.75        10.39        15.06 
TCGA-08-0355 TCGA-08-0389 TCGA-08-0392 TCGA-08-0512 TCGA-08-0517 TCGA-08-0520 
       22.52         3.19         0.30        11.77        58.19        10.75 
TCGA-08-0525 TCGA-12-0615 TCGA-12-0821 TCGA-12-0827 TCGA-12-1091 TCGA-12-3644 
       15.98        14.01        10.62        38.76        30.54        59.41 
TCGA-12-3646 TCGA-12-3652 TCGA-12-5295 TCGA-14-0736 TCGA-14-0740 TCGA-14-0787 
       43.23        34.52        13.12        15.12        11.97         2.24 
TCGA-14-0862 TCGA-14-0865 TCGA-14-1453 TCGA-14-3477 TCGA-15-0742 TCGA-15-1447 
        2.89        16.50         1.15         3.78         9.86        53.19 
TCGA-16-0861 TCGA-16-1045 TCGA-19-1388 TCGA-19-1390 TCGA-19-1392 TCGA-19-1786 
        4.31        29.03        12.95        25.38         3.48         7.17 
TCGA-19-2619 TCGA-19-2621 TCGA-19-2623 TCGA-19-2625 TCGA-19-2629 TCGA-19-5947 
        9.67         1.08         7.53         4.08        16.47         6.64 
TCGA-19-5956 TCGA-19-5960 TCGA-26-1439 TCGA-26-1440 TCGA-26-5133 TCGA-27-2524 
        6.51         5.42        13.87         9.73        14.86         7.59 
TCGA-28-1750 TCGA-28-2514 TCGA-28-5204 TCGA-28-5220 TCGA-32-1973 TCGA-32-1977 
        8.35         5.26         3.91        10.49        21.07         0.10 
TCGA-32-1978 TCGA-32-2494 TCGA-32-2615 TCGA-32-2634 TCGA-32-4208 TCGA-32-4213 
       15.85        20.78        15.95        22.78        21.14        19.86 
TCGA-32-4719 TCGA-41-2572 TCGA-41-2575 TCGA-41-3392 TCGA-74-6575 TCGA-76-4925 
       10.85        13.35         9.53         0.99        20.91         4.80 
TCGA-76-4926 TCGA-76-4929 TCGA-76-4931 TCGA-76-4934 TCGA-76-4935 TCGA-76-6285 
        4.54         3.65         9.17         2.53        10.78         8.35 
TCGA-76-6286 TCGA-OX-A56R 
       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 
        9.17         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        55.86        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 
       10.36        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-02-0069 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         0.23        51.32         8.81        57.76 
TCGA-02-0089 TCGA-02-0102 TCGA-02-0104 TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 
       16.96        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         0.16 
TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 TCGA-02-0422 TCGA-02-0430 
       25.71         4.37        25.12        10.59        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-02-2483 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 
       15.32        15.45        16.21         2.70         0.26         4.04 
TCGA-06-0125 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0130 TCGA-06-0132 
       47.31         0.10         3.58        22.72        10.52        18.74 
TCGA-06-0133 TCGA-06-0137 TCGA-06-0138 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 
       14.07        23.08        22.16        10.75         0.20         9.21 
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        16.70         9.80 
TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 
        7.86        19.46        46.59        12.79         8.65         3.19 
TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0164 TCGA-06-0165 TCGA-06-0166 
        5.46         9.44        11.80        56.88        10.65         5.29 
TCGA-06-0168 TCGA-06-0169 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 
       19.04         3.12         0.23         2.20         2.73        91.00 
TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0187 TCGA-06-0188 
        2.01        53.98        19.00         2.53        26.33        28.47 
TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 
       14.93        10.29        18.31         4.67         7.04         2.60 
TCGA-06-0201 TCGA-06-0206 TCGA-06-0208 TCGA-06-0209 TCGA-06-0210 TCGA-06-0211 
        0.39         6.48         5.49         3.91         4.96        11.84 
TCGA-06-0213 TCGA-06-0216 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 
        0.20        22.49        10.36        11.80        20.42        14.96 
TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 TCGA-06-0412 
       10.32         5.52         0.26        70.52         4.70         8.05 
TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 
        0.16        35.01        12.33         3.22         4.47         9.67 
TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 
        2.04        23.57         9.40        22.32        19.56         5.39 
TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0876 TCGA-06-0877 TCGA-06-0878 
        2.70         2.17         0.92        46.19         5.65         7.17 
TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 TCGA-06-1086 
       22.98         5.85         5.42        20.94         7.43         6.35 
TCGA-06-1087 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 TCGA-06-1806 
        3.58         8.65         7.89        13.61        33.90        15.32 
TCGA-06-2557 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2565 
        1.08         4.93         9.27         2.83        30.64         6.81 
TCGA-06-2566 TCGA-06-2567 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 
        5.98         4.37         3.55         8.35         4.54         8.81 
TCGA-06-5414 TCGA-06-5415 TCGA-06-5858 TCGA-06-6388 TCGA-06-6389 TCGA-06-6390 
        8.98         8.55         6.15         3.95         7.79         5.39 
TCGA-06-6391 TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 
        1.48         7.36         8.32        12.85         4.77         1.55 
TCGA-06-6700 TCGA-06-6701 TCGA-06-A6S0 TCGA-08-0244 TCGA-08-0246 TCGA-08-0344 
        4.77         4.96         3.12        22.68         3.91       108.82 
TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 
        1.74         4.34        13.78         7.59         3.42        53.82 
TCGA-08-0352 TCGA-08-0353 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 
        1.28         6.41        14.70        35.64        19.53         0.95 
TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 TCGA-08-0390 TCGA-08-0509 TCGA-08-0510 
        9.17        10.85        15.72        10.59         0.56         3.52 
TCGA-08-0514 TCGA-08-0516 TCGA-08-0518 TCGA-08-0521 TCGA-08-0524 TCGA-08-0529 
        8.52        18.44         1.28         4.80         6.54        17.33 
TCGA-08-0531 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 
        5.52        14.43         1.64        10.39         5.95         7.17 
TCGA-12-0656 TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 
       65.92         0.10        38.17        25.97        24.13         6.12 
TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 
        2.63        18.12        28.41        12.43        53.10        43.10 
TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0818 TCGA-12-0819 
        5.49         9.11        14.86        14.27        91.76        24.79 
TCGA-12-0820 TCGA-12-0822 TCGA-12-0826 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 
       18.48        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         6.25        21.63        11.97        11.38        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         3.42         9.44        25.28 
TCGA-12-1600 TCGA-12-1602 TCGA-12-3648 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 
       13.61         6.41        25.78        11.54        10.95        11.77 
TCGA-12-3653 TCGA-12-5299 TCGA-12-5301 TCGA-14-0781 TCGA-14-0783 TCGA-14-0786 
       11.74         3.22         2.04         0.95         6.21        23.05 
TCGA-14-0789 TCGA-14-0790 TCGA-14-0812 TCGA-14-0813 TCGA-14-0817 TCGA-14-0866 
       11.24        13.78         3.25         1.35         5.39        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-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 TCGA-14-1794 
       30.18         0.92        40.96         6.15        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-15-1444 TCGA-15-1446 TCGA-15-1449 
       17.49         7.96         3.42        50.53        19.10         5.52 
TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 TCGA-16-1047 TCGA-16-1055 
        3.91         9.93        26.07        16.31         0.82         9.90 
TCGA-16-1056 TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 
       13.35         3.65        18.28        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         0.43        14.27         3.39        10.75 
TCGA-19-1386 TCGA-19-1387 TCGA-19-1389 TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 
        9.07         5.95         4.64        12.66         3.25         0.13 
TCGA-19-2620 TCGA-19-2624 TCGA-19-2631 TCGA-19-4065 TCGA-19-5950 TCGA-19-5951 
        4.87         0.16         7.00         7.04        11.28         8.02 
TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5958 TCGA-19-5959 
       18.64         4.73         7.96         1.78         5.39         5.29 
TCGA-19-A6J4 TCGA-19-A6J5 TCGA-26-1438 TCGA-26-1442 TCGA-26-1443 TCGA-26-1799 
        3.98        16.57        10.03        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         1.22         1.58         7.92 
TCGA-26-6174 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 
        2.33         4.80        16.60         9.86        18.25        33.14 
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-28-2502 TCGA-28-2506 TCGA-28-2509 TCGA-28-2513 
        2.83         0.13         0.66         6.74         4.77         7.30 
TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 
        9.04        15.58        14.53        11.77        31.27        14.20 
TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-6450 TCGA-32-1970 
        7.79        13.64         4.21        22.68         5.42        15.39 
TCGA-32-1976 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 
        0.49        19.50         1.18         4.67        12.69        14.86 
TCGA-32-1991 TCGA-32-2491 TCGA-32-2495 TCGA-32-2616 TCGA-32-2632 TCGA-32-2638 
       16.93        12.23        15.02         7.36         8.84        21.17 
TCGA-32-4210 TCGA-32-4211 TCGA-32-5222 TCGA-41-2571 TCGA-41-2573 TCGA-41-3393 
        3.72        12.59        10.62         0.85         8.94         4.44 
TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 TCGA-74-6573 TCGA-74-6577 
       11.84         0.20        11.54         7.76         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 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
              0.1               0.1 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            73.84            127.59 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           10.815             9.735 
[1] "0.1 - 73.8 (10.8)" "0.1 - 127.6 (9.7)"
[1] "hr=" "1.1"
D80V2, continuous
D80V3, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    44  60
  XQ LOSS WILD-TYPE 176 280
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     44   60
  XQ LOSS WILD-TYPE  176  280
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE              44               176
  MALE                60               280
[1] 2 2
[1] FALSE
D80V4, continuous
                   vv
clus                GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  XQ LOSS MUTATED                               3                   2
  XQ LOSS WILD-TYPE                            14                  16
                   vv
clus                UNTREATED PRIMARY (DE NOVO) GBM
  XQ LOSS MUTATED                                99
  XQ LOSS WILD-TYPE                             426
D80V5, multiclass
                                 clus
vv                                XQ LOSS MUTATED XQ LOSS WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                 3                14
  TREATED PRIMARY GBM                           2                16
  UNTREATED PRIMARY (DE NOVO) GBM              99               426
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V6, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    73  31
  XQ LOSS WILD-TYPE 309 147
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     73   31
  XQ LOSS WILD-TYPE  309  147
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  NO               73               309
  YES              31               147
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XQ LOSS MUTATED       4                        10    86
  XQ LOSS WILD-TYPE     9                        29   399
D80V7, multiclass
                           clus
vv                          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  ASIAN                                   4                 9
  BLACK OR AFRICAN AMERICAN              10                29
  WHITE                                  86               399
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V8, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     3  85
  XQ LOSS WILD-TYPE   9 377
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      3   85
  XQ LOSS WILD-TYPE    9  377
                        clus
vv                       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                 9
  NOT HISPANIC OR LATINO              85               377
[1] 2 2
[1] FALSE
