[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"       "-oTLGG-TP"
[1] "opt"       "-OPMUTSIG"
[1] "tl" ""  
[1] "dx" ""  
[1] "opt"    "MUTSIG"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/LGG-TP/11541557/LGG-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LGG-TP/11544935/transformed.cor.cli.txt"

nPatients in clinical file=433, in cluster file=513, common to both=430
[1] "Reduce the number of clustering variables from 80 to 78."
[1]  78 430
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               11               419 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               11               419 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               18               412 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               18               412 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               11               419 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               11               419 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               10               420 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               10               420 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               11               419 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               11               419 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                8               422 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                8               422 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               11               419 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               11               419 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                4               426 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                4               426 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                8               422 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                8               422 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                5               425 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                5               425 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                7               423 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                7               423 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               96               334 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               96               334 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              127               303 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              127               303 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               39               391 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               39               391 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               46               384 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               46               384 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               14               416 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               14               416 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               20               410 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               20               410 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                44                386 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                44                386 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 8                422 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 8                422 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                27                403 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                27                403 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                49                381 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                49                381 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                27                403 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                27                403 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                13                417 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                13                417 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 6                424 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 6                424 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 3                427 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 3                427 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 8                422 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 8                422 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                16                414 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                16                414 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                18                412 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                18                412 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                17                413 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                17                413 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                19                411 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                19                411 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                13                417 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                13                417 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 9                421 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 9                421 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                84                346 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                84                346 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                20                410 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                20                410 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                37                393 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                37                393 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                37                393 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                37                393 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                21                409 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                21                409 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                15                415 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                15                415 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               30               400 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               30               400 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
              159               271 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
              159               271 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               23               407 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               23               407 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               16               414 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               16               414 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               13               417 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               13               417 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               21               409 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               21               409 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               23               407 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               23               407 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               58               372 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               58               372 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               74               356 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               74               356 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               28               402 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               28               402 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               28               402 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               28               402 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               25               405 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               25               405 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               50               380 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               50               380 
[1] "7P LOSS MUTATION ANALYSIS"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                3               427 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                3               427 
[1] "7Q LOSS MUTATION ANALYSIS"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                3               427 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                3               427 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               13               417 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               13               417 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                9               421 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                9               421 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               96               334 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               96               334 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               38               392 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               38               392 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                68                362 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                68                362 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                80                350 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                80                350 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                53                377 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                53                377 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                19                411 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                19                411 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                21                409 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                21                409 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                40                390 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                40                390 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                98                332 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                98                332 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                65                365 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                65                365 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                39                391 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                39                391 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                11                419 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                11                419 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                19                411 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                19                411 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                12                418 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                12                418 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 8                422 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 8                422 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                59                371 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                59                371 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                54                376 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                54                376 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                19                411 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                19                411 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
               177                253 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
               177                253 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 5                425 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 5                425 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                26                404 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                26                404 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                46                384 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                46                384 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               56               374 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               56               374 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDISEASE"                  
 [6] "DCCUPLOADDATE"                         
 [7] "GENDER"                                
 [8] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
 [9] "DAYSTOLASTKNOWNALIVE"                  
[10] "RADIATIONTHERAPY"                      
[11] "KARNOFSKYPERFORMANCESCORE"             
[12] "HISTOLOGICALTYPE"                      
[13] "RADIATIONS.RADIATION.REGIMENINDICATION"
[14] "RACE"                                  
[15] "ETHNICITY"                             
[16] "BATCHNUMBER"                           

Input Data has 16 rows and 430 columns.

[1] "Batch" "16"   
[1] "Last Follow UP"
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
         143           NA           NA          552          323         1966 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
        1222            3           NA          303           NA           NA 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
         725          546          378          258          230          244 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
         225          201         3733         2493         2289         1458 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
        2218         1419         1526         1354         1112         2381 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
         915          313          387          840          822          573 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
         559         2219          383          335          573          511 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
         182          489          469          846          448          415 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
         332          225          196          313          935          116 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
          NA          968          922          438          244           NA 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
        1279          846          523          523         1650          311 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
         200          105          189          548          443          531 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
          NA          407          257          207         5546          576 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 
         532          461         6423         1585          682         1491 
TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 
        2286         1401           NA           NA         2660          214 
TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 
          NA           NA          605           NA           NA         3470 
TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 
         242          235           NA           NA         4752         4206 
TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 
          NA           NA           NA           NA           NA         2761 
TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 
          NA          800           NA           NA         2869           NA 
TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 
          NA           NA           NA         1834           NA         1277 
TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 
          84           NA           NA          121          629          651 
TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR 
         582          516          471          431          433          383 
TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 
         460          151          111          172          371          263 
TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L 
          82         2372          220          182           NA           NA 
TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 TCGA-DU-A7TG TCGA-E1-5302 TCGA-E1-5303 
         217           NA         3787           NA         1525         2052 
TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 
        1251         2433         1762         4084         2379         2907 
TCGA-E1-5322 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 
        3978          436            7            6         1453          547 
TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 
        1045          979          571          454          760          729 
TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 
         413          467          544          686          627          611 
TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 
         394          416          433          487          611          455 
TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX 
         685          472         1164          326          160          569 
TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 
         721          449          542          499          457          500 
TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 
         322          868          328          698         1329          159 
TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 
         226          174            4            3          203          238 
TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 
         268            4            1          503          114          530 
TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 
         199          738          194          216         2287         1800 
TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 
        1826         4690          122          153          908          705 
TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 
        3283          139          526           NA          671         1399 
TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 
        1706         1752           NA          434            5          494 
TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 
          23         1359          184         1300            3          964 
TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 
         455            3            3           90          533          210 
TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 
         442         1201          585         1189            7         1540 
TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 
          15          718         1130           10            4          112 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 
         162           89           52          343          956           50 
TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 
         494          286           NA            3          654         1004 
TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 
         372          190            3           14           76          120 
TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 
         143            7          900          118          488          478 
TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA 
           7          319            4          426            2          447 
TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 
           3           NA           82          396           55          491 
TCGA-HT-A618 TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 
         162            3          910          409          253          585 
TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 
        1222         1092          131          660          657          596 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 
         542          619          240          633          630           NA 
TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5ET TCGA-P5-A5EU TCGA-P5-A5EV 
        1301          159          144           NA           NA            7 
TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 
         204           50           72           70          125          179 
TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V 
         232           23           39          175           77          147 
TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW 
         237          125          127          451          442           NA 
TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 
          NA           67           96           18          192          119 
TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 
         144           58            7          153          106            2 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TS TCGA-S9-A6TU 
        2702         2860          993         1806           NA         2101 
TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 
         571         1151         1049          953          658          498 
TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
         536          719          992          300         2878         2546 
TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH 
          NA         3236         1897         2208         2437          987 
TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP 
        2585          331          604          484          231          461 
TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ 
         428          434           NA          597          383          128 
TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX 
         285          249           62          247          109          123 
TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 
         863          396         5000           NA         3013          530 
TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 
        2549           NA          569          152         1504         1470 
TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F 
        1500         1058         1472          365          459         1544 
TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M 
        1045          738          589          532           NA          502 
TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-VM-A8C8 
         910          575          287          139          365         1006 
TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH 
         915          411            3           NA          815          333 
TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-W9-A837 
         823          214          706         1371 
Variable 1:'AGE':	nDistinctValues=59,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=75,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=323,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'DCCUPLOADDAY':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 7:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=21,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=5,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 10:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=7,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 12:'HISTOLOGICAL.TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'BATCH.NUMBER':	nDistinctValues=18,	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 430 columns, 1 survival variables, and 7 non-survival variables.
AGE, nv=59, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY.PERFORMANCE.SCORE, nv=7, binary=FALSE, numeric=TRUE
HISTOLOGICAL.TYPE, nv=3, binary=FALSE, numeric=FALSE
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
RACE, nv=4, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1P GAIN MUTATION ANALYSIS
D1V1, survival
                   sevent
clus2                 0   1
  1P GAIN MUTATED     7   4
  1P GAIN WILD-TYPE 345  71
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               11               416 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                4                71 
$`1P GAIN MUTATED`
TCGA-CS-4941 TCGA-CS-6665 TCGA-DU-7010 TCGA-DU-7290 TCGA-DU-8165 TCGA-DU-A5TT 
        7.69        12.43        14.99        10.36        19.13         4.96 
TCGA-E1-5304 TCGA-HT-7686 TCGA-HT-A4DS TCGA-S9-A6WM TCGA-TM-A84I 
       41.13        42.74         0.23        19.86        19.36 

$`1P GAIN WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5393 
        4.70        43.89        18.15        10.62        64.64        40.18 
TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
        0.10        21.01         9.96         6.38        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 
       17.95         8.48         7.56         8.02         7.40         6.61 
TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 
      122.73        81.96        75.25        47.93        72.92        46.65 
TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA 
       50.17        44.52        36.56        78.28        30.08        10.29 
TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG 
       12.72        27.62        27.02        18.84        18.38        72.95 
TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R 
       12.59        11.01        18.84        16.80         5.98        16.08 
TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K 
       15.42        27.81        14.73        13.64        10.92         7.40 
TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 
        6.44        10.29        30.74         3.81        19.96        31.82 
TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D 
       30.31        14.40         8.02        30.21        42.05        27.81 
TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU 
       17.19        17.19        54.25        10.22         6.58         3.45 
TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 
        6.21        18.02        14.56        17.46         6.74        13.38 
TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 
        8.45         6.81       182.33        18.94        17.49        15.16 
TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 
      211.17        52.11        22.42        49.02        75.16        46.06 
TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 
       65.75         1.22        87.45         7.04        11.64       133.74 
TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 
       19.89        16.83        94.52       114.08         7.96         7.73 
TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7011 TCGA-DU-7012 
       11.47        62.96       156.23       138.28       105.21         6.54 
TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7292 
        8.84       117.40        90.77        30.67        26.30         7.96 
TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 
       94.32        18.94        44.02        62.01        25.91        60.30 
TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 
       23.31        41.98         2.76         5.10        23.74         3.98 
TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP 
       20.68        21.40        16.96        15.48        14.17        14.24 
TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 
       12.59        15.12         3.65         5.65        12.20         8.65 
TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L 
        2.70        77.98         7.23         5.98        11.41        26.76 
TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 TCGA-DU-A7TG TCGA-E1-5302 TCGA-E1-5303 
        7.13        21.30       124.50        44.42        50.14        67.46 
TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 
       79.99        57.93       134.27        78.21        95.57       130.78 
TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 
       14.33         0.23         0.20        47.77        17.98        34.36 
TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 
       32.19        18.77        14.93        24.99        23.97        13.58 
TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 
       15.35        17.88        22.55        20.61        20.09        12.95 
TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 
       13.68        14.24        16.01        20.09        14.96        22.52 
TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY 
       15.52        38.27        10.72         5.26        18.71        23.70 
TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 
       14.76        17.82        16.41        15.02        16.44        10.59 
TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N 
       28.54        10.78        22.95        43.69         5.23         7.43 
TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 
        5.72         0.13         0.10         6.67         7.82         8.81 
TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 
        0.13         0.03        16.54         3.75        17.42         6.54 
TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 
       24.26         6.38         7.10        75.19        59.18        60.03 
TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 
      154.19         4.01         5.03        29.85        23.18       107.93 
TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 
        4.57        17.29         3.16        22.06        45.99        56.09 
TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 
       57.60         0.23        14.27         0.16        16.24         0.76 
TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 
       44.68         6.05         0.10        31.69        14.96         0.10 
TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 
        0.10         2.96        17.52         6.90        14.53        39.48 
TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 
       19.23        39.09         0.23        50.63         0.49        23.61 
TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 
       37.15         0.33         0.13         3.68         5.33         2.93 
TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 
        1.71        11.28        31.43         1.64        16.24         9.40 
TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 
       63.55         0.10        21.50        33.01        12.23         6.25 
TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 
        0.10         0.46         2.50         3.95         4.70         0.23 
TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DV TCGA-HT-A5R5 
       29.59         3.88        16.04        15.72        10.49         0.13 
TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 
       14.01         0.07        14.70         0.10         5.33         2.70 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A74O TCGA-HW-7486 
       13.02         1.81        16.14         5.33         0.10        29.92 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 
       13.45         8.32        19.23        40.18        35.90         4.31 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
       21.70        21.60        19.59        17.82        20.35         7.89 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 
       20.81        20.71        19.00        42.77         5.23         4.73 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 
        0.23         6.71         1.64         2.37         2.30         4.11 
TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-QH-A65R TCGA-QH-A65S 
        5.88         7.63         0.76         1.28         5.75         2.53 
TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV 
        4.83         7.79         4.11         4.18        14.83        14.53 
TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 
       12.23         2.20         3.16         0.59         6.31         3.91 
TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 
        4.73         1.91         0.23         5.03         3.48         0.07 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TS TCGA-S9-A6TU 
       88.83        94.03        32.65        59.38        62.17        69.07 
TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 
       18.77        37.84        34.49        31.33        21.63        16.37 
TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
       17.62        23.64        32.61         9.86        94.62        83.70 
TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH 
        5.85       106.39        62.37        72.59        80.12        32.45 
TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ 
       84.99        10.88        15.91         7.59        15.16        14.07 
TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 
       14.27         7.92        19.63        12.59         4.21         9.37 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY 
        8.19         2.04         8.12         3.58         4.04        28.37 
TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 
       13.02       164.38        10.39        99.06        17.42        83.80 
TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 
       31.59        18.71         5.00        49.45        48.33        49.32 
TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G 
       34.78        48.39        12.00        15.09        50.76        34.36 
TCGA-TM-A84H TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q 
       24.26        17.49        40.83        16.50        29.92        18.90 
TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA 
        9.44         4.57        12.00        33.07        30.08        13.51 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M 
        0.10         7.89        26.79        10.95        27.06         7.04 
TCGA-VW-A7QS TCGA-W9-A837 
       23.21        45.07 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             0.23              0.03 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            42.74            211.17 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            14.99             15.96 
[1] "0.2 - 42.7 (15.0)"  "0.0 - 211.2 (16.0)"
[1] "hr=" "3.8"
D1V2, continuous
D1V3, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     7   4
  1P GAIN WILD-TYPE 183 236
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      7    4
  1P GAIN WILD-TYPE  183  236
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE               7               183
  MALE                 4               236
[1] 2 2
[1] FALSE
D1V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  1P GAIN MUTATED             9                0                 2
  1P GAIN WILD-TYPE         150              107               162
D1V5, multiclass
                   clus
vv                  1P GAIN MUTATED 1P GAIN WILD-TYPE
  ASTROCYTOMA                     9               150
  OLIGOASTROCYTOMA                0               107
  OLIGODENDROGLIOMA               2               162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V6, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     3   8
  1P GAIN WILD-TYPE  86 333
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      3    8
  1P GAIN WILD-TYPE   86  333
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  NO                3                86
  YES               8               333
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1P GAIN MUTATED                                  0     0
  1P GAIN WILD-TYPE                                1     6
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1P GAIN MUTATED                           0    11
  1P GAIN WILD-TYPE                        14   389
D1V7, multiclass
                                  clus
vv                                 1P GAIN MUTATED 1P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 6
  BLACK OR AFRICAN AMERICAN                      0                14
  WHITE                                         11               389
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V8, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     0  11
  1P GAIN WILD-TYPE  16 376
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      0   11
  1P GAIN WILD-TYPE   16  376
                        clus
vv                       1P GAIN MUTATED 1P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                16
  NOT HISPANIC OR LATINO              11               376
[1] 2 2
[1] FALSE

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                 0   1
  1Q GAIN MUTATED    13   5
  1Q GAIN WILD-TYPE 339  70
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               18               409 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                5                70 
$`1Q GAIN MUTATED`
TCGA-CS-4941 TCGA-CS-6665 TCGA-DB-A64L TCGA-DU-6392 TCGA-DU-7010 TCGA-DU-7015 
        7.69        12.43        11.01       211.17        14.99        90.77 
TCGA-DU-7290 TCGA-DU-8162 TCGA-DU-8165 TCGA-DU-A5TT TCGA-E1-5304 TCGA-HT-7475 
       10.36         3.98        19.13         4.96        41.13        17.42 
TCGA-HT-7688 TCGA-HT-A4DS TCGA-S9-A6WM TCGA-TM-A84B TCGA-TM-A84I TCGA-VM-A8CA 
       31.69         0.23        19.86        12.00        19.36        13.51 

$`1Q GAIN WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5393 
        4.70        43.89        18.15        10.62        64.64        40.18 
TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
        0.10        21.01         9.96         6.38        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 
       17.95         8.48         7.56         8.02         7.40         6.61 
TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 
      122.73        81.96        75.25        47.93        72.92        46.65 
TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA 
       50.17        44.52        36.56        78.28        30.08        10.29 
TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG 
       12.72        27.62        27.02        18.84        18.38        72.95 
TCGA-DB-A4XH TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S 
       12.59        18.84        16.80         5.98        16.08        15.42 
TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L 
       27.81        14.73        13.64        10.92         7.40         6.44 
TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 
       10.29        30.74         3.81        19.96        31.82        30.31 
TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F 
       14.40         8.02        30.21        42.05        27.81        17.19 
TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV 
       17.19        54.25        10.22         6.58         3.45         6.21 
TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 
       18.02        14.56        17.46         6.74        13.38         8.45 
TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6393 
        6.81       182.33        18.94        17.49        15.16        52.11 
TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 
       22.42        49.02        75.16        46.06        65.75         1.22 
TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 
       87.45         7.04        11.64       133.74        19.89        16.83 
TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 
       94.52       114.08         7.96         7.73        11.47        62.96 
TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 
      156.23       138.28       105.21         6.54         8.84       117.40 
TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 
       30.67        26.30         7.96        94.32        18.94        44.02 
TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 
       62.01        25.91        60.30        23.31        41.98         2.76 
TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-8167 
        5.10        23.74        20.68        21.40        16.96        15.48 
TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TU TCGA-DU-A5TW 
       14.17        14.24        12.59        15.12         3.65         5.65 
TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 
       12.20         8.65         2.70        77.98         7.23         5.98 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 TCGA-DU-A7TG 
       11.41        26.76         7.13        21.30       124.50        44.42 
TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 
       50.14        67.46        79.99        57.93       134.27        78.21 
TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 
       95.57       130.78        14.33         0.23         0.20        47.77 
TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 
       17.98        34.36        32.19        18.77        14.93        24.99 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 
       23.97        13.58        15.35        17.88        22.55        20.61 
TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 
       20.09        12.95        13.68        14.24        16.01        20.09 
TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW 
       14.96        22.52        15.52        38.27        10.72         5.26 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ 
       18.71        23.70        14.76        17.82        16.41        15.02 
TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 
       16.44        10.59        28.54        10.78        22.95        43.69 
TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 
        5.23         7.43         5.72         0.13         0.10         6.67 
TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 
        7.82         8.81         0.13         0.03        16.54         3.75 
TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 
        6.54        24.26         6.38         7.10        75.19        59.18 
TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 
       60.03       154.19         4.01         5.03        29.85        23.18 
TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 
      107.93         4.57        17.29         3.16        22.06        45.99 
TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 
       56.09        57.60         0.23        14.27         0.16        16.24 
TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7689 
        0.76        44.68         6.05        42.74         0.10        14.96 
TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 
        0.10         0.10         2.96        17.52         6.90        14.53 
TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 
       39.48        19.23        39.09         0.23        50.63         0.49 
TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 
       23.61        37.15         0.33         0.13         3.68         5.33 
TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 
        2.93         1.71        11.28        31.43         1.64        16.24 
TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 
        9.40        63.55         0.10        21.50        33.01        12.23 
TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 
        6.25         0.10         0.46         2.50         3.95         4.70 
TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DV 
        0.23        29.59         3.88        16.04        15.72        10.49 
TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC 
        0.13        14.01         0.07        14.70         0.10         5.33 
TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A74O 
        2.70        13.02         1.81        16.14         5.33         0.10 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 
       29.92        13.45         8.32        19.23        40.18        35.90 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
        4.31        21.70        21.60        19.59        17.82        20.35 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X 
        7.89        20.81        20.71        19.00        42.77         5.23 
TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ 
        4.73         0.23         6.71         1.64         2.37         2.30 
TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-QH-A65R 
        4.11         5.88         7.63         0.76         1.28         5.75 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU 
        2.53         4.83         7.79         4.11         4.18        14.83 
TCGA-QH-A6CV TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
       14.53        12.23         2.20         3.16         0.59         6.31 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X 
        3.91         4.73         1.91         0.23         5.03         3.48 
TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TS 
        0.07        88.83        94.03        32.65        59.38        62.17 
TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ 
       69.07        18.77        37.84        34.49        31.33        21.63 
TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       16.37        17.62        23.64        32.61         9.86        94.62 
TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG 
       83.70         5.85       106.39        62.37        72.59        80.12 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP 
       32.45        84.99        10.88        15.91         7.59        15.16 
TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ 
       14.07        14.27         7.92        19.63        12.59         4.21 
TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX 
        9.37         8.19         2.04         8.12         3.58         4.04 
TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 
       28.37        13.02       164.38        10.39        99.06        17.42 
TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 
       83.80        31.59        18.71         5.00        49.45        48.33 
TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G 
       49.32        34.78        48.39        15.09        50.76        34.36 
TCGA-TM-A84H TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q 
       24.26        17.49        40.83        16.50        29.92        18.90 
TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CB 
        9.44         4.57        12.00        33.07        30.08         0.10 
TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS 
        7.89        26.79        10.95        27.06         7.04        23.21 
TCGA-W9-A837 
       45.07 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             0.23              0.03 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           211.17            182.33 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            14.25             16.01 
[1] "0.2 - 211.2 (14.2)" "0.0 - 182.3 (16.0)"
[1] "hr=" "1.5"
D2V2, continuous
D2V3, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    10   8
  1Q GAIN WILD-TYPE 180 232
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     10    8
  1Q GAIN WILD-TYPE  180  232
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE              10               180
  MALE                 8               232
[1] 2 2
[1] FALSE
D2V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  1Q GAIN MUTATED            10                2                 6
  1Q GAIN WILD-TYPE         149              105               158
D2V5, multiclass
                   clus
vv                  1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  ASTROCYTOMA                    10               149
  OLIGOASTROCYTOMA                2               105
  OLIGODENDROGLIOMA               6               158
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V6, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED     5  13
  1Q GAIN WILD-TYPE  84 328
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      5   13
  1Q GAIN WILD-TYPE   84  328
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  NO                5                84
  YES              13               328
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1Q GAIN MUTATED                                  0     0
  1Q GAIN WILD-TYPE                                1     6
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1Q GAIN MUTATED                           0    17
  1Q GAIN WILD-TYPE                        14   383
D2V7, multiclass
                                  clus
vv                                 1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 6
  BLACK OR AFRICAN AMERICAN                      0                14
  WHITE                                         17               383
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V8, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED     0  17
  1Q GAIN WILD-TYPE  16 370
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      0   17
  1Q GAIN WILD-TYPE   16  370
                        clus
vv                       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                16
  NOT HISPANIC OR LATINO              17               370
[1] 2 2
[1] FALSE

Clustering(3) Variable = 2P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                 0   1
  2P GAIN MUTATED     9   2
  2P GAIN WILD-TYPE 343  73
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               11               416 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                2                73 
$`2P GAIN MUTATED`
TCGA-DB-5274 TCGA-DH-A669 TCGA-DH-A7UR TCGA-DU-8165 TCGA-E1-5304 TCGA-HT-8564 
       75.25        30.21        54.25        19.13        41.13        15.72 
TCGA-HT-A4DS TCGA-S9-A6WM TCGA-S9-A7J0 TCGA-TM-A84Q TCGA-VM-A8CA 
        0.23        19.86         9.37        18.90        13.51 

$`2P GAIN WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5275 TCGA-DB-5276 
        7.40         6.61       122.73        81.96        47.93        72.92 
TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 
       46.65        50.17        44.52        36.56        78.28        30.08 
TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF 
       10.29        12.72        27.62        27.02        18.84        18.38 
TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q 
       72.95        12.59        11.01        18.84        16.80         5.98 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X 
       16.08        15.42        27.81        14.73        13.64        10.92 
TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 
        7.40         6.44        10.29        30.74         3.81        19.96 
TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A66B TCGA-DH-A66D 
       31.82        30.31        14.40         8.02        42.05        27.81 
TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV 
       17.19        17.19        10.22         6.58         3.45         6.21 
TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 
       18.02        14.56        17.46         6.74        13.38         8.45 
TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 
        6.81       182.33        18.94        17.49        15.16       211.17 
TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 
       52.11        22.42        49.02        75.16        46.06        65.75 
TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 
        1.22        87.45         7.04        11.64       133.74        19.89 
TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 
       16.83        94.52       114.08         7.96         7.73        11.47 
TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 
       62.96       156.23       138.28        14.99       105.21         6.54 
TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 
        8.84       117.40        90.77        30.67        26.30        10.36 
TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 
        7.96        94.32        18.94        44.02        62.01        25.91 
TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 
       60.30        23.31        41.98         2.76         5.10        23.74 
TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 
        3.98        20.68        21.40        16.96        15.48        14.17 
TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW 
       14.24        12.59        15.12         4.96         3.65         5.65 
TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 
       12.20         8.65         2.70        77.98         7.23         5.98 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 TCGA-DU-A7TG 
       11.41        26.76         7.13        21.30       124.50        44.42 
TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 
       50.14        67.46        79.99        57.93       134.27        78.21 
TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 
       95.57       130.78        14.33         0.23         0.20        47.77 
TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 
       17.98        34.36        32.19        18.77        14.93        24.99 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 
       23.97        13.58        15.35        17.88        22.55        20.61 
TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 
       20.09        12.95        13.68        14.24        16.01        20.09 
TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW 
       14.96        22.52        15.52        38.27        10.72         5.26 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ 
       18.71        23.70        14.76        17.82        16.41        15.02 
TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 
       16.44        10.59        28.54        10.78        22.95        43.69 
TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 
        5.23         7.43         5.72         0.13         0.10         6.67 
TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 
        7.82         8.81         0.13         0.03        16.54         3.75 
TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 
       17.42         6.54        24.26         6.38         7.10        75.19 
TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 
       59.18        60.03       154.19         4.01         5.03        29.85 
TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 
       23.18       107.93         4.57        17.29         3.16        22.06 
TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 
       45.99        56.09        57.60         0.23        14.27         0.16 
TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 
       16.24         0.76        44.68         6.05        42.74         0.10 
TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 
       31.69        14.96         0.10         0.10         2.96        17.52 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 
        6.90        14.53        39.48        19.23        39.09         0.23 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
       50.63         0.49        23.61        37.15         0.33         0.13 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 
        3.68         5.33         2.93         1.71        11.28        31.43 
TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 
        1.64        16.24         9.40        63.55         0.10        21.50 
TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 
       33.01        12.23         6.25         0.10         0.46         2.50 
TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 
        3.95         4.70         0.23        29.59         3.88        16.04 
TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB 
       10.49         0.13        14.01         0.07        14.70         0.10 
TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 
        5.33         2.70        13.02         1.81        16.14         5.33 
TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 
        0.10        29.92        13.45         8.32        19.23        40.18 
TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 
       35.90         4.31        21.70        21.60        19.59        17.82 
TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 
       20.35         7.89        20.81        20.71        19.00        42.77 
TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY 
        5.23         4.73         0.23         6.71         1.64         2.37 
TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 
        2.30         4.11         5.88         7.63         0.76         1.28 
TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS 
        5.75         2.53         4.83         7.79         4.11         4.18 
TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
       14.83        14.53        12.23         2.20         3.16         0.59 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC 
        6.31         3.91         4.73         1.91         0.23         5.03 
TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
        3.48         0.07        88.83        94.03        32.65        59.38 
TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY 
       62.17        69.07        18.77        37.84        34.49        31.33 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       21.63        16.37        17.62        23.64        32.61         9.86 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE 
       94.62        83.70         5.85       106.39        62.37        72.59 
TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WO 
       80.12        32.45        84.99        10.88        15.91         7.59 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY 
       15.16        14.07        14.27         7.92        19.63        12.59 
TCGA-S9-A7IZ TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX 
        4.21         8.19         2.04         8.12         3.58         4.04 
TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 
       28.37        13.02       164.38        10.39        99.06        17.42 
TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 
       83.80        31.59        18.71         5.00        49.45        48.33 
TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F 
       49.32        34.78        48.39        12.00        15.09        50.76 
TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M 
       34.36        24.26        19.36        17.49        40.83        16.50 
TCGA-TM-A84O TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-VM-A8C8 TCGA-VM-A8C9 
       29.92         9.44         4.57        12.00        33.07        30.08 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M 
        0.10         7.89        26.79        10.95        27.06         7.04 
TCGA-VW-A7QS TCGA-W9-A837 
       23.21        45.07 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             0.23              0.03 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            75.25            211.17 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            19.13             15.50 
[1] "0.2 - 75.2 (19.1)"  "0.0 - 211.2 (15.5)"
[1] "hr=" "1.1"
D3V2, continuous
D3V3, binary
                   cls
clus                  0   1
  2P GAIN MUTATED     6   5
  2P GAIN WILD-TYPE 184 235
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      6    5
  2P GAIN WILD-TYPE  184  235
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE               6               184
  MALE                 5               235
[1] 2 2
[1] FALSE
D3V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  2P GAIN MUTATED             5                1                 5
  2P GAIN WILD-TYPE         154              106               159
D3V5, multiclass
                   clus
vv                  2P GAIN MUTATED 2P GAIN WILD-TYPE
  ASTROCYTOMA                     5               154
  OLIGOASTROCYTOMA                1               106
  OLIGODENDROGLIOMA               5               159
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V6, binary
                   cls
clus                  0   1
  2P GAIN MUTATED     2   9
  2P GAIN WILD-TYPE  87 332
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      2    9
  2P GAIN WILD-TYPE   87  332
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  NO                2                87
  YES               9               332
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2P GAIN MUTATED                                  0     0
  2P GAIN WILD-TYPE                                1     6
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2P GAIN MUTATED                           0    10
  2P GAIN WILD-TYPE                        14   390
D3V7, multiclass
                                  clus
vv                                 2P GAIN MUTATED 2P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 6
  BLACK OR AFRICAN AMERICAN                      0                14
  WHITE                                         10               390
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V8, binary
                   cls
clus                  0   1
  2P GAIN MUTATED     1   9
  2P GAIN WILD-TYPE  15 378
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      1    9
  2P GAIN WILD-TYPE   15  378
                        clus
vv                       2P GAIN MUTATED 2P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                15
  NOT HISPANIC OR LATINO               9               378
[1] 2 2
[1] FALSE

Clustering(4) Variable = 2Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                 0   1
  2Q GAIN MUTATED     9   1
  2Q GAIN WILD-TYPE 343  74
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               10               417 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                1                74 
$`2Q GAIN MUTATED`
TCGA-DB-5274 TCGA-DH-A7UR TCGA-DU-8165 TCGA-E1-5304 TCGA-HT-8564 TCGA-HT-A4DS 
       75.25        54.25        19.13        41.13        15.72         0.23 
TCGA-S9-A6WM TCGA-S9-A7J0 TCGA-TM-A84Q TCGA-VM-A8CA 
       19.86         9.37        18.90        13.51 

$`2Q GAIN WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5275 TCGA-DB-5276 
        7.40         6.61       122.73        81.96        47.93        72.92 
TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 
       46.65        50.17        44.52        36.56        78.28        30.08 
TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF 
       10.29        12.72        27.62        27.02        18.84        18.38 
TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q 
       72.95        12.59        11.01        18.84        16.80         5.98 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X 
       16.08        15.42        27.81        14.73        13.64        10.92 
TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 
        7.40         6.44        10.29        30.74         3.81        19.96 
TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B 
       31.82        30.31        14.40         8.02        30.21        42.05 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU 
       27.81        17.19        17.19        10.22         6.58         3.45 
TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 
        6.21        18.02        14.56        17.46         6.74        13.38 
TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 
        8.45         6.81       182.33        18.94        17.49        15.16 
TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 
      211.17        52.11        22.42        49.02        75.16        46.06 
TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 
       65.75         1.22        87.45         7.04        11.64       133.74 
TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 
       19.89        16.83        94.52       114.08         7.96         7.73 
TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 
       11.47        62.96       156.23       138.28        14.99       105.21 
TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 
        6.54         8.84       117.40        90.77        30.67        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 
       10.36         7.96        94.32        18.94        44.02        62.01 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 
       25.91        60.30        23.31        41.98         2.76         5.10 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-8167 
       23.74         3.98        20.68        21.40        16.96        15.48 
TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU 
       14.17        14.24        12.59        15.12         4.96         3.65 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
        5.65        12.20         8.65         2.70        77.98         7.23 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 
        5.98        11.41        26.76         7.13        21.30       124.50 
TCGA-DU-A7TG TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 
       44.42        50.14        67.46        79.99        57.93       134.27 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 
       78.21        95.57       130.78        14.33         0.23         0.20 
TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 
       47.77        17.98        34.36        32.19        18.77        14.93 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 
       24.99        23.97        13.58        15.35        17.88        22.55 
TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 
       20.61        20.09        12.95        13.68        14.24        16.01 
TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU 
       20.09        14.96        22.52        15.52        38.27        10.72 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
        5.26        18.71        23.70        14.76        17.82        16.41 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 
       15.02        16.44        10.59        28.54        10.78        22.95 
TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 
       43.69         5.23         7.43         5.72         0.13         0.10 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 
        6.67         7.82         8.81         0.13         0.03        16.54 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 
        3.75        17.42         6.54        24.26         6.38         7.10 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
       75.19        59.18        60.03       154.19         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 
       29.85        23.18       107.93         4.57        17.29         3.16 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
       22.06        45.99        56.09        57.60         0.23        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 
        0.16        16.24         0.76        44.68         6.05        42.74 
TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 
        0.10        31.69        14.96         0.10         0.10         2.96 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 
       17.52         6.90        14.53        39.48        19.23        39.09 
TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 
        0.23        50.63         0.49        23.61        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 
        0.13         3.68         5.33         2.93         1.71        11.28 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 
       31.43         1.64        16.24         9.40        63.55         0.10 
TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 
       21.50        33.01        12.23         6.25         0.10         0.46 
TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 
        2.50         3.95         4.70         0.23        29.59         3.88 
TCGA-HT-8563 TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA 
       16.04        10.49         0.13        14.01         0.07        14.70 
TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 
        0.10         5.33         2.70        13.02         1.81        16.14 
TCGA-HT-A618 TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 
        5.33         0.10        29.92        13.45         8.32        19.23 
TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 
       40.18        35.90         4.31        21.70        21.60        19.59 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 
       17.82        20.35         7.89        20.81        20.71        19.00 
TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX 
       42.77         5.23         4.73         0.23         6.71         1.64 
TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 
        2.37         2.30         4.11         5.88         7.63         0.76 
TCGA-P5-A5F6 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z 
        1.28         5.75         2.53         4.83         7.79         4.11 
TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ 
        4.18        14.83        14.53        12.23         2.20         3.16 
TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA 
        0.59         6.31         3.91         4.73         1.91         0.23 
TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO 
        5.03         3.48         0.07        88.83        94.03        32.65 
TCGA-R8-A73M TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX 
       59.38        62.17        69.07        18.77        37.84        34.49 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       31.33        21.63        16.37        17.62        23.64        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
        9.86        94.62        83.70         5.85       106.39        62.37 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN 
       72.59        80.12        32.45        84.99        10.88        15.91 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX 
        7.59        15.16        14.07        14.27         7.92        19.63 
TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW 
       12.59         4.21         8.19         2.04         8.12         3.58 
TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 
        4.04        28.37        13.02       164.38        10.39        99.06 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 
       17.42        83.80        31.59        18.71         5.00        49.45 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
       48.33        49.32        34.78        48.39        12.00        15.09 
TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L 
       50.76        34.36        24.26        19.36        17.49        40.83 
TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-VM-A8C8 
       16.50        29.92         9.44         4.57        12.00        33.07 
TCGA-VM-A8C9 TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 
       30.08         0.10         7.89        26.79        10.95        27.06 
TCGA-VV-A86M TCGA-VW-A7QS TCGA-W9-A837 
        7.04        23.21        45.07 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             0.23              0.03 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            75.25            211.17 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
           19.015            15.520 
[1] "0.2 - 75.2 (19.0)"  "0.0 - 211.2 (15.5)"
[1] "hr=" "1.7"
D4V2, continuous
D4V3, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED     6   4
  2Q GAIN WILD-TYPE 184 236
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      6    4
  2Q GAIN WILD-TYPE  184  236
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE               6               184
  MALE                 4               236
[1] 2 2
[1] FALSE
D4V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  2Q GAIN MUTATED             5                1                 4
  2Q GAIN WILD-TYPE         154              106               160
D4V5, multiclass
                   clus
vv                  2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  ASTROCYTOMA                     5               154
  OLIGOASTROCYTOMA                1               106
  OLIGODENDROGLIOMA               4               160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V6, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED     2   8
  2Q GAIN WILD-TYPE  87 333
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      2    8
  2Q GAIN WILD-TYPE   87  333
     clus
vv    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  NO                2                87
  YES               8               333
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2Q GAIN MUTATED                                  0     0
  2Q GAIN WILD-TYPE                                1     6
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2Q GAIN MUTATED                           0     9
  2Q GAIN WILD-TYPE                        14   391
D4V7, multiclass
                                  clus
vv                                 2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 6
  BLACK OR AFRICAN AMERICAN                      0                14
  WHITE                                          9               391
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V8, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED     1   8
  2Q GAIN WILD-TYPE  15 379
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      1    8
  2Q GAIN WILD-TYPE   15  379
                        clus
vv                       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                15
  NOT HISPANIC OR LATINO               8               379
[1] 2 2
[1] FALSE

Clustering(5) Variable = 3P GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                 0   1
  3P GAIN MUTATED     7   4
  3P GAIN WILD-TYPE 345  71
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               11               416 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                4                71 
$`3P GAIN MUTATED`
TCGA-CS-6668 TCGA-DU-6400 TCGA-DU-7013 TCGA-DU-8158 TCGA-E1-5304 TCGA-FG-5962 
        8.02         1.22         8.84         5.10        41.13        47.77 
TCGA-HT-7606 TCGA-HT-A4DS TCGA-P5-A5EZ TCGA-S9-A6WM TCGA-S9-A6WO 
       17.29         0.23         2.30        19.86         7.59 

$`3P GAIN WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6669 
       23.84        17.95        12.43         8.48         7.56         7.40 
TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 
        6.61       122.73        81.96        75.25        47.93        72.92 
TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 
       46.65        50.17        44.52        36.56        78.28        30.08 
TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF 
       10.29        12.72        27.62        27.02        18.84        18.38 
TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q 
       72.95        12.59        11.01        18.84        16.80         5.98 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X 
       16.08        15.42        27.81        14.73        13.64        10.92 
TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 
        7.40         6.44        10.29        30.74         3.81        19.96 
TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B 
       31.82        30.31        14.40         8.02        30.21        42.05 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT 
       27.81        17.19        17.19        54.25        10.22         6.58 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
        3.45         6.21        18.02        14.56        17.46         6.74 
TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 
       13.38         8.45         6.81       182.33        18.94        17.49 
TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       15.16       211.17        52.11        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 
       46.06        65.75        87.45         7.04        11.64       133.74 
TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 
       19.89        16.83        94.52       114.08         7.96         7.73 
TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 
       11.47        62.96       156.23       138.28        14.99       105.21 
TCGA-DU-7012 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 
        6.54       117.40        90.77        30.67        26.30        10.36 
TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 
        7.96        94.32        18.94        44.02        62.01        25.91 
TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8161 TCGA-DU-8162 
       60.30        23.31        41.98         2.76        23.74         3.98 
TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 
       20.68        21.40        19.13        16.96        15.48        14.17 
TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW 
       14.24        12.59        15.12         4.96         3.65         5.65 
TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 
       12.20         8.65         2.70        77.98         7.23         5.98 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 TCGA-DU-A7TG 
       11.41        26.76         7.13        21.30       124.50        44.42 
TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 
       50.14        67.46        79.99        57.93       134.27        78.21 
TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5963 
       95.57       130.78        14.33         0.23         0.20        17.98 
TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 
       34.36        32.19        18.77        14.93        24.99        23.97 
TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 
       13.58        15.35        17.88        22.55        20.61        20.09 
TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 
       12.95        13.68        14.24        16.01        20.09        14.96 
TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX 
       22.52        15.52        38.27        10.72         5.26        18.71 
TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 
       23.70        14.76        17.82        16.41        15.02        16.44 
TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 
       10.59        28.54        10.78        22.95        43.69         5.23 
TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 
        7.43         5.72         0.13         0.10         6.67         7.82 
TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 
        8.81         0.13         0.03        16.54         3.75        17.42 
TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 
        6.54        24.26         6.38         7.10        75.19        59.18 
TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 
       60.03       154.19         4.01         5.03        29.85        23.18 
TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 
      107.93         4.57         3.16        22.06        45.99        56.09 
TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 
       57.60         0.23        14.27         0.16        16.24         0.76 
TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 
       44.68         6.05        42.74         0.10        31.69        14.96 
TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 
        0.10         0.10         2.96        17.52         6.90        14.53 
TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 
       39.48        19.23        39.09         0.23        50.63         0.49 
TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 
       23.61        37.15         0.33         0.13         3.68         5.33 
TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 
        2.93         1.71        11.28        31.43         1.64        16.24 
TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 
        9.40        63.55         0.10        21.50        33.01        12.23 
TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 
        6.25         0.10         0.46         2.50         3.95         4.70 
TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DV 
        0.23        29.59         3.88        16.04        15.72        10.49 
TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC 
        0.13        14.01         0.07        14.70         0.10         5.33 
TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A74O 
        2.70        13.02         1.81        16.14         5.33         0.10 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 
       29.92        13.45         8.32        19.23        40.18        35.90 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
        4.31        21.70        21.60        19.59        17.82        20.35 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X 
        7.89        20.81        20.71        19.00        42.77         5.23 
TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5F0 
        4.73         0.23         6.71         1.64         2.37         4.11 
TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-QH-A65R TCGA-QH-A65S 
        5.88         7.63         0.76         1.28         5.75         2.53 
TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV 
        4.83         7.79         4.11         4.18        14.83        14.53 
TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 
       12.23         2.20         3.16         0.59         6.31         3.91 
TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 
        4.73         1.91         0.23         5.03         3.48         0.07 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TS TCGA-S9-A6TU 
       88.83        94.03        32.65        59.38        62.17        69.07 
TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 
       18.77        37.84        34.49        31.33        21.63        16.37 
TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
       17.62        23.64        32.61         9.86        94.62        83.70 
TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH 
        5.85       106.39        62.37        72.59        80.12        32.45 
TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ 
       84.99        10.88        15.91        15.16        14.07        14.27 
TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 
        7.92        19.63        12.59         4.21         9.37         8.19 
TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ 
        2.04         8.12         3.58         4.04        28.37        13.02 
TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 
      164.38        10.39        99.06        17.42        83.80        31.59 
TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA 
       18.71         5.00        49.45        48.33        49.32        34.78 
TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H 
       48.39        12.00        15.09        50.76        34.36        24.26 
TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q 
       19.36        17.49        40.83        16.50        29.92        18.90 
TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA 
        9.44         4.57        12.00        33.07        30.08        13.51 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M 
        0.10         7.89        26.79        10.95        27.06         7.04 
TCGA-VW-A7QS TCGA-W9-A837 
       23.21        45.07 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             0.23              0.03 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            47.77            211.17 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            8.020            16.025 
[1] "0.2 - 47.8 (8.0)"   "0.0 - 211.2 (16.0)"
[1] "hr=" "4.5"
D5V2, continuous
D5V3, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     6   5
  3P GAIN WILD-TYPE 184 235
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      6    5
  3P GAIN WILD-TYPE  184  235
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE               6               184
  MALE                 5               235
[1] 2 2
[1] FALSE
D5V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  3P GAIN MUTATED             8                0                 3
  3P GAIN WILD-TYPE         151              107               161
D5V5, multiclass
                   clus
vv                  3P GAIN MUTATED 3P GAIN WILD-TYPE
  ASTROCYTOMA                     8               151
  OLIGOASTROCYTOMA                0               107
  OLIGODENDROGLIOMA               3               161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V6, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     3   8
  3P GAIN WILD-TYPE  86 333
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      3    8
  3P GAIN WILD-TYPE   86  333
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  NO                3                86
  YES               8               333
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3P GAIN MUTATED                                  0     0
  3P GAIN WILD-TYPE                                1     6
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3P GAIN MUTATED                           0    11
  3P GAIN WILD-TYPE                        14   389
D5V7, multiclass
                                  clus
vv                                 3P GAIN MUTATED 3P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 6
  BLACK OR AFRICAN AMERICAN                      0                14
  WHITE                                         11               389
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V8, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     0  11
  3P GAIN WILD-TYPE  16 376
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      0   11
  3P GAIN WILD-TYPE   16  376
                        clus
vv                       3P GAIN MUTATED 3P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                16
  NOT HISPANIC OR LATINO              11               376
[1] 2 2
[1] FALSE

Clustering(6) Variable = 3Q GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                 0   1
  3Q GAIN MUTATED     4   4
  3Q GAIN WILD-TYPE 348  71
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                8               419 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                4                71 
$`3Q GAIN MUTATED`
TCGA-DU-6400 TCGA-DU-7013 TCGA-DU-8158 TCGA-E1-5304 TCGA-FG-5962 TCGA-HT-7606 
        1.22         8.84         5.10        41.13        47.77        17.29 
TCGA-HT-A4DS TCGA-S9-A6WM 
        0.23        19.86 

$`3Q GAIN WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        46.65        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       30.08        10.29        12.72        27.62        27.02        18.84 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       18.38        72.95        12.59        11.01        18.84        16.80 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        16.08        15.42        27.81        14.73        13.64 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       10.92         7.40         6.44        10.29        30.74         3.81 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       42.05        27.81        17.19        17.19        54.25        10.22 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
        6.58         3.45         6.21        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
        6.74        13.38         8.45         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 
       17.49        15.16       211.17        52.11        22.42        49.02 
TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       75.16        46.06        65.75        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 
      133.74        19.89        16.83        94.52       114.08         7.96 
TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 
        7.73        11.47        62.96       156.23       138.28        14.99 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 
      105.21         6.54       117.40        90.77        30.67        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 
       10.36         7.96        94.32        18.94        44.02        62.01 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8161 
       25.91        60.30        23.31        41.98         2.76        23.74 
TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 
        3.98        20.68        21.40        19.13        16.96        15.48 
TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU 
       14.17        14.24        12.59        15.12         4.96         3.65 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
        5.65        12.20         8.65         2.70        77.98         7.23 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 
        5.98        11.41        26.76         7.13        21.30       124.50 
TCGA-DU-A7TG TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 
       44.42        50.14        67.46        79.99        57.93       134.27 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 
       78.21        95.57       130.78        14.33         0.23         0.20 
TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 
       17.98        34.36        32.19        18.77        14.93        24.99 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 
       23.97        13.58        15.35        17.88        22.55        20.61 
TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 
       20.09        12.95        13.68        14.24        16.01        20.09 
TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW 
       14.96        22.52        15.52        38.27        10.72         5.26 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ 
       18.71        23.70        14.76        17.82        16.41        15.02 
TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 
       16.44        10.59        28.54        10.78        22.95        43.69 
TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 
        5.23         7.43         5.72         0.13         0.10         6.67 
TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 
        7.82         8.81         0.13         0.03        16.54         3.75 
TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 
       17.42         6.54        24.26         6.38         7.10        75.19 
TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 
       59.18        60.03       154.19         4.01         5.03        29.85 
TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 
       23.18       107.93         4.57         3.16        22.06        45.99 
TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 
       56.09        57.60         0.23        14.27         0.16        16.24 
TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 
        0.76        44.68         6.05        42.74         0.10        31.69 
TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 
       14.96         0.10         0.10         2.96        17.52         6.90 
TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 
       14.53        39.48        19.23        39.09         0.23        50.63 
TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 
        0.49        23.61        37.15         0.33         0.13         3.68 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 
        5.33         2.93         1.71        11.28        31.43         1.64 
TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 
       16.24         9.40        63.55         0.10        21.50        33.01 
TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 
       12.23         6.25         0.10         0.46         2.50         3.95 
TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 
        4.70         0.23        29.59         3.88        16.04        15.72 
TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB 
       10.49         0.13        14.01         0.07        14.70         0.10 
TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 
        5.33         2.70        13.02         1.81        16.14         5.33 
TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 
        0.10        29.92        13.45         8.32        19.23        40.18 
TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 
       35.90         4.31        21.70        21.60        19.59        17.82 
TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 
       20.35         7.89        20.81        20.71        19.00        42.77 
TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY 
        5.23         4.73         0.23         6.71         1.64         2.37 
TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 
        2.30         4.11         5.88         7.63         0.76         1.28 
TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS 
        5.75         2.53         4.83         7.79         4.11         4.18 
TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
       14.83        14.53        12.23         2.20         3.16         0.59 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC 
        6.31         3.91         4.73         1.91         0.23         5.03 
TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
        3.48         0.07        88.83        94.03        32.65        59.38 
TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY 
       62.17        69.07        18.77        37.84        34.49        31.33 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       21.63        16.37        17.62        23.64        32.61         9.86 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE 
       94.62        83.70         5.85       106.39        62.37        72.59 
TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WO 
       80.12        32.45        84.99        10.88        15.91         7.59 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY 
       15.16        14.07        14.27         7.92        19.63        12.59 
TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW 
        4.21         9.37         8.19         2.04         8.12         3.58 
TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 
        4.04        28.37        13.02       164.38        10.39        99.06 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 
       17.42        83.80        31.59        18.71         5.00        49.45 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
       48.33        49.32        34.78        48.39        12.00        15.09 
TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L 
       50.76        34.36        24.26        19.36        17.49        40.83 
TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T 
       16.50        29.92        18.90         9.44         4.57        12.00 
TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE 
       33.07        30.08        13.51         0.10         7.89        26.79 
TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-W9-A837 
       10.95        27.06         7.04        23.21        45.07 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             0.23              0.03 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            47.77            211.17 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
           13.065            15.910 
[1] "0.2 - 47.8 (13.1)"  "0.0 - 211.2 (15.9)"
[1] "hr=" "5"  
D6V2, continuous
D6V3, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED     5   3
  3Q GAIN WILD-TYPE 185 237
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      5    3
  3Q GAIN WILD-TYPE  185  237
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE               5               185
  MALE                 3               237
[1] 2 2
[1] FALSE
D6V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  3Q GAIN MUTATED             6                0                 2
  3Q GAIN WILD-TYPE         153              107               162
D6V5, multiclass
                   clus
vv                  3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  ASTROCYTOMA                     6               153
  OLIGOASTROCYTOMA                0               107
  OLIGODENDROGLIOMA               2               162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V6, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED     3   5
  3Q GAIN WILD-TYPE  86 336
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      3    5
  3Q GAIN WILD-TYPE   86  336
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  NO                3                86
  YES               5               336
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3Q GAIN MUTATED                                  0     0
  3Q GAIN WILD-TYPE                                1     6
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3Q GAIN MUTATED                           0     8
  3Q GAIN WILD-TYPE                        14   392
D6V7, multiclass
                                  clus
vv                                 3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 6
  BLACK OR AFRICAN AMERICAN                      0                14
  WHITE                                          8               392
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V8, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED     0   8
  3Q GAIN WILD-TYPE  16 379
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      0    8
  3Q GAIN WILD-TYPE   16  379
                        clus
vv                       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                16
  NOT HISPANIC OR LATINO               8               379
[1] 2 2
[1] FALSE

Clustering(7) Variable = 4P GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                 0   1
  4P GAIN MUTATED    11   0
  4P GAIN WILD-TYPE 341  75
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               11               416 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                0                75 
$`4P GAIN MUTATED`
TCGA-CS-4943 TCGA-CS-6665 TCGA-CS-6666 TCGA-DU-A5TS TCGA-DU-A5TT TCGA-FG-A87Q 
       18.15        12.43         8.48        15.12         4.96         5.72 
TCGA-HT-7477 TCGA-HT-7857 TCGA-HT-A5R7 TCGA-S9-A6TU TCGA-S9-A7J0 
       24.26         0.23        14.01        69.07         9.37 

$`4P GAIN WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5393 
        4.70         7.69        43.89        10.62        64.64        40.18 
TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
        0.10        21.01         9.96         6.38        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 
       17.95         7.56         8.02         7.40         6.61       122.73 
TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 
       81.96        75.25        47.93        72.92        46.65        50.17 
TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB 
       44.52        36.56        78.28        30.08        10.29        12.72 
TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH 
       27.62        27.02        18.84        18.38        72.95        12.59 
TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S 
       11.01        18.84        16.80         5.98        16.08        15.42 
TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L 
       27.81        14.73        13.64        10.92         7.40         6.44 
TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 
       10.29        30.74         3.81        19.96        31.82        30.31 
TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F 
       14.40         8.02        30.21        42.05        27.81        17.19 
TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV 
       17.19        54.25        10.22         6.58         3.45         6.21 
TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 
       18.02        14.56        17.46         6.74        13.38         8.45 
TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 
        6.81       182.33        18.94        17.49        15.16       211.17 
TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 
       52.11        22.42        49.02        75.16        46.06        65.75 
TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 
        1.22        87.45         7.04        11.64       133.74        19.89 
TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 
       16.83        94.52       114.08         7.96         7.73        11.47 
TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 
       62.96       156.23       138.28        14.99       105.21         6.54 
TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 
        8.84       117.40        90.77        30.67        26.30        10.36 
TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 
        7.96        94.32        18.94        44.02        62.01        25.91 
TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 
       60.30        23.31        41.98         2.76         5.10        23.74 
TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 
        3.98        20.68        21.40        19.13        16.96        15.48 
TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY 
       14.17        14.24        12.59         3.65         5.65        12.20 
TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K 
        8.65         2.70        77.98         7.23         5.98        11.41 
TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 TCGA-DU-A7TG TCGA-E1-5302 
       26.76         7.13        21.30       124.50        44.42        50.14 
TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 
       67.46        41.13        79.99        57.93       134.27        78.21 
TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 
       95.57       130.78        14.33         0.23         0.20        47.77 
TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 
       17.98        34.36        32.19        18.77        14.93        24.99 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 
       23.97        13.58        15.35        17.88        22.55        20.61 
TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 
       20.09        12.95        13.68        14.24        16.01        20.09 
TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW 
       14.96        22.52        15.52        38.27        10.72         5.26 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ 
       18.71        23.70        14.76        17.82        16.41        15.02 
TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 
       16.44        10.59        28.54        10.78        22.95        43.69 
TCGA-FG-A713 TCGA-FG-A87N TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 
        5.23         7.43         0.13         0.10         6.67         7.82 
TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 
        8.81         0.13         0.03        16.54         3.75        17.42 
TCGA-HT-7476 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 
        6.54         6.38         7.10        75.19        59.18        60.03 
TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 
      154.19         4.01         5.03        29.85        23.18       107.93 
TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 
        4.57        17.29         3.16        22.06        45.99        56.09 
TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 
       57.60         0.23        14.27         0.16        16.24         0.76 
TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 
       44.68         6.05        42.74         0.10        31.69        14.96 
TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 
        0.10         0.10         2.96        17.52         6.90        14.53 
TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 
       39.48        19.23        39.09        50.63         0.49        23.61 
TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 
       37.15         0.33         0.13         3.68         5.33         2.93 
TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 
        1.71        11.28        31.43         1.64        16.24         9.40 
TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 
       63.55         0.10        21.50        33.01        12.23         6.25 
TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 
        0.10         0.46         2.50         3.95         4.70         0.23 
TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV 
       29.59         3.88        16.04        15.72         0.23        10.49 
TCGA-HT-A5R5 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 
        0.13         0.07        14.70         0.10         5.33         2.70 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A74O TCGA-HW-7486 
       13.02         1.81        16.14         5.33         0.10        29.92 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 
       13.45         8.32        19.23        40.18        35.90         4.31 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
       21.70        21.60        19.59        17.82        20.35         7.89 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 
       20.81        20.71        19.00        42.77         5.23         4.73 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 
        0.23         6.71         1.64         2.37         2.30         4.11 
TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-QH-A65R TCGA-QH-A65S 
        5.88         7.63         0.76         1.28         5.75         2.53 
TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV 
        4.83         7.79         4.11         4.18        14.83        14.53 
TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 
       12.23         2.20         3.16         0.59         6.31         3.91 
TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 
        4.73         1.91         0.23         5.03         3.48         0.07 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TS TCGA-S9-A6TV 
       88.83        94.03        32.65        59.38        62.17        18.77 
TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 
       37.84        34.49        31.33        21.63        16.37        17.62 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA 
       23.64        32.61         9.86        94.62        83.70         5.85 
TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI 
      106.39        62.37        72.59        80.12        32.45        84.99 
TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ 
       10.88        19.86        15.91         7.59        15.16        14.07 
TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J1 
       14.27         7.92        19.63        12.59         4.21         8.19 
TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ 
        2.04         8.12         3.58         4.04        28.37        13.02 
TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 
      164.38        10.39        99.06        17.42        83.80        31.59 
TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA 
       18.71         5.00        49.45        48.33        49.32        34.78 
TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H 
       48.39        12.00        15.09        50.76        34.36        24.26 
TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q 
       19.36        17.49        40.83        16.50        29.92        18.90 
TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA 
        9.44         4.57        12.00        33.07        30.08        13.51 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M 
        0.10         7.89        26.79        10.95        27.06         7.04 
TCGA-VW-A7QS TCGA-W9-A837 
       23.21        45.07 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
             0.23              0.03 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            69.07            211.17 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            12.43             16.06 
[1] "0.2 - 69.1 (12.4)"  "0.0 - 211.2 (16.1)"
[1] "hr="     "9200000"
D7V2, continuous
D7V3, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     5   6
  4P GAIN WILD-TYPE 185 234
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      5    6
  4P GAIN WILD-TYPE  185  234
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE               5               185
  MALE                 6               234
[1] 2 2
[1] FALSE
D7V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  4P GAIN MUTATED             8                0                 3
  4P GAIN WILD-TYPE         151              107               161
D7V5, multiclass
                   clus
vv                  4P GAIN MUTATED 4P GAIN WILD-TYPE
  ASTROCYTOMA                     8               151
  OLIGOASTROCYTOMA                0               107
  OLIGODENDROGLIOMA               3               161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V6, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     1  10
  4P GAIN WILD-TYPE  88 331
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      1   10
  4P GAIN WILD-TYPE   88  331
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  NO                1                88
  YES              10               331
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4P GAIN MUTATED                                  0     0
  4P GAIN WILD-TYPE                                1     6
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4P GAIN MUTATED                           1    10
  4P GAIN WILD-TYPE                        13   390
D7V7, multiclass
                                  clus
vv                                 4P GAIN MUTATED 4P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 6
  BLACK OR AFRICAN AMERICAN                      1                13
  WHITE                                         10               390
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V8, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     0  10
  4P GAIN WILD-TYPE  16 377
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      0   10
  4P GAIN WILD-TYPE   16  377
                        clus
vv                       4P GAIN MUTATED 4P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                16
  NOT HISPANIC OR LATINO              10               377
[1] 2 2
[1] FALSE

Clustering(8) Variable = 4Q GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                 0   1
  4Q GAIN MUTATED     4   0
  4Q GAIN WILD-TYPE 348  75
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                4               423 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                0                75 
$`4Q GAIN MUTATED`
TCGA-DU-A5TT TCGA-HT-7477 TCGA-HT-7857 TCGA-HT-A5R7 
        4.96        24.26         0.23        14.01 

$`4Q GAIN WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        46.65        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       30.08        10.29        12.72        27.62        27.02        18.84 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       18.38        72.95        12.59        11.01        18.84        16.80 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        16.08        15.42        27.81        14.73        13.64 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       10.92         7.40         6.44        10.29        30.74         3.81 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       42.05        27.81        17.19        17.19        54.25        10.22 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
        6.58         3.45         6.21        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
        6.74        13.38         8.45         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 
       17.49        15.16       211.17        52.11        22.42        49.02 
TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 
       75.16        46.06        65.75         1.22        87.45         7.04 
TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 
       11.64       133.74        19.89        16.83        94.52       114.08 
TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 
        7.96         7.73        11.47        62.96       156.23       138.28 
TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 
       14.99       105.21         6.54         8.84       117.40        90.77 
TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 
       30.67        26.30        10.36         7.96        94.32        18.94 
TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 
       44.02        62.01        25.91        60.30        23.31        41.98 
TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 
        2.76         5.10        23.74         3.98        20.68        21.40 
TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR 
       19.13        16.96        15.48        14.17        14.24        12.59 
TCGA-DU-A5TS TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 
       15.12         3.65         5.65        12.20         8.65         2.70 
TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O 
       77.98         7.23         5.98        11.41        26.76         7.13 
TCGA-DU-A76R TCGA-DU-A7T8 TCGA-DU-A7TG TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 
       21.30       124.50        44.42        50.14        67.46        41.13 
TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 
       79.99        57.93       134.27        78.21        95.57       130.78 
TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 
       14.33         0.23         0.20        47.77        17.98        34.36 
TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 
       32.19        18.77        14.93        24.99        23.97        13.58 
TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 
       15.35        17.88        22.55        20.61        20.09        12.95 
TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 
       13.68        14.24        16.01        20.09        14.96        22.52 
TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY 
       15.52        38.27        10.72         5.26        18.71        23.70 
TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 
       14.76        17.82        16.41        15.02        16.44        10.59 
TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N 
       28.54        10.78        22.95        43.69         5.23         7.43 
TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 
        5.72         0.13         0.10         6.67         7.82         8.81 
TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 
        0.13         0.03        16.54         3.75        17.42         6.54 
TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 
        6.38         7.10        75.19        59.18        60.03       154.19 
TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 
        4.01         5.03        29.85        23.18       107.93         4.57 
TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 
       17.29         3.16        22.06        45.99        56.09        57.60 
TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 
        0.23        14.27         0.16        16.24         0.76        44.68 
TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 
        6.05        42.74         0.10        31.69        14.96         0.10 
TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 
        0.10         2.96        17.52         6.90        14.53        39.48 
TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 
       19.23        39.09        50.63         0.49        23.61        37.15 
TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 
        0.33         0.13         3.68         5.33         2.93         1.71 
TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 
       11.28        31.43         1.64        16.24         9.40        63.55 
TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 
        0.10        21.50        33.01        12.23         6.25         0.10 
TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 
        0.46         2.50         3.95         4.70         0.23        29.59 
TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
        3.88        16.04        15.72         0.23        10.49         0.13 
TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 
        0.07        14.70         0.10         5.33         2.70        13.02 
TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 
        1.81        16.14         5.33         0.10        29.92        13.45 
TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 
        8.32        19.23        40.18        35.90         4.31        21.70 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
       21.60        19.59        17.82        20.35         7.89        20.81 
TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV 
       20.71        19.00        42.77         5.23         4.73         0.23 
TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 
        6.71         1.64         2.37         2.30         4.11         5.88 
TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V 
        7.63         0.76         1.28         5.75         2.53         4.83 
TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CX 
        7.79         4.11         4.18        14.83        14.53        12.23 
TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 
        2.20         3.16         0.59         6.31         3.91         4.73 
TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK 
        1.91         0.23         5.03         3.48         0.07        88.83 
TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV 
       94.03        32.65        59.38        62.17        69.07        18.77 
TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 
       37.84        34.49        31.33        21.63        16.37        17.62 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA 
       23.64        32.61         9.86        94.62        83.70         5.85 
TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI 
      106.39        62.37        72.59        80.12        32.45        84.99 
TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ 
       10.88        19.86        15.91         7.59        15.16        14.07 
TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 
       14.27         7.92        19.63        12.59         4.21         9.37 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY 
        8.19         2.04         8.12         3.58         4.04        28.37 
TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 
       13.02       164.38        10.39        99.06        17.42        83.80 
TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 
       31.59        18.71         5.00        49.45        48.33        49.32 
TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G 
       34.78        48.39        12.00        15.09        50.76        34.36 
TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O 
       24.26        19.36        17.49        40.83        16.50        29.92 
TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-VM-A8C8 TCGA-VM-A8C9 
       18.90         9.44         4.57        12.00        33.07        30.08 
TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 
       13.51         0.10         7.89        26.79        10.95        27.06 
TCGA-VV-A86M TCGA-VW-A7QS TCGA-W9-A837 
        7.04        23.21        45.07 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
             0.23              0.03 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            24.26            211.17 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            9.485            16.010 
[1] "0.2 - 24.3 (9.5)"   "0.0 - 211.2 (16.0)"
[1] "hr="     "3300000"
D8V2, continuous
D8V3, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     2   2
  4Q GAIN WILD-TYPE 188 238
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      2    2
  4Q GAIN WILD-TYPE  188  238
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE               2               188
  MALE                 2               238
[1] 2 2
[1] FALSE
D8V4, continuous
[1] "Remove cluster labels:" "4Q GAIN MUTATED"       
clus
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                2               247 
       TCGA-CS-4938        TCGA-CS-4941        TCGA-CS-4942        TCGA-CS-4943 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CS-4944        TCGA-CS-5390        TCGA-CS-5393        TCGA-CS-5395 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CS-5396        TCGA-CS-5397        TCGA-CS-6186        TCGA-CS-6188 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CS-6290        TCGA-CS-6665        TCGA-CS-6666        TCGA-CS-6667 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CS-6668        TCGA-CS-6669        TCGA-DB-5274        TCGA-DB-A4XE 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DB-A64L        TCGA-DB-A64Q        TCGA-DB-A64R        TCGA-DB-A64S 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DB-A64U        TCGA-DB-A64V        TCGA-DB-A64W        TCGA-DB-A64X 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DB-A75L        TCGA-DB-A75O        TCGA-DH-5140        TCGA-DH-5142 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DH-5143        TCGA-DH-5144        TCGA-DH-A66B        TCGA-DH-A66D 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DH-A66F        TCGA-DH-A66G        TCGA-DH-A7UR        TCGA-DH-A7UU 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DH-A7UV        TCGA-DU-5851        TCGA-DU-5852        TCGA-DU-5853 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DU-5854        TCGA-DU-5855        TCGA-DU-5870        TCGA-DU-5871 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DU-5874        TCGA-DU-6396        TCGA-DU-6403        TCGA-DU-6404 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DU-6405        TCGA-DU-6407        TCGA-DU-6408        TCGA-DU-6410 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DU-7011        TCGA-DU-7013        TCGA-DU-7014        TCGA-DU-7015 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DU-7018        TCGA-DU-7019        TCGA-DU-7294        TCGA-DU-7298 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DU-7299        TCGA-DU-7300        TCGA-DU-7301        TCGA-DU-7302 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DU-7304        TCGA-DU-7306        TCGA-DU-7309        TCGA-DU-8158 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DU-8161        TCGA-DU-8162        TCGA-DU-8163        TCGA-DU-8165 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DU-8167        TCGA-DU-8168        TCGA-DU-A5TP        TCGA-DU-A5TR 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DU-A5TS        TCGA-DU-A5TU        TCGA-DU-A5TW        TCGA-DU-A6S2 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DU-A6S6        TCGA-DU-A6S7        TCGA-DU-A6S8        TCGA-DU-A76R 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DU-A7T8        TCGA-DU-A7TG        TCGA-E1-5302        TCGA-E1-5303 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-E1-5304        TCGA-E1-5305        TCGA-E1-5307        TCGA-E1-5311 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-E1-5318        TCGA-E1-5319        TCGA-E1-5322        TCGA-FG-5963 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-FG-5965        TCGA-FG-6688        TCGA-FG-6689        TCGA-FG-6690 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-FG-6691        TCGA-FG-7636        TCGA-FG-7638        TCGA-FG-8181 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-FG-8185        TCGA-FG-8186        TCGA-FG-8187        TCGA-FG-8188 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-FG-8189        TCGA-FG-A4MT        TCGA-FG-A4MW        TCGA-FG-A4MX 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-FG-A60J        TCGA-FG-A60L        TCGA-FG-A6J1        TCGA-FG-A6J3 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-FG-A711        TCGA-FG-A713        TCGA-FG-A87Q        TCGA-HT-7468 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-HT-7470        TCGA-HT-7475        TCGA-HT-7485        TCGA-HT-7607 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-HT-7609        TCGA-HT-7611        TCGA-HT-7689        TCGA-HT-7692 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-HT-7693        TCGA-HT-7694        TCGA-HT-7854        TCGA-HT-7875 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-HT-7884        TCGA-HT-8564        TCGA-HT-A4DV        TCGA-HT-A5RA 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-HT-A5RC        TCGA-HT-A615        TCGA-HT-A617        TCGA-HT-A618 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-IK-7675        TCGA-KT-A74X        TCGA-KT-A7W1        TCGA-P5-A5EU 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-P5-A5EV        TCGA-P5-A5EW        TCGA-P5-A5EX        TCGA-P5-A5F0 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-P5-A5F2        TCGA-P5-A5F4        TCGA-P5-A5F6        TCGA-QH-A65R 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-QH-A65S        TCGA-QH-A65V        TCGA-QH-A65X        TCGA-QH-A65Z 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-QH-A6CS        TCGA-QH-A6CU        TCGA-QH-A6CV        TCGA-QH-A6CW 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-QH-A6CX        TCGA-QH-A6CY        TCGA-QH-A6CZ        TCGA-QH-A6X3 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-QH-A6X4        TCGA-QH-A6X5        TCGA-QH-A6X8        TCGA-QH-A6X9 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-QH-A6XA        TCGA-QH-A6XC        TCGA-QH-A86X        TCGA-QH-A870 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-S9-A6TS        TCGA-S9-A6TU        TCGA-S9-A6TV        TCGA-S9-A6TW 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-S9-A6TX        TCGA-S9-A6TY        TCGA-S9-A6TZ        TCGA-S9-A6U0 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-S9-A6U1        TCGA-S9-A6U2        TCGA-S9-A6U5        TCGA-S9-A6U6 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-S9-A6U8        TCGA-S9-A6UA        TCGA-S9-A6UB        TCGA-S9-A6WD 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-S9-A6WE        TCGA-S9-A6WG        TCGA-S9-A6WH        TCGA-S9-A6WI 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-S9-A6WL        TCGA-S9-A6WM        TCGA-S9-A6WN        TCGA-S9-A6WO 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-S9-A6WP        TCGA-S9-A6WQ        TCGA-S9-A7IQ        TCGA-S9-A7IS 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-S9-A7IX        TCGA-S9-A7IY        TCGA-S9-A7IZ        TCGA-S9-A7J0 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-S9-A7J1        TCGA-S9-A7J2        TCGA-S9-A7J3        TCGA-S9-A7QW 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-S9-A7QX        TCGA-S9-A7QY        TCGA-S9-A7QZ        TCGA-S9-A7R1 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-S9-A7R2        TCGA-S9-A7R3        TCGA-S9-A7R4        TCGA-S9-A7R7 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-S9-A7R8        TCGA-S9-A89V        TCGA-S9-A89Z        TCGA-TM-A7C3 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-TM-A7C4        TCGA-TM-A7C5        TCGA-TM-A7CA        TCGA-TM-A7CF 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-TM-A84B        TCGA-TM-A84C        TCGA-TM-A84F        TCGA-TM-A84G 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-TM-A84H        TCGA-TM-A84I        TCGA-TM-A84J        TCGA-TM-A84L 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-TM-A84M        TCGA-TM-A84O        TCGA-TM-A84Q        TCGA-TM-A84R 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-TM-A84S        TCGA-TM-A84T        TCGA-VM-A8C8        TCGA-VM-A8CA 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-VM-A8CD        TCGA-VM-A8CE        TCGA-VM-A8CH 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  4Q GAIN MUTATED             3                0                 1
  4Q GAIN WILD-TYPE         156              107               163
D8V5, multiclass
                   clus
vv                  4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  ASTROCYTOMA                     3               156
  OLIGOASTROCYTOMA                0               107
  OLIGODENDROGLIOMA               1               163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V6, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     0   4
  4Q GAIN WILD-TYPE  89 337
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      0    4
  4Q GAIN WILD-TYPE   89  337
     clus
vv    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  NO                0                89
  YES               4               337
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4Q GAIN MUTATED                                  0     0
  4Q GAIN WILD-TYPE                                1     6
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4Q GAIN MUTATED                           0     4
  4Q GAIN WILD-TYPE                        14   396
D8V7, multiclass
                                  clus
vv                                 4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 6
  BLACK OR AFRICAN AMERICAN                      0                14
  WHITE                                          4               396
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V8, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     0   4
  4Q GAIN WILD-TYPE  16 383
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      0    4
  4Q GAIN WILD-TYPE   16  383
                        clus
vv                       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                16
  NOT HISPANIC OR LATINO               4               383
[1] 2 2
[1] FALSE

Clustering(9) Variable = 5P GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                 0   1
  5P GAIN MUTATED     6   2
  5P GAIN WILD-TYPE 346  73
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                8               419 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                2                73 
$`5P GAIN MUTATED`
TCGA-DU-A5TT TCGA-E1-5304 TCGA-HT-7477 TCGA-QH-A65S TCGA-QH-A6CV TCGA-S9-A6TS 
        4.96        41.13        24.26         2.53        14.53        62.17 
TCGA-TM-A7C3 TCGA-VM-A8C9 
       49.45        30.08 

$`5P GAIN WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        46.65        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       30.08        10.29        12.72        27.62        27.02        18.84 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       18.38        72.95        12.59        11.01        18.84        16.80 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        16.08        15.42        27.81        14.73        13.64 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       10.92         7.40         6.44        10.29        30.74         3.81 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       42.05        27.81        17.19        17.19        54.25        10.22 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
        6.58         3.45         6.21        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
        6.74        13.38         8.45         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 
       17.49        15.16       211.17        52.11        22.42        49.02 
TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 
       75.16        46.06        65.75         1.22        87.45         7.04 
TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 
       11.64       133.74        19.89        16.83        94.52       114.08 
TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 
        7.96         7.73        11.47        62.96       156.23       138.28 
TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 
       14.99       105.21         6.54         8.84       117.40        90.77 
TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 
       30.67        26.30        10.36         7.96        94.32        18.94 
TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 
       44.02        62.01        25.91        60.30        23.31        41.98 
TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 
        2.76         5.10        23.74         3.98        20.68        21.40 
TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR 
       19.13        16.96        15.48        14.17        14.24        12.59 
TCGA-DU-A5TS TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 
       15.12         3.65         5.65        12.20         8.65         2.70 
TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O 
       77.98         7.23         5.98        11.41        26.76         7.13 
TCGA-DU-A76R TCGA-DU-A7T8 TCGA-DU-A7TG TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5305 
       21.30       124.50        44.42        50.14        67.46        79.99 
TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 
       57.93       134.27        78.21        95.57       130.78        14.33 
TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 
        0.23         0.20        47.77        17.98        34.36        32.19 
TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 
       18.77        14.93        24.99        23.97        13.58        15.35 
TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 
       17.88        22.55        20.61        20.09        12.95        13.68 
TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 
       14.24        16.01        20.09        14.96        22.52        15.52 
TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J 
       38.27        10.72         5.26        18.71        23.70        14.76 
TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y 
       17.82        16.41        15.02        16.44        10.59        28.54 
TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q 
       10.78        22.95        43.69         5.23         7.43         5.72 
TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 
        0.13         0.10         6.67         7.82         8.81         0.13 
TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7478 
        0.03        16.54         3.75        17.42         6.54         6.38 
TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 
        7.10        75.19        59.18        60.03       154.19         4.01 
TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 
        5.03        29.85        23.18       107.93         4.57        17.29 
TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 
        3.16        22.06        45.99        56.09        57.60         0.23 
TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 
       14.27         0.16        16.24         0.76        44.68         6.05 
TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 
       42.74         0.10        31.69        14.96         0.10         0.10 
TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 
        2.96        17.52         6.90        14.53        39.48        19.23 
TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 
       39.09         0.23        50.63         0.49        23.61        37.15 
TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 
        0.33         0.13         3.68         5.33         2.93         1.71 
TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 
       11.28        31.43         1.64        16.24         9.40        63.55 
TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 
        0.10        21.50        33.01        12.23         6.25         0.10 
TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 
        0.46         2.50         3.95         4.70         0.23        29.59 
TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
        3.88        16.04        15.72         0.23        10.49         0.13 
TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 
       14.01         0.07        14.70         0.10         5.33         2.70 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A74O TCGA-HW-7486 
       13.02         1.81        16.14         5.33         0.10        29.92 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 
       13.45         8.32        19.23        40.18        35.90         4.31 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
       21.70        21.60        19.59        17.82        20.35         7.89 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 
       20.81        20.71        19.00        42.77         5.23         4.73 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 
        0.23         6.71         1.64         2.37         2.30         4.11 
TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-QH-A65R TCGA-QH-A65V 
        5.88         7.63         0.76         1.28         5.75         4.83 
TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CX TCGA-QH-A6CY 
        7.79         4.11         4.18        14.83        12.23         2.20 
TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 
        3.16         0.59         6.31         3.91         4.73         1.91 
TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML 
        0.23         5.03         3.48         0.07        88.83        94.03 
TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX 
       32.65        59.38        69.07        18.77        37.84        34.49 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       31.33        21.63        16.37        17.62        23.64        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
        9.86        94.62        83.70         5.85       106.39        62.37 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM 
       72.59        80.12        32.45        84.99        10.88        19.86 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
       15.91         7.59        15.16        14.07        14.27         7.92 
TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 
       19.63        12.59         4.21         9.37         8.19         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 
        8.12         3.58         4.04        28.37        13.02       164.38 
TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V 
       10.39        99.06        17.42        83.80        31.59        18.71 
TCGA-S9-A89Z TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B 
        5.00        48.33        49.32        34.78        48.39        12.00 
TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J 
       15.09        50.76        34.36        24.26        19.36        17.49 
TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S 
       40.83        16.50        29.92        18.90         9.44         4.57 
TCGA-TM-A84T TCGA-VM-A8C8 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE 
       12.00        33.07        13.51         0.10         7.89        26.79 
TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-W9-A837 
       10.95        27.06         7.04        23.21        45.07 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             2.53              0.03 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            62.17            211.17 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            27.17             15.72 
[1] "2.5 - 62.2 (27.2)"  "0.0 - 211.2 (15.7)"
[1] "hr=" "1.4"
D9V2, continuous
D9V3, binary
                   cls
clus                  0   1
  5P GAIN MUTATED     4   4
  5P GAIN WILD-TYPE 186 236
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      4    4
  5P GAIN WILD-TYPE  186  236
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE               4               186
  MALE                 4               236
[1] 2 2
[1] FALSE
D9V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  5P GAIN MUTATED             5                2                 1
  5P GAIN WILD-TYPE         154              105               163
D9V5, multiclass
                   clus
vv                  5P GAIN MUTATED 5P GAIN WILD-TYPE
  ASTROCYTOMA                     5               154
  OLIGOASTROCYTOMA                2               105
  OLIGODENDROGLIOMA               1               163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V6, binary
                   cls
clus                  0   1
  5P GAIN MUTATED     1   7
  5P GAIN WILD-TYPE  88 334
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      1    7
  5P GAIN WILD-TYPE   88  334
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  NO                1                88
  YES               7               334
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5P GAIN MUTATED                                  0     1
  5P GAIN WILD-TYPE                                1     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5P GAIN MUTATED                           0     6
  5P GAIN WILD-TYPE                        14   394
D9V7, multiclass
                                  clus
vv                                 5P GAIN MUTATED 5P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 5
  BLACK OR AFRICAN AMERICAN                      0                14
  WHITE                                          6               394
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V8, binary
                   cls
clus                  0   1
  5P GAIN MUTATED     0   7
  5P GAIN WILD-TYPE  16 380
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      0    7
  5P GAIN WILD-TYPE   16  380
                        clus
vv                       5P GAIN MUTATED 5P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                16
  NOT HISPANIC OR LATINO               7               380
[1] 2 2
[1] FALSE

Clustering(10) Variable = 5Q GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                 0   1
  5Q GAIN MUTATED     5   0
  5Q GAIN WILD-TYPE 347  75
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                5               422 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                0                75 
$`5Q GAIN MUTATED`
TCGA-DU-A5TT TCGA-QH-A65S TCGA-QH-A6CV TCGA-TM-A7C3 TCGA-VM-A8C9 
        4.96         2.53        14.53        49.45        30.08 

$`5Q GAIN WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        46.65        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       30.08        10.29        12.72        27.62        27.02        18.84 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       18.38        72.95        12.59        11.01        18.84        16.80 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        16.08        15.42        27.81        14.73        13.64 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       10.92         7.40         6.44        10.29        30.74         3.81 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       42.05        27.81        17.19        17.19        54.25        10.22 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
        6.58         3.45         6.21        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
        6.74        13.38         8.45         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 
       17.49        15.16       211.17        52.11        22.42        49.02 
TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 
       75.16        46.06        65.75         1.22        87.45         7.04 
TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 
       11.64       133.74        19.89        16.83        94.52       114.08 
TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 
        7.96         7.73        11.47        62.96       156.23       138.28 
TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 
       14.99       105.21         6.54         8.84       117.40        90.77 
TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 
       30.67        26.30        10.36         7.96        94.32        18.94 
TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 
       44.02        62.01        25.91        60.30        23.31        41.98 
TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 
        2.76         5.10        23.74         3.98        20.68        21.40 
TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR 
       19.13        16.96        15.48        14.17        14.24        12.59 
TCGA-DU-A5TS TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 
       15.12         3.65         5.65        12.20         8.65         2.70 
TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O 
       77.98         7.23         5.98        11.41        26.76         7.13 
TCGA-DU-A76R TCGA-DU-A7T8 TCGA-DU-A7TG TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 
       21.30       124.50        44.42        50.14        67.46        41.13 
TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 
       79.99        57.93       134.27        78.21        95.57       130.78 
TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 
       14.33         0.23         0.20        47.77        17.98        34.36 
TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 
       32.19        18.77        14.93        24.99        23.97        13.58 
TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 
       15.35        17.88        22.55        20.61        20.09        12.95 
TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 
       13.68        14.24        16.01        20.09        14.96        22.52 
TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY 
       15.52        38.27        10.72         5.26        18.71        23.70 
TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 
       14.76        17.82        16.41        15.02        16.44        10.59 
TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N 
       28.54        10.78        22.95        43.69         5.23         7.43 
TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 
        5.72         0.13         0.10         6.67         7.82         8.81 
TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 
        0.13         0.03        16.54         3.75        17.42         6.54 
TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 
       24.26         6.38         7.10        75.19        59.18        60.03 
TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 
      154.19         4.01         5.03        29.85        23.18       107.93 
TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 
        4.57        17.29         3.16        22.06        45.99        56.09 
TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 
       57.60         0.23        14.27         0.16        16.24         0.76 
TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 
       44.68         6.05        42.74         0.10        31.69        14.96 
TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 
        0.10         0.10         2.96        17.52         6.90        14.53 
TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 
       39.48        19.23        39.09         0.23        50.63         0.49 
TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 
       23.61        37.15         0.33         0.13         3.68         5.33 
TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 
        2.93         1.71        11.28        31.43         1.64        16.24 
TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 
        9.40        63.55         0.10        21.50        33.01        12.23 
TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 
        6.25         0.10         0.46         2.50         3.95         4.70 
TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS 
        0.23        29.59         3.88        16.04        15.72         0.23 
TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB 
       10.49         0.13        14.01         0.07        14.70         0.10 
TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 
        5.33         2.70        13.02         1.81        16.14         5.33 
TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 
        0.10        29.92        13.45         8.32        19.23        40.18 
TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 
       35.90         4.31        21.70        21.60        19.59        17.82 
TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 
       20.35         7.89        20.81        20.71        19.00        42.77 
TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY 
        5.23         4.73         0.23         6.71         1.64         2.37 
TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 
        2.30         4.11         5.88         7.63         0.76         1.28 
TCGA-QH-A65R TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU 
        5.75         4.83         7.79         4.11         4.18        14.83 
TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 
       12.23         2.20         3.16         0.59         6.31         3.91 
TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 
        4.73         1.91         0.23         5.03         3.48         0.07 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TS TCGA-S9-A6TU 
       88.83        94.03        32.65        59.38        62.17        69.07 
TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 
       18.77        37.84        34.49        31.33        21.63        16.37 
TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
       17.62        23.64        32.61         9.86        94.62        83.70 
TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH 
        5.85       106.39        62.37        72.59        80.12        32.45 
TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP 
       84.99        10.88        19.86        15.91         7.59        15.16 
TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ 
       14.07        14.27         7.92        19.63        12.59         4.21 
TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX 
        9.37         8.19         2.04         8.12         3.58         4.04 
TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 
       28.37        13.02       164.38        10.39        99.06        17.42 
TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C4 TCGA-TM-A7C5 
       83.80        31.59        18.71         5.00        48.33        49.32 
TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G 
       34.78        48.39        12.00        15.09        50.76        34.36 
TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O 
       24.26        19.36        17.49        40.83        16.50        29.92 
TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-VM-A8C8 TCGA-VM-A8CA 
       18.90         9.44         4.57        12.00        33.07        13.51 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M 
        0.10         7.89        26.79        10.95        27.06         7.04 
TCGA-VW-A7QS TCGA-W9-A837 
       23.21        45.07 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             2.53              0.03 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            49.45            211.17 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            14.53             15.96 
[1] "2.5 - 49.5 (14.5)"  "0.0 - 211.2 (16.0)"
[1] "hr="     "3300000"
D10V2, continuous
D10V3, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     3   2
  5Q GAIN WILD-TYPE 187 238
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      3    2
  5Q GAIN WILD-TYPE  187  238
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE               3               187
  MALE                 2               238
[1] 2 2
[1] FALSE
D10V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  5Q GAIN MUTATED             2                2                 1
  5Q GAIN WILD-TYPE         157              105               163
D10V5, multiclass
                   clus
vv                  5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  ASTROCYTOMA                     2               157
  OLIGOASTROCYTOMA                2               105
  OLIGODENDROGLIOMA               1               163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V6, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     0   5
  5Q GAIN WILD-TYPE  89 336
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      0    5
  5Q GAIN WILD-TYPE   89  336
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  NO                0                89
  YES               5               336
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5Q GAIN MUTATED                                  0     1
  5Q GAIN WILD-TYPE                                1     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5Q GAIN MUTATED                           0     3
  5Q GAIN WILD-TYPE                        14   397
D10V7, multiclass
                                  clus
vv                                 5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 5
  BLACK OR AFRICAN AMERICAN                      0                14
  WHITE                                          3               397
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V8, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     0   4
  5Q GAIN WILD-TYPE  16 383
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      0    4
  5Q GAIN WILD-TYPE   16  383
                        clus
vv                       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                16
  NOT HISPANIC OR LATINO               4               383
[1] 2 2
[1] FALSE

Clustering(11) Variable = 6P GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                 0   1
  6P GAIN MUTATED     6   1
  6P GAIN WILD-TYPE 346  74
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                7               420 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                1                74 
$`6P GAIN MUTATED`
TCGA-CS-6665 TCGA-DU-6408 TCGA-DU-6542 TCGA-FG-A6J3 TCGA-HT-7606 TCGA-HT-8563 
       12.43       114.08         7.73        10.59        17.29        16.04 
TCGA-P5-A5EZ 
        2.30 

$`6P GAIN WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 
       23.84        17.95         8.48         7.56         8.02         7.40 
TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 
        6.61       122.73        81.96        75.25        47.93        72.92 
TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 
       46.65        50.17        44.52        36.56        78.28        30.08 
TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF 
       10.29        12.72        27.62        27.02        18.84        18.38 
TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q 
       72.95        12.59        11.01        18.84        16.80         5.98 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X 
       16.08        15.42        27.81        14.73        13.64        10.92 
TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 
        7.40         6.44        10.29        30.74         3.81        19.96 
TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B 
       31.82        30.31        14.40         8.02        30.21        42.05 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT 
       27.81        17.19        17.19        54.25        10.22         6.58 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
        3.45         6.21        18.02        14.56        17.46         6.74 
TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 
       13.38         8.45         6.81       182.33        18.94        17.49 
TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       15.16       211.17        52.11        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       46.06        65.75         1.22        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6410 TCGA-DU-7006 
      133.74        19.89        16.83        94.52         7.96        11.47 
TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 
       62.96       156.23       138.28        14.99       105.21         6.54 
TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 
        8.84       117.40        90.77        30.67        26.30        10.36 
TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 
        7.96        94.32        18.94        44.02        62.01        25.91 
TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 
       60.30        23.31        41.98         2.76         5.10        23.74 
TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 
        3.98        20.68        21.40        19.13        16.96        15.48 
TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU 
       14.17        14.24        12.59        15.12         4.96         3.65 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
        5.65        12.20         8.65         2.70        77.98         7.23 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 
        5.98        11.41        26.76         7.13        21.30       124.50 
TCGA-DU-A7TG TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 
       44.42        50.14        67.46        41.13        79.99        57.93 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 TCGA-F6-A8O3 
      134.27        78.21        95.57       130.78        14.33         0.23 
TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 
        0.20        47.77        17.98        34.36        32.19        18.77 
TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 
       14.93        24.99        23.97        13.58        15.35        17.88 
TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 
       22.55        20.61        20.09        12.95        13.68        14.24 
TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT 
       16.01        20.09        14.96        22.52        15.52        38.27 
TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K 
       10.72         5.26        18.71        23.70        14.76        17.82 
TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 
       16.41        15.02        16.44        28.54        10.78        22.95 
TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 
       43.69         5.23         7.43         5.72         0.13         0.10 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 
        6.67         7.82         8.81         0.13         0.03        16.54 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 
        3.75        17.42         6.54        24.26         6.38         7.10 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
       75.19        59.18        60.03       154.19         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7607 TCGA-HT-7608 
       29.85        23.18       107.93         4.57         3.16        22.06 
TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 
       45.99        56.09        57.60         0.23        14.27         0.16 
TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 
       16.24         0.76        44.68         6.05        42.74         0.10 
TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 
       31.69        14.96         0.10         0.10         2.96        17.52 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 
        6.90        14.53        39.48        19.23        39.09         0.23 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
       50.63         0.49        23.61        37.15         0.33         0.13 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 
        3.68         5.33         2.93         1.71        11.28        31.43 
TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 
        1.64        16.24         9.40        63.55         0.10        21.50 
TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 
       33.01        12.23         6.25         0.10         0.46         2.50 
TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8564 
        3.95         4.70         0.23        29.59         3.88        15.72 
TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA 
        0.23        10.49         0.13        14.01         0.07        14.70 
TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 
        0.10         5.33         2.70        13.02         1.81        16.14 
TCGA-HT-A618 TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 
        5.33         0.10        29.92        13.45         8.32        19.23 
TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 
       40.18        35.90         4.31        21.70        21.60        19.59 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 
       17.82        20.35         7.89        20.81        20.71        19.00 
TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX 
       42.77         5.23         4.73         0.23         6.71         1.64 
TCGA-P5-A5EY TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 
        2.37         4.11         5.88         7.63         0.76         1.28 
TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS 
        5.75         2.53         4.83         7.79         4.11         4.18 
TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
       14.83        14.53        12.23         2.20         3.16         0.59 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC 
        6.31         3.91         4.73         1.91         0.23         5.03 
TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
        3.48         0.07        88.83        94.03        32.65        59.38 
TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY 
       62.17        69.07        18.77        37.84        34.49        31.33 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       21.63        16.37        17.62        23.64        32.61         9.86 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE 
       94.62        83.70         5.85       106.39        62.37        72.59 
TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN 
       80.12        32.45        84.99        10.88        19.86        15.91 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX 
        7.59        15.16        14.07        14.27         7.92        19.63 
TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       12.59         4.21         9.37         8.19         2.04         8.12 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 
        3.58         4.04        28.37        13.02       164.38        10.39 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z 
       99.06        17.42        83.80        31.59        18.71         5.00 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B 
       49.45        48.33        49.32        34.78        48.39        12.00 
TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J 
       15.09        50.76        34.36        24.26        19.36        17.49 
TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S 
       40.83        16.50        29.92        18.90         9.44         4.57 
TCGA-TM-A84T TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD 
       12.00        33.07        30.08        13.51         0.10         7.89 
TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-W9-A837 
       26.79        10.95        27.06         7.04        23.21        45.07 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             2.30              0.03 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           114.08            211.17 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            12.43             15.96 
[1] "2.3 - 114.1 (12.4)" "0.0 - 211.2 (16.0)"
[1] "hr=" "1.3"
D11V2, continuous
D11V3, binary
                   cls
clus                  0   1
  6P GAIN MUTATED     5   2
  6P GAIN WILD-TYPE 185 238
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      5    2
  6P GAIN WILD-TYPE  185  238
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE               5               185
  MALE                 2               238
[1] 2 2
[1] FALSE
D11V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  6P GAIN MUTATED             5                1                 1
  6P GAIN WILD-TYPE         154              106               163
D11V5, multiclass
                   clus
vv                  6P GAIN MUTATED 6P GAIN WILD-TYPE
  ASTROCYTOMA                     5               154
  OLIGOASTROCYTOMA                1               106
  OLIGODENDROGLIOMA               1               163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V6, binary
                   cls
clus                  0   1
  6P GAIN MUTATED     2   5
  6P GAIN WILD-TYPE  87 336
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      2    5
  6P GAIN WILD-TYPE   87  336
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  NO                2                87
  YES               5               336
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6P GAIN MUTATED                                  0     0
  6P GAIN WILD-TYPE                                1     6
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6P GAIN MUTATED                           0     7
  6P GAIN WILD-TYPE                        14   393
D11V7, multiclass
                                  clus
vv                                 6P GAIN MUTATED 6P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 6
  BLACK OR AFRICAN AMERICAN                      0                14
  WHITE                                          7               393
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V8, binary
                   cls
clus                  0   1
  6P GAIN MUTATED     0   7
  6P GAIN WILD-TYPE  16 380
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      0    7
  6P GAIN WILD-TYPE   16  380
                        clus
vv                       6P GAIN MUTATED 6P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                16
  NOT HISPANIC OR LATINO               7               380
[1] 2 2
[1] FALSE

Clustering(12) Variable = 7P GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                 0   1
  7P GAIN MUTATED    64  32
  7P GAIN WILD-TYPE 288  43
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               96               331 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               32                43 
$`7P GAIN MUTATED`
TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-5393 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 
        7.69        43.89        40.18        21.01         9.96         6.38 
TCGA-CS-6186 TCGA-CS-6665 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5277 TCGA-DB-A4X9 
       17.69        12.43         6.61       122.73        46.65        30.08 
TCGA-DB-A4XE TCGA-DB-A64O TCGA-DB-A75O TCGA-DH-A669 TCGA-DH-A66G TCGA-DH-A7UT 
       18.84        18.84        30.74        30.21        17.19         6.58 
TCGA-DH-A7UV TCGA-DU-5854 TCGA-DU-6392 TCGA-DU-6395 TCGA-DU-6400 TCGA-DU-6402 
        6.21         8.45       211.17        49.02         1.22         7.04 
TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6410 
       11.64       133.74        19.89        16.83        94.52         7.96 
TCGA-DU-7006 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 
       11.47       105.21         6.54         8.84       117.40        90.77 
TCGA-DU-8161 TCGA-DU-8163 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-A5TR TCGA-DU-A5TT 
       23.74        20.68        19.13        16.96        12.59         4.96 
TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76R 
        3.65         5.65        12.20        11.41        26.76        21.30 
TCGA-E1-5304 TCGA-E1-5322 TCGA-FG-5962 TCGA-FG-6688 TCGA-FG-6691 TCGA-FG-6692 
       41.13       130.78        47.77        18.77        23.97        13.58 
TCGA-FG-7634 TCGA-FG-7643 TCGA-FG-8182 TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A70Z 
       15.35        20.09        13.68        10.72         5.26        10.78 
TCGA-FG-A87Q TCGA-HT-7473 TCGA-HT-7477 TCGA-HT-7860 TCGA-HT-7882 TCGA-HT-7884 
        5.72        16.54        24.26         0.49         1.71        11.28 
TCGA-HT-8011 TCGA-HT-8013 TCGA-HT-8104 TCGA-HT-8110 TCGA-HT-8564 TCGA-HT-A4DS 
       16.24        63.55        12.23         4.70        15.72         0.23 
TCGA-HT-A5R5 TCGA-HT-A5R9 TCGA-HT-A5RC TCGA-HT-A617 TCGA-KT-A7W1 TCGA-P5-A5F0 
        0.13         0.07         5.33        16.14         4.73         4.11 
TCGA-QH-A6CS TCGA-QH-A6CV TCGA-QH-A6X9 TCGA-QH-A6XC TCGA-S9-A6TY TCGA-S9-A6U0 
        4.18        14.53         1.91         5.03        31.33        16.37 
TCGA-S9-A6WM TCGA-S9-A7IQ TCGA-S9-A7IX TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7QW 
       19.86        14.27        19.63         4.21         9.37         3.58 
TCGA-S9-A7R2 TCGA-TM-A7C3 TCGA-TM-A7CA TCGA-TM-A84B TCGA-TM-A84H TCGA-TM-A84M 
       10.39        49.45        34.78        12.00        24.26        16.50 

$`7P GAIN WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5394 TCGA-CS-6188 
        4.70        18.15        10.62        64.64         0.10        23.84 
TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-DB-5273 
       17.95         8.48         7.56         8.02         7.40        81.96 
TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 
       75.25        47.93        72.92        50.17        44.52        36.56 
TCGA-DB-5281 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XF 
       78.28        10.29        12.72        27.62        27.02        18.38 
TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R 
       72.95        12.59        11.01        16.80         5.98        16.08 
TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K 
       15.42        27.81        14.73        13.64        10.92         7.40 
TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 
        6.44        10.29         3.81        19.96        31.82        30.31 
TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A7UR 
       14.40         8.02        42.05        27.81        17.19        54.25 
TCGA-DH-A7US TCGA-DH-A7UU TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
       10.22         3.45        18.02        14.56        17.46         6.74 
TCGA-DU-5853 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 
       13.38         6.81       182.33        18.94        17.49        15.16 
TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6401 
       52.11        22.42        75.16        46.06        65.75        87.45 
TCGA-DU-6408 TCGA-DU-6542 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 
      114.08         7.73        62.96       156.23       138.28        14.99 
TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 
       30.67        26.30        10.36         7.96        94.32        18.94 
TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 
       44.02        62.01        25.91        60.30        23.31        41.98 
TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8162 TCGA-DU-8164 TCGA-DU-8167 TCGA-DU-8168 
        2.76         5.10         3.98        21.40        15.48        14.17 
TCGA-DU-A5TP TCGA-DU-A5TS TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
       14.24        15.12         8.65         2.70        77.98         7.23 
TCGA-DU-A6S8 TCGA-DU-A76O TCGA-DU-A7T8 TCGA-DU-A7TG TCGA-E1-5302 TCGA-E1-5303 
        5.98         7.13       124.50        44.42        50.14        67.46 
TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-EZ-7264 
       79.99        57.93       134.27        78.21        95.57        14.33 
TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6689 
        0.23         0.20        17.98        34.36        32.19        14.93 
TCGA-FG-6690 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-8181 TCGA-FG-8185 
       24.99        17.88        22.55        20.61        12.95        14.24 
TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT 
       16.01        20.09        14.96        22.52        15.52        38.27 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ 
       18.71        23.70        14.76        17.82        16.41        15.02 
TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 
       16.44        10.59        28.54        22.95        43.69         5.23 
TCGA-FG-A87N TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 
        7.43         0.13         0.10         6.67         7.82         8.81 
TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7478 
        0.13         0.03         3.75        17.42         6.54         6.38 
TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 
        7.10        75.19        59.18        60.03       154.19         4.01 
TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 
        5.03        29.85        23.18       107.93         4.57        17.29 
TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 
        3.16        22.06        45.99        56.09        57.60         0.23 
TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 
       14.27         0.16        16.24         0.76        44.68         6.05 
TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 
       42.74         0.10        31.69        14.96         0.10         0.10 
TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 
        2.96        17.52         6.90        14.53        39.48        19.23 
TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 
       39.09         0.23        50.63        23.61        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7902 TCGA-HT-8010 
        0.13         3.68         5.33         2.93        31.43         1.64 
TCGA-HT-8012 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8105 TCGA-HT-8106 
        9.40         0.10        21.50        33.01         6.25         0.10 
TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 
        0.46         2.50         3.95         0.23        29.59         3.88 
TCGA-HT-8563 TCGA-HT-A4DV TCGA-HT-A5R7 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A614 
       16.04        10.49        14.01        14.70         0.10         2.70 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A618 TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 
       13.02         1.81         5.33         0.10        29.92        13.45 
TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 
        8.32        19.23        40.18        35.90         4.31        21.70 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
       21.60        19.59        17.82        20.35         7.89        20.81 
TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-P5-A5EV TCGA-P5-A5EW 
       20.71        19.00        42.77         5.23         0.23         6.71 
TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 
        1.64         2.37         2.30         5.88         7.63         0.76 
TCGA-P5-A5F6 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z 
        1.28         5.75         2.53         4.83         7.79         4.11 
TCGA-QH-A6CU TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
       14.83        12.23         2.20         3.16         0.59         6.31 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6XA TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK 
        3.91         4.73         0.23         3.48         0.07        88.83 
TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV 
       94.03        32.65        59.38        62.17        69.07        18.77 
TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TZ TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       37.84        34.49        21.63        17.62        23.64        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
        9.86        94.62        83.70         5.85       106.39        62.37 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN 
       72.59        80.12        32.45        84.99        10.88        15.91 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IS TCGA-S9-A7IY TCGA-S9-A7J1 
        7.59        15.16        14.07         7.92        12.59         8.19 
TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 
        2.04         8.12         4.04        28.37        13.02       164.38 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z 
       99.06        17.42        83.80        31.59        18.71         5.00 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CF TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G 
       48.33        49.32        48.39        15.09        50.76        34.36 
TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R 
       19.36        17.49        40.83        29.92        18.90         9.44 
TCGA-TM-A84S TCGA-TM-A84T TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB 
        4.57        12.00        33.07        30.08        13.51         0.10 
TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS 
        7.89        26.79        10.95        27.06         7.04        23.21 
TCGA-W9-A837 
       45.07 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             0.07              0.03 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           211.17            182.33 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            14.94             16.04 
[1] "0.1 - 211.2 (14.9)" "0.0 - 182.3 (16.0)"
[1] "hr=" "2.7"
D12V2, continuous
D12V3, binary
                   cls
clus                  0   1
  7P GAIN MUTATED    48  48
  7P GAIN WILD-TYPE 142 192
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     48   48
  7P GAIN WILD-TYPE  142  192
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE              48               142
  MALE                48               192
[1] 2 2
[1] FALSE
D12V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  7P GAIN MUTATED            44               23                29
  7P GAIN WILD-TYPE         115               84               135
D12V5, multiclass
                   clus
vv                  7P GAIN MUTATED 7P GAIN WILD-TYPE
  ASTROCYTOMA                    44               115
  OLIGOASTROCYTOMA               23                84
  OLIGODENDROGLIOMA              29               135
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V6, binary
                   cls
clus                  0   1
  7P GAIN MUTATED    22  74
  7P GAIN WILD-TYPE  67 267
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     22   74
  7P GAIN WILD-TYPE   67  267
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  NO               22                67
  YES              74               267
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7P GAIN MUTATED                                  1     1
  7P GAIN WILD-TYPE                                0     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7P GAIN MUTATED                           6    88
  7P GAIN WILD-TYPE                         8   312
D12V7, multiclass
                                  clus
vv                                 7P GAIN MUTATED 7P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          1                 5
  BLACK OR AFRICAN AMERICAN                      6                 8
  WHITE                                         88               312
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V8, binary
                   cls
clus                  0   1
  7P GAIN MUTATED     4  88
  7P GAIN WILD-TYPE  12 299
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      4   88
  7P GAIN WILD-TYPE   12  299
                        clus
vv                       7P GAIN MUTATED 7P GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                12
  NOT HISPANIC OR LATINO              88               299
[1] 2 2
[1] FALSE

Clustering(13) Variable = 7Q GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                 0   1
  7Q GAIN MUTATED    89  38
  7Q GAIN WILD-TYPE 263  37
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              127               300 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               38                37 
$`7Q GAIN MUTATED`
TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
        7.69        43.89        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6665 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5277 TCGA-DB-A4X9 
       23.84        12.43         6.61       122.73        46.65        30.08 
TCGA-DB-A4XB TCGA-DB-A4XE TCGA-DB-A64O TCGA-DB-A64X TCGA-DB-A75O TCGA-DH-A669 
       12.72        18.84        18.84        10.92        30.74        30.21 
TCGA-DH-A66G TCGA-DH-A7UT TCGA-DH-A7UV TCGA-DU-5849 TCGA-DU-5854 TCGA-DU-6392 
       17.19         6.58         6.21        14.56         8.45       211.17 
TCGA-DU-6395 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 
       49.02        65.75         1.22         7.04        11.64       133.74 
TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6410 TCGA-DU-7006 TCGA-DU-7011 
       19.89        16.83        94.52         7.96        11.47       105.21 
TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7292 TCGA-DU-7301 TCGA-DU-7306 
        6.54         8.84       117.40         7.96        25.91        41.98 
TCGA-DU-8161 TCGA-DU-8163 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-A5TR TCGA-DU-A5TT 
       23.74        20.68        19.13        16.96        12.59         4.96 
TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S6 TCGA-DU-A76K TCGA-DU-A76L 
        3.65         5.65        12.20        77.98        11.41        26.76 
TCGA-DU-A76R TCGA-DU-A7T8 TCGA-E1-5302 TCGA-E1-5304 TCGA-E1-5322 TCGA-F6-A8O4 
       21.30       124.50        50.14        41.13       130.78         0.20 
TCGA-FG-5962 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 
       47.77        32.19        18.77        24.99        23.97        13.58 
TCGA-FG-7634 TCGA-FG-7643 TCGA-FG-8182 TCGA-FG-8186 TCGA-FG-A4MU TCGA-FG-A4MW 
       15.35        20.09        13.68        16.01        10.72         5.26 
TCGA-FG-A70Z TCGA-FG-A87Q TCGA-HT-7473 TCGA-HT-7475 TCGA-HT-7477 TCGA-HT-7604 
       10.78         5.72        16.54        17.42        24.26       107.93 
TCGA-HT-7610 TCGA-HT-7693 TCGA-HT-7860 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-8011 
       56.09        17.52         0.49         1.71        11.28        16.24 
TCGA-HT-8013 TCGA-HT-8104 TCGA-HT-8108 TCGA-HT-8110 TCGA-HT-8564 TCGA-HT-A4DS 
       63.55        12.23         2.50         4.70        15.72         0.23 
TCGA-HT-A5R5 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RC TCGA-HT-A616 TCGA-HT-A617 
        0.13         0.07        14.70         5.33         1.81        16.14 
TCGA-HT-A74O TCGA-HW-7495 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-KT-A7W1 TCGA-P5-A5EV 
        0.10         4.31        17.82        20.35         4.73         0.23 
TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CX 
        2.30         4.11         4.18        14.83        14.53        12.23 
TCGA-QH-A6XA TCGA-QH-A6XC TCGA-S9-A6TY TCGA-S9-A6U0 TCGA-S9-A6WM TCGA-S9-A6WO 
        0.23         5.03        31.33        16.37        19.86         7.59 
TCGA-S9-A7IQ TCGA-S9-A7IX TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7QW TCGA-S9-A7QY 
       14.27        19.63         4.21         9.37         3.58        28.37 
TCGA-S9-A7R2 TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7CA TCGA-TM-A84B TCGA-TM-A84H 
       10.39        49.45        48.33        34.78        12.00        24.26 
TCGA-TM-A84M 
       16.50 

$`7Q GAIN WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5393 TCGA-CS-5394 
        4.70        18.15        10.62        64.64        40.18         0.10 
TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-DB-5273 
       17.95         8.48         7.56         8.02         7.40        81.96 
TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 
       75.25        47.93        72.92        50.17        44.52        36.56 
TCGA-DB-5281 TCGA-DB-A4XA TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XF TCGA-DB-A4XG 
       78.28        10.29        27.62        27.02        18.38        72.95 
TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S 
       12.59        11.01        16.80         5.98        16.08        15.42 
TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M 
       27.81        14.73        13.64         7.40         6.44        10.29 
TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 
        3.81        19.96        31.82        30.31        14.40         8.02 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UU 
       42.05        27.81        17.19        54.25        10.22         3.45 
TCGA-DU-5847 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5855 TCGA-DU-5870 
       18.02        17.46         6.74        13.38         6.81       182.33 
TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6396 
       18.94        17.49        15.16        52.11        22.42        75.16 
TCGA-DU-6397 TCGA-DU-6401 TCGA-DU-6408 TCGA-DU-6542 TCGA-DU-7007 TCGA-DU-7008 
       46.06        87.45       114.08         7.73        62.96       156.23 
TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 
      138.28        14.99        90.77        30.67        26.30        10.36 
TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7302 TCGA-DU-7304 
       94.32        18.94        44.02        62.01        60.30        23.31 
TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8162 TCGA-DU-8164 TCGA-DU-8167 TCGA-DU-8168 
        2.76         5.10         3.98        21.40        15.48        14.17 
TCGA-DU-A5TP TCGA-DU-A5TS TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S7 TCGA-DU-A6S8 
       14.24        15.12         8.65         2.70         7.23         5.98 
TCGA-DU-A76O TCGA-DU-A7TG TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 
        7.13        44.42        67.46        79.99        57.93       134.27 
TCGA-E1-5318 TCGA-E1-5319 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-FG-5963 TCGA-FG-5964 
       78.21        95.57        14.33         0.23        17.98        34.36 
TCGA-FG-6689 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-8181 TCGA-FG-8185 
       14.93        17.88        22.55        20.61        12.95        14.24 
TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MX 
       20.09        14.96        22.52        15.52        38.27        18.71 
TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 
       23.70        14.76        17.82        16.41        15.02        16.44 
TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N 
       10.59        28.54        22.95        43.69         5.23         7.43 
TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 
        0.13         0.10         6.67         7.82         8.81         0.13 
TCGA-HT-7472 TCGA-HT-7474 TCGA-HT-7476 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 
        0.03         3.75         6.54         6.38         7.10        75.19 
TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 
       59.18        60.03       154.19         4.01         5.03        29.85 
TCGA-HT-7603 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 
       23.18         4.57        17.29         3.16        22.06        45.99 
TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 
       57.60         0.23        14.27         0.16        16.24         0.76 
TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 
       44.68         6.05        42.74         0.10        31.69        14.96 
TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 
        0.10         0.10         2.96         6.90        14.53        39.48 
TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7873 TCGA-HT-7874 
       19.23        39.09         0.23        50.63        23.61        37.15 
TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7902 
        0.33         0.13         3.68         5.33         2.93        31.43 
TCGA-HT-8010 TCGA-HT-8012 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8105 
        1.64         9.40         0.10        21.50        33.01         6.25 
TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8109 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 
        0.10         0.46         3.95         0.23        29.59         3.88 
TCGA-HT-8563 TCGA-HT-A4DV TCGA-HT-A5R7 TCGA-HT-A5RB TCGA-HT-A614 TCGA-HT-A615 
       16.04        10.49        14.01         0.10         2.70        13.02 
TCGA-HT-A618 TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 
        5.33        29.92        13.45         8.32        19.23        40.18 
TCGA-HW-7493 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-A5KK TCGA-HW-A5KL 
       35.90        21.70        21.60        19.59         7.89        20.81 
TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-P5-A5EW TCGA-P5-A5EX 
       20.71        19.00        42.77         5.23         6.71         1.64 
TCGA-P5-A5EY TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-QH-A65R 
        2.37         5.88         7.63         0.76         1.28         5.75 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CY TCGA-QH-A6CZ 
        2.53         4.83         7.79         4.11         2.20         3.16 
TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A86X 
        0.59         6.31         3.91         4.73         1.91         3.48 
TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TS 
        0.07        88.83        94.03        32.65        59.38        62.17 
TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TZ TCGA-S9-A6U1 
       69.07        18.77        37.84        34.49        21.63        17.62 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA 
       23.64        32.61         9.86        94.62        83.70         5.85 
TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI 
      106.39        62.37        72.59        80.12        32.45        84.99 
TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IS TCGA-S9-A7IY 
       10.88        15.91        15.16        14.07         7.92        12.59 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QX TCGA-S9-A7QZ TCGA-S9-A7R1 
        8.19         2.04         8.12         4.04        13.02       164.38 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z 
       99.06        17.42        83.80        31.59        18.71         5.00 
TCGA-TM-A7C5 TCGA-TM-A7CF TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84I 
       49.32        48.39        15.09        50.76        34.36        19.36 
TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S 
       17.49        40.83        29.92        18.90         9.44         4.57 
TCGA-TM-A84T TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD 
       12.00        33.07        30.08        13.51         0.10         7.89 
TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-W9-A837 
       26.79        10.95        27.06         7.04        23.21        45.07 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             0.07              0.03 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           211.17            182.33 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            15.35             16.06 
[1] "0.1 - 211.2 (15.3)" "0.0 - 182.3 (16.1)"
[1] "hr=" "2.6"
D13V2, continuous
D13V3, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED    60  67
  7Q GAIN WILD-TYPE 130 173
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     60   67
  7Q GAIN WILD-TYPE  130  173
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE              60               130
  MALE                67               173
[1] 2 2
[1] FALSE
D13V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  7Q GAIN MUTATED            58               32                37
  7Q GAIN WILD-TYPE         101               75               127
D13V5, multiclass
                   clus
vv                  7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  ASTROCYTOMA                    58               101
  OLIGOASTROCYTOMA               32                75
  OLIGODENDROGLIOMA              37               127
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V6, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED    28  99
  7Q GAIN WILD-TYPE  61 242
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     28   99
  7Q GAIN WILD-TYPE   61  242
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  NO               28                61
  YES              99               242
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7Q GAIN MUTATED                                  1     2
  7Q GAIN WILD-TYPE                                0     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7Q GAIN MUTATED                           7   117
  7Q GAIN WILD-TYPE                         7   283
D13V7, multiclass
                                  clus
vv                                 7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          2                 4
  BLACK OR AFRICAN AMERICAN                      7                 7
  WHITE                                        117               283
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V8, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED     5 118
  7Q GAIN WILD-TYPE  11 269
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      5  118
  7Q GAIN WILD-TYPE   11  269
                        clus
vv                       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   5                11
  NOT HISPANIC OR LATINO             118               269
[1] 2 2
[1] FALSE

Clustering(14) Variable = 8P GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                 0   1
  8P GAIN MUTATED    31   8
  8P GAIN WILD-TYPE 321  67
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               39               388 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                8                67 
$`8P GAIN MUTATED`
TCGA-CS-6665 TCGA-CS-6666 TCGA-DB-5281 TCGA-DB-A64X TCGA-DH-A669 TCGA-DH-A7UT 
       12.43         8.48        78.28        10.92        30.21         6.58 
TCGA-DU-5871 TCGA-DU-6407 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7304 TCGA-DU-8158 
       18.94        94.52         8.84       117.40        23.31         5.10 
TCGA-DU-8163 TCGA-DU-A5TS TCGA-DU-A6S7 TCGA-E1-5303 TCGA-FG-5962 TCGA-FG-7634 
       20.68        15.12         7.23        67.46        47.77        15.35 
TCGA-FG-A4MT TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7479 TCGA-HT-7482 TCGA-HT-7855 
       38.27         6.54        24.26         7.10        60.03        19.23 
TCGA-HT-8011 TCGA-HT-8013 TCGA-HT-8106 TCGA-HT-8111 TCGA-HT-A5R7 TCGA-S9-A6TY 
       16.24        63.55         0.10         0.23        14.01        31.33 
TCGA-S9-A6WH TCGA-S9-A6WO TCGA-S9-A7QX TCGA-S9-A89Z TCGA-TM-A7CF TCGA-TM-A84H 
       32.45         7.59         4.04         5.00        48.39        24.26 
TCGA-TM-A84Q TCGA-VM-A8C8 TCGA-VM-A8CA 
       18.90        33.07        13.51 

$`8P GAIN WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 
       23.84        17.95         7.56         8.02         7.40         6.61 
TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 
      122.73        81.96        75.25        47.93        72.92        46.65 
TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB 
       50.17        44.52        36.56        30.08        10.29        12.72 
TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH 
       27.62        27.02        18.84        18.38        72.95        12.59 
TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S 
       11.01        18.84        16.80         5.98        16.08        15.42 
TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M 
       27.81        14.73        13.64         7.40         6.44        10.29 
TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 
       30.74         3.81        19.96        31.82        30.31        14.40 
TCGA-DH-5144 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR 
        8.02        42.05        27.81        17.19        17.19        54.25 
TCGA-DH-A7US TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       10.22         3.45         6.21        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5872 
        6.74        13.38         8.45         6.81       182.33        17.49 
TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       15.16       211.17        52.11        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       46.06        65.75         1.22        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 
      133.74        19.89        16.83       114.08         7.96         7.73 
TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 
       11.47        62.96       156.23       138.28        14.99       105.21 
TCGA-DU-7012 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 
        6.54        90.77        30.67        26.30        10.36         7.96 
TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 
       94.32        18.94        44.02        62.01        25.91        60.30 
TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8164 TCGA-DU-8165 
       41.98         2.76        23.74         3.98        21.40        19.13 
TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TT 
       16.96        15.48        14.17        14.24        12.59         4.96 
TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
        3.65         5.65        12.20         8.65         2.70        77.98 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 
        5.98        11.41        26.76         7.13        21.30       124.50 
TCGA-DU-A7TG TCGA-E1-5302 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 
       44.42        50.14        41.13        79.99        57.93       134.27 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 
       78.21        95.57       130.78        14.33         0.23         0.20 
TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 
       17.98        34.36        32.19        18.77        14.93        24.99 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 
       23.97        13.58        17.88        22.55        20.61        20.09 
TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 
       12.95        13.68        14.24        16.01        20.09        14.96 
TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY 
       22.52        15.52        10.72         5.26        18.71        23.70 
TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 
       14.76        17.82        16.41        15.02        16.44        10.59 
TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N 
       28.54        10.78        22.95        43.69         5.23         7.43 
TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 
        5.72         0.13         0.10         6.67         7.82         8.81 
TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7478 
        0.13         0.03        16.54         3.75        17.42         6.38 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 
       75.19        59.18       154.19         4.01         5.03        29.85 
TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 
       23.18       107.93         4.57        17.29         3.16        22.06 
TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 
       45.99        56.09        57.60         0.23        14.27         0.16 
TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 
       16.24         0.76        44.68         6.05        42.74         0.10 
TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 
       31.69        14.96         0.10         0.10         2.96        17.52 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 
        6.90        14.53        39.48        39.09         0.23        50.63 
TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 
        0.49        23.61        37.15         0.33         0.13         3.68 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 
        5.33         2.93         1.71        11.28        31.43         1.64 
TCGA-HT-8012 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 
        9.40         0.10        21.50        33.01        12.23         6.25 
TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8113 TCGA-HT-8114 
        0.46         2.50         3.95         4.70        29.59         3.88 
TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R9 
       16.04        15.72         0.23        10.49         0.13         0.07 
TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 
       14.70         0.10         5.33         2.70        13.02         1.81 
TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 
       16.14         5.33         0.10        29.92        13.45         8.32 
TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 
       19.23        40.18        35.90         4.31        21.70        21.60 
TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM 
       19.59        17.82        20.35         7.89        20.81        20.71 
TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW 
       19.00        42.77         5.23         4.73         0.23         6.71 
TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 
        1.64         2.37         2.30         4.11         5.88         7.63 
TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X 
        0.76         1.28         5.75         2.53         4.83         7.79 
TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CX TCGA-QH-A6CY 
        4.11         4.18        14.83        14.53        12.23         2.20 
TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 
        3.16         0.59         6.31         3.91         4.73         1.91 
TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML 
        0.23         5.03         3.48         0.07        88.83        94.03 
TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW 
       32.65        59.38        62.17        69.07        18.77        37.84 
TCGA-S9-A6TX TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       34.49        21.63        16.37        17.62        23.64        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
        9.86        94.62        83.70         5.85       106.39        62.37 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN 
       72.59        80.12        84.99        10.88        19.86        15.91 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY 
       15.16        14.07        14.27         7.92        19.63        12.59 
TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW 
        4.21         9.37         8.19         2.04         8.12         3.58 
TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 
       28.37        13.02       164.38        10.39        99.06        17.42 
TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 
       83.80        31.59        18.71        49.45        48.33        49.32 
TCGA-TM-A7CA TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84I 
       34.78        12.00        15.09        50.76        34.36        19.36 
TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84R TCGA-TM-A84S 
       17.49        40.83        16.50        29.92         9.44         4.57 
TCGA-TM-A84T TCGA-VM-A8C9 TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH 
       12.00        30.08         0.10         7.89        26.79        10.95 
TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-W9-A837 
       27.06         7.04        23.21        45.07 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             0.10              0.03 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           117.40            211.17 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            18.90             15.62 
[1] "0.1 - 117.4 (18.9)" "0.0 - 211.2 (15.6)"
[1] "hr=" "1.1"
D14V2, continuous
D14V3, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    15  24
  8P GAIN WILD-TYPE 175 216
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     15   24
  8P GAIN WILD-TYPE  175  216
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE              15               175
  MALE                24               216
[1] 2 2
[1] FALSE
D14V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  8P GAIN MUTATED            20                9                10
  8P GAIN WILD-TYPE         139               98               154
D14V5, multiclass
                   clus
vv                  8P GAIN MUTATED 8P GAIN WILD-TYPE
  ASTROCYTOMA                    20               139
  OLIGOASTROCYTOMA                9                98
  OLIGODENDROGLIOMA              10               154
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V6, binary
                   cls
clus                  0   1
  8P GAIN MUTATED     7  32
  8P GAIN WILD-TYPE  82 309
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      7   32
  8P GAIN WILD-TYPE   82  309
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  NO                7                82
  YES              32               309
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8P GAIN MUTATED                                  0     0
  8P GAIN WILD-TYPE                                1     6
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8P GAIN MUTATED                           1    37
  8P GAIN WILD-TYPE                        13   363
D14V7, multiclass
                                  clus
vv                                 8P GAIN MUTATED 8P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 6
  BLACK OR AFRICAN AMERICAN                      1                13
  WHITE                                         37               363
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V8, binary
                   cls
clus                  0   1
  8P GAIN MUTATED     1  36
  8P GAIN WILD-TYPE  15 351
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      1   36
  8P GAIN WILD-TYPE   15  351
                        clus
vv                       8P GAIN MUTATED 8P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                15
  NOT HISPANIC OR LATINO              36               351
[1] 2 2
[1] FALSE

Clustering(15) Variable = 8Q GAIN MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                 0   1
  8Q GAIN MUTATED    37   9
  8Q GAIN WILD-TYPE 315  66
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               46               381 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                9                66 
$`8Q GAIN MUTATED`
TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-DB-5277 TCGA-DB-5281 TCGA-DB-A64X 
       17.95        12.43         8.48        46.65        78.28        10.92 
TCGA-DH-5143 TCGA-DH-A669 TCGA-DH-A7UT TCGA-DU-5871 TCGA-DU-6407 TCGA-DU-7013 
       14.40        30.21         6.58        18.94        94.52         8.84 
TCGA-DU-7014 TCGA-DU-7304 TCGA-DU-8158 TCGA-DU-8163 TCGA-DU-A5TS TCGA-DU-A5TW 
      117.40        23.31         5.10        20.68        15.12         5.65 
TCGA-DU-A6S7 TCGA-E1-5303 TCGA-FG-5962 TCGA-FG-6691 TCGA-FG-7634 TCGA-FG-A4MT 
        7.23        67.46        47.77        23.97        15.35        38.27 
TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7479 TCGA-HT-7482 TCGA-HT-7855 TCGA-HT-8011 
        6.54        24.26         7.10        60.03        19.23        16.24 
TCGA-HT-8013 TCGA-HT-8106 TCGA-HT-8111 TCGA-HT-A5R7 TCGA-P5-A5F1 TCGA-S9-A6TY 
       63.55         0.10         0.23        14.01         5.88        31.33 
TCGA-S9-A6WH TCGA-S9-A6WO TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A89Z TCGA-TM-A7CF 
       32.45         7.59         3.58         4.04         5.00        48.39 
TCGA-TM-A84H TCGA-TM-A84Q TCGA-VM-A8C8 TCGA-VM-A8CA 
       24.26        18.90        33.07        13.51 

$`8Q GAIN WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 
       23.84         7.56         8.02         7.40         6.61       122.73 
TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5278 TCGA-DB-5279 
       81.96        75.25        47.93        72.92        50.17        44.52 
TCGA-DB-5280 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD 
       36.56        30.08        10.29        12.72        27.62        27.02 
TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O 
       18.84        18.38        72.95        12.59        11.01        18.84 
TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V 
       16.80         5.98        16.08        15.42        27.81        14.73 
TCGA-DB-A64W TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       13.64         7.40         6.44        10.29        30.74         3.81 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5144 TCGA-DH-A66B TCGA-DH-A66D 
       19.96        31.82        30.31         8.02        42.05        27.81 
TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UU TCGA-DH-A7UV 
       17.19        17.19        54.25        10.22         3.45         6.21 
TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 
       18.02        14.56        17.46         6.74        13.38         8.45 
TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 
        6.81       182.33        17.49        15.16       211.17        52.11 
TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 
       22.42        49.02        75.16        46.06        65.75         1.22 
TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 
       87.45         7.04        11.64       133.74        19.89        16.83 
TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 
      114.08         7.96         7.73        11.47        62.96       156.23 
TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7015 TCGA-DU-7018 
      138.28        14.99       105.21         6.54        90.77        30.67 
TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 
       26.30        10.36         7.96        94.32        18.94        44.02 
TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8161 
       62.01        25.91        60.30        41.98         2.76        23.74 
TCGA-DU-8162 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 
        3.98        21.40        19.13        16.96        15.48        14.17 
TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TY TCGA-DU-A6S2 
       14.24        12.59         4.96         3.65        12.20         8.65 
TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O 
        2.70        77.98         5.98        11.41        26.76         7.13 
TCGA-DU-A76R TCGA-DU-A7T8 TCGA-DU-A7TG TCGA-E1-5302 TCGA-E1-5304 TCGA-E1-5305 
       21.30       124.50        44.42        50.14        41.13        79.99 
TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 
       57.93       134.27        78.21        95.57       130.78        14.33 
TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 
        0.23         0.20        17.98        34.36        32.19        18.77 
TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6692 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 
       14.93        24.99        13.58        17.88        22.55        20.61 
TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 
       20.09        12.95        13.68        14.24        16.01        20.09 
TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX 
       14.96        22.52        15.52        10.72         5.26        18.71 
TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 
       23.70        14.76        17.82        16.41        15.02        16.44 
TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 
       10.59        28.54        10.78        22.95        43.69         5.23 
TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 
        7.43         5.72         0.13         0.10         6.67         7.82 
TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 
        8.81         0.13         0.03        16.54         3.75        17.42 
TCGA-HT-7478 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
        6.38        75.19        59.18       154.19         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 
       29.85        23.18       107.93         4.57        17.29         3.16 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
       22.06        45.99        56.09        57.60         0.23        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 
        0.16        16.24         0.76        44.68         6.05        42.74 
TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 
        0.10        31.69        14.96         0.10         0.10         2.96 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7856 TCGA-HT-7857 
       17.52         6.90        14.53        39.48        39.09         0.23 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
       50.63         0.49        23.61        37.15         0.33         0.13 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 
        3.68         5.33         2.93         1.71        11.28        31.43 
TCGA-HT-8010 TCGA-HT-8012 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 
        1.64         9.40         0.10        21.50        33.01        12.23 
TCGA-HT-8105 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8113 
        6.25         0.46         2.50         3.95         4.70        29.59 
TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
        3.88        16.04        15.72         0.23        10.49         0.13 
TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 
        0.07        14.70         0.10         5.33         2.70        13.02 
TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 
        1.81        16.14         5.33         0.10        29.92        13.45 
TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 
        8.32        19.23        40.18        35.90         4.31        21.70 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
       21.60        19.59        17.82        20.35         7.89        20.81 
TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV 
       20.71        19.00        42.77         5.23         4.73         0.23 
TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F2 
        6.71         1.64         2.37         2.30         4.11         7.63 
TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X 
        0.76         1.28         5.75         2.53         4.83         7.79 
TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CX TCGA-QH-A6CY 
        4.11         4.18        14.83        14.53        12.23         2.20 
TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 
        3.16         0.59         6.31         3.91         4.73         1.91 
TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML 
        0.23         5.03         3.48         0.07        88.83        94.03 
TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW 
       32.65        59.38        62.17        69.07        18.77        37.84 
TCGA-S9-A6TX TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       34.49        21.63        16.37        17.62        23.64        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
        9.86        94.62        83.70         5.85       106.39        62.37 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN 
       72.59        80.12        84.99        10.88        19.86        15.91 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY 
       15.16        14.07        14.27         7.92        19.63        12.59 
TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QY 
        4.21         9.37         8.19         2.04         8.12        28.37 
TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 
       13.02       164.38        10.39        99.06        17.42        83.80 
TCGA-S9-A7R8 TCGA-S9-A89V TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA 
       31.59        18.71        49.45        48.33        49.32        34.78 
TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84I TCGA-TM-A84J 
       12.00        15.09        50.76        34.36        19.36        17.49 
TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T 
       40.83        16.50        29.92         9.44         4.57        12.00 
TCGA-VM-A8C9 TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 
       30.08         0.10         7.89        26.79        10.95        27.06 
TCGA-VV-A86M TCGA-VW-A7QS TCGA-W9-A837 
        7.04        23.21        45.07 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             0.10              0.03 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           117.40            211.17 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           17.095            15.720 
[1] "0.1 - 117.4 (17.1)" "0.0 - 211.2 (15.7)"
[1] "hr=" "1.2"
D15V2, continuous
D15V3, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED    18  28
  8Q GAIN WILD-TYPE 172 212
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     18   28
  8Q GAIN WILD-TYPE  172  212
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE              18               172
  MALE                28               212
[1] 2 2
[1] FALSE
D15V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  8Q GAIN MUTATED            26               10                10
  8Q GAIN WILD-TYPE         133               97               154
D15V5, multiclass
                   clus
vv                  8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  ASTROCYTOMA                    26               133
  OLIGOASTROCYTOMA               10                97
  OLIGODENDROGLIOMA              10               154
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V6, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED    10  36
  8Q GAIN WILD-TYPE  79 305
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     10   36
  8Q GAIN WILD-TYPE   79  305
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  NO               10                79
  YES              36               305
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8Q GAIN MUTATED                                  0     0
  8Q GAIN WILD-TYPE                                1     6
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8Q GAIN MUTATED                           2    42
  8Q GAIN WILD-TYPE                        12   358
D15V7, multiclass
                                  clus
vv                                 8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 6
  BLACK OR AFRICAN AMERICAN                      2                12
  WHITE                                         42               358
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V8, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED     1  42
  8Q GAIN WILD-TYPE  15 345
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      1   42
  8Q GAIN WILD-TYPE   15  345
                        clus
vv                       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                15
  NOT HISPANIC OR LATINO              42               345
[1] 2 2
[1] FALSE

Clustering(16) Variable = 9P GAIN MUTATION ANALYSIS
D16V1, survival
                   sevent
clus2                 0   1
  9P GAIN MUTATED    10   4
  9P GAIN WILD-TYPE 342  71
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               14               413 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                4                71 
$`9P GAIN MUTATED`
TCGA-CS-5396 TCGA-CS-6665 TCGA-DB-A4XE TCGA-DU-7010 TCGA-DU-8158 TCGA-DU-8161 
        9.96        12.43        18.84        14.99         5.10        23.74 
TCGA-DU-8165 TCGA-DU-A5TT TCGA-DU-A76O TCGA-E1-5302 TCGA-HT-7474 TCGA-S9-A6WH 
       19.13         4.96         7.13        50.14         3.75        32.45 
TCGA-S9-A6WM TCGA-TM-A7C4 
       19.86        48.33 

$`9P GAIN WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
       40.18         0.10        21.01         6.38        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 
       17.95         8.48         7.56         8.02         7.40         6.61 
TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 
      122.73        81.96        75.25        47.93        72.92        46.65 
TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA 
       50.17        44.52        36.56        78.28        30.08        10.29 
TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH 
       12.72        27.62        27.02        18.38        72.95        12.59 
TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S 
       11.01        18.84        16.80         5.98        16.08        15.42 
TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L 
       27.81        14.73        13.64        10.92         7.40         6.44 
TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 
       10.29        30.74         3.81        19.96        31.82        30.31 
TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F 
       14.40         8.02        30.21        42.05        27.81        17.19 
TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV 
       17.19        54.25        10.22         6.58         3.45         6.21 
TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 
       18.02        14.56        17.46         6.74        13.38         8.45 
TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 
        6.81       182.33        18.94        17.49        15.16       211.17 
TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 
       52.11        22.42        49.02        75.16        46.06        65.75 
TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 
        1.22        87.45         7.04        11.64       133.74        19.89 
TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 
       16.83        94.52       114.08         7.96         7.73        11.47 
TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 
       62.96       156.23       138.28       105.21         6.54         8.84 
TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 
      117.40        90.77        30.67        26.30        10.36         7.96 
TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 
       94.32        18.94        44.02        62.01        25.91        60.30 
TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 
       23.31        41.98         2.76         3.98        20.68        21.40 
TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS 
       16.96        15.48        14.17        14.24        12.59        15.12 
TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
        3.65         5.65        12.20         8.65         2.70        77.98 
TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76R TCGA-DU-A7T8 
        7.23         5.98        11.41        26.76        21.30       124.50 
TCGA-DU-A7TG TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 
       44.42        67.46        41.13        79.99        57.93       134.27 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 
       78.21        95.57       130.78        14.33         0.23         0.20 
TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 
       47.77        17.98        34.36        32.19        18.77        14.93 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 
       24.99        23.97        13.58        15.35        17.88        22.55 
TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 
       20.61        20.09        12.95        13.68        14.24        16.01 
TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU 
       20.09        14.96        22.52        15.52        38.27        10.72 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
        5.26        18.71        23.70        14.76        17.82        16.41 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 
       15.02        16.44        10.59        28.54        10.78        22.95 
TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 
       43.69         5.23         7.43         5.72         0.13         0.10 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 
        6.67         7.82         8.81         0.13         0.03        16.54 
TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 
       17.42         6.54        24.26         6.38         7.10        75.19 
TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 
       59.18        60.03       154.19         4.01         5.03        29.85 
TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 
       23.18       107.93         4.57        17.29         3.16        22.06 
TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 
       45.99        56.09        57.60         0.23        14.27         0.16 
TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 
       16.24         0.76        44.68         6.05        42.74         0.10 
TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 
       31.69        14.96         0.10         0.10         2.96        17.52 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 
        6.90        14.53        39.48        19.23        39.09         0.23 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
       50.63         0.49        23.61        37.15         0.33         0.13 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 
        3.68         5.33         2.93         1.71        11.28        31.43 
TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 
        1.64        16.24         9.40        63.55         0.10        21.50 
TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 
       33.01        12.23         6.25         0.10         0.46         2.50 
TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 
        3.95         4.70         0.23        29.59         3.88        16.04 
TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 
       15.72         0.23        10.49         0.13        14.01         0.07 
TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 
       14.70         0.10         5.33         2.70        13.02         1.81 
TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 
       16.14         5.33         0.10        29.92        13.45         8.32 
TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 
       19.23        40.18        35.90         4.31        21.70        21.60 
TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM 
       19.59        17.82        20.35         7.89        20.81        20.71 
TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW 
       19.00        42.77         5.23         4.73         0.23         6.71 
TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 
        1.64         2.37         2.30         4.11         5.88         7.63 
TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X 
        0.76         1.28         5.75         2.53         4.83         7.79 
TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CX TCGA-QH-A6CY 
        4.11         4.18        14.83        14.53        12.23         2.20 
TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 
        3.16         0.59         6.31         3.91         4.73         1.91 
TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML 
        0.23         5.03         3.48         0.07        88.83        94.03 
TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW 
       32.65        59.38        62.17        69.07        18.77        37.84 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 
       34.49        31.33        21.63        16.37        17.62        23.64 
TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB 
       32.61         9.86        94.62        83.70         5.85       106.39 
TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN 
       62.37        72.59        80.12        84.99        10.88        15.91 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX 
        7.59        15.16        14.07        14.27         7.92        19.63 
TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       12.59         4.21         9.37         8.19         2.04         8.12 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 
        3.58         4.04        28.37        13.02       164.38        10.39 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z 
       99.06        17.42        83.80        31.59        18.71         5.00 
TCGA-TM-A7C3 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
       49.45        49.32        34.78        48.39        12.00        15.09 
TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L 
       50.76        34.36        24.26        19.36        17.49        40.83 
TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T 
       16.50        29.92        18.90         9.44         4.57        12.00 
TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE 
       33.07        30.08        13.51         0.10         7.89        26.79 
TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-W9-A837 
       10.95        27.06         7.04        23.21        45.07 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
             3.75              0.03 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            50.14            211.17 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           16.915            15.910 
[1] "3.8 - 50.1 (16.9)"  "0.0 - 211.2 (15.9)"
[1] "hr=" "2.5"
D16V2, continuous
D16V3, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    10   4
  9P GAIN WILD-TYPE 180 236
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     10    4
  9P GAIN WILD-TYPE  180  236
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE              10               180
  MALE                 4               236
[1] 2 2
[1] FALSE
D16V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  9P GAIN MUTATED             7                4                 3
  9P GAIN WILD-TYPE         152              103               161
D16V5, multiclass
                   clus
vv                  9P GAIN MUTATED 9P GAIN WILD-TYPE
  ASTROCYTOMA                     7               152
  OLIGOASTROCYTOMA                4               103
  OLIGODENDROGLIOMA               3               161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V6, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     3  11
  9P GAIN WILD-TYPE  86 330
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      3   11
  9P GAIN WILD-TYPE   86  330
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  NO                3                86
  YES              11               330
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9P GAIN MUTATED                                  0     0
  9P GAIN WILD-TYPE                                1     6
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9P GAIN MUTATED                           0    14
  9P GAIN WILD-TYPE                        14   386
D16V7, multiclass
                                  clus
vv                                 9P GAIN MUTATED 9P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 6
  BLACK OR AFRICAN AMERICAN                      0                14
  WHITE                                         14               386
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V8, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     0  14
  9P GAIN WILD-TYPE  16 373
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      0   14
  9P GAIN WILD-TYPE   16  373
                        clus
vv                       9P GAIN MUTATED 9P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                16
  NOT HISPANIC OR LATINO              14               373
[1] 2 2
[1] FALSE

Clustering(17) Variable = 9Q GAIN MUTATION ANALYSIS
D17V1, survival
                   sevent
clus2                 0   1
  9Q GAIN MUTATED    15   5
  9Q GAIN WILD-TYPE 337  70
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               20               407 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                5                70 
$`9Q GAIN MUTATED`
TCGA-CS-5396 TCGA-CS-6665 TCGA-DB-A4XE TCGA-DU-7010 TCGA-DU-7298 TCGA-DU-8158 
        9.96        12.43        18.84        14.99        18.94         5.10 
TCGA-DU-8161 TCGA-DU-8165 TCGA-DU-A5TT TCGA-DU-A76O TCGA-E1-5302 TCGA-FG-A4MY 
       23.74        19.13         4.96         7.13        50.14        23.70 
TCGA-FG-A6J3 TCGA-FG-A87N TCGA-HT-7477 TCGA-HW-8319 TCGA-S9-A6TW TCGA-S9-A6WH 
       10.59         7.43        24.26        21.70        37.84        32.45 
TCGA-S9-A6WM TCGA-S9-A7QW 
       19.86         3.58 

$`9Q GAIN WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
       40.18         0.10        21.01         6.38        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 
       17.95         8.48         7.56         8.02         7.40         6.61 
TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 
      122.73        81.96        75.25        47.93        72.92        46.65 
TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA 
       50.17        44.52        36.56        78.28        30.08        10.29 
TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH 
       12.72        27.62        27.02        18.38        72.95        12.59 
TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S 
       11.01        18.84        16.80         5.98        16.08        15.42 
TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L 
       27.81        14.73        13.64        10.92         7.40         6.44 
TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 
       10.29        30.74         3.81        19.96        31.82        30.31 
TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F 
       14.40         8.02        30.21        42.05        27.81        17.19 
TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV 
       17.19        54.25        10.22         6.58         3.45         6.21 
TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 
       18.02        14.56        17.46         6.74        13.38         8.45 
TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 
        6.81       182.33        18.94        17.49        15.16       211.17 
TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 
       52.11        22.42        49.02        75.16        46.06        65.75 
TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 
        1.22        87.45         7.04        11.64       133.74        19.89 
TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 
       16.83        94.52       114.08         7.96         7.73        11.47 
TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 
       62.96       156.23       138.28       105.21         6.54         8.84 
TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 
      117.40        90.77        30.67        26.30        10.36         7.96 
TCGA-DU-7294 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 
       94.32        44.02        62.01        25.91        60.30        23.31 
TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8166 
       41.98         2.76         3.98        20.68        21.40        16.96 
TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TU 
       15.48        14.17        14.24        12.59        15.12         3.65 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
        5.65        12.20         8.65         2.70        77.98         7.23 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76R TCGA-DU-A7T8 TCGA-DU-A7TG 
        5.98        11.41        26.76        21.30       124.50        44.42 
TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 
       67.46        41.13        79.99        57.93       134.27        78.21 
TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 
       95.57       130.78        14.33         0.23         0.20        47.77 
TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 
       17.98        34.36        32.19        18.77        14.93        24.99 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 
       23.97        13.58        15.35        17.88        22.55        20.61 
TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 
       20.09        12.95        13.68        14.24        16.01        20.09 
TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW 
       14.96        22.52        15.52        38.27        10.72         5.26 
TCGA-FG-A4MX TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 
       18.71        14.76        17.82        16.41        15.02        16.44 
TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87Q 
       28.54        10.78        22.95        43.69         5.23         5.72 
TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 
        0.13         0.10         6.67         7.82         8.81         0.13 
TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7478 
        0.03        16.54         3.75        17.42         6.54         6.38 
TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 
        7.10        75.19        59.18        60.03       154.19         4.01 
TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 
        5.03        29.85        23.18       107.93         4.57        17.29 
TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 
        3.16        22.06        45.99        56.09        57.60         0.23 
TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 
       14.27         0.16        16.24         0.76        44.68         6.05 
TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 
       42.74         0.10        31.69        14.96         0.10         0.10 
TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 
        2.96        17.52         6.90        14.53        39.48        19.23 
TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 
       39.09         0.23        50.63         0.49        23.61        37.15 
TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 
        0.33         0.13         3.68         5.33         2.93         1.71 
TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 
       11.28        31.43         1.64        16.24         9.40        63.55 
TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 
        0.10        21.50        33.01        12.23         6.25         0.10 
TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 
        0.46         2.50         3.95         4.70         0.23        29.59 
TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
        3.88        16.04        15.72         0.23        10.49         0.13 
TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 
       14.01         0.07        14.70         0.10         5.33         2.70 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A74O TCGA-HW-7486 
       13.02         1.81        16.14         5.33         0.10        29.92 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 
       13.45         8.32        19.23        40.18        35.90         4.31 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
       21.60        19.59        17.82        20.35         7.89        20.81 
TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV 
       20.71        19.00        42.77         5.23         4.73         0.23 
TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 
        6.71         1.64         2.37         2.30         4.11         5.88 
TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V 
        7.63         0.76         1.28         5.75         2.53         4.83 
TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CX 
        7.79         4.11         4.18        14.83        14.53        12.23 
TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 
        2.20         3.16         0.59         6.31         3.91         4.73 
TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK 
        1.91         0.23         5.03         3.48         0.07        88.83 
TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV 
       94.03        32.65        59.38        62.17        69.07        18.77 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 
       34.49        31.33        21.63        16.37        17.62        23.64 
TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB 
       32.61         9.86        94.62        83.70         5.85       106.39 
TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN 
       62.37        72.59        80.12        84.99        10.88        15.91 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX 
        7.59        15.16        14.07        14.27         7.92        19.63 
TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       12.59         4.21         9.37         8.19         2.04         8.12 
TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 
        4.04        28.37        13.02       164.38        10.39        99.06 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 
       17.42        83.80        31.59        18.71         5.00        49.45 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
       48.33        49.32        34.78        48.39        12.00        15.09 
TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L 
       50.76        34.36        24.26        19.36        17.49        40.83 
TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T 
       16.50        29.92        18.90         9.44         4.57        12.00 
TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE 
       33.07        30.08        13.51         0.10         7.89        26.79 
TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-W9-A837 
       10.95        27.06         7.04        23.21        45.07 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
             3.58              0.03 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            50.14            211.17 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            18.89             15.72 
[1] "3.6 - 50.1 (18.9)"  "0.0 - 211.2 (15.7)"
[1] "hr=" "2.3"
D17V2, continuous
D17V3, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    15   5
  9Q GAIN WILD-TYPE 175 235
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     15    5
  9Q GAIN WILD-TYPE  175  235
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE              15               175
  MALE                 5               235
[1] 2 2
[1] FALSE
D17V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  9Q GAIN MUTATED            12                4                 4
  9Q GAIN WILD-TYPE         147              103               160
D17V5, multiclass
                   clus
vv                  9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  ASTROCYTOMA                    12               147
  OLIGOASTROCYTOMA                4               103
  OLIGODENDROGLIOMA               4               160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V6, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     3  17
  9Q GAIN WILD-TYPE  86 324
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      3   17
  9Q GAIN WILD-TYPE   86  324
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  NO                3                86
  YES              17               324
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9Q GAIN MUTATED                                  0     1
  9Q GAIN WILD-TYPE                                1     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9Q GAIN MUTATED                           1    18
  9Q GAIN WILD-TYPE                        13   382
D17V7, multiclass
                                  clus
vv                                 9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 5
  BLACK OR AFRICAN AMERICAN                      1                13
  WHITE                                         18               382
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V8, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     1  19
  9Q GAIN WILD-TYPE  15 368
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      1   19
  9Q GAIN WILD-TYPE   15  368
                        clus
vv                       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                15
  NOT HISPANIC OR LATINO              19               368
[1] 2 2
[1] FALSE

Clustering(18) Variable = 10P GAIN MUTATION ANALYSIS
D18V1, survival
                    sevent
clus2                  0   1
  10P GAIN MUTATED    35   9
  10P GAIN WILD-TYPE 317  66
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                44                383 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 9                 66 
$`10P GAIN MUTATED`
TCGA-CS-5393 TCGA-CS-6665 TCGA-CS-6667 TCGA-DB-5277 TCGA-DB-A75M TCGA-DH-A66B 
       40.18        12.43         7.56        46.65        10.29        42.05 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-6396 TCGA-DU-7014 TCGA-DU-7019 TCGA-DU-7299 
        3.45         6.21        75.16       117.40        26.30        44.02 
TCGA-DU-7304 TCGA-DU-A5TR TCGA-DU-A5TS TCGA-E1-5304 TCGA-E1-5322 TCGA-FG-A4MY 
       23.31        12.59        15.12        41.13       130.78        23.70 
TCGA-FG-A60L TCGA-FG-A70Y TCGA-FG-A87N TCGA-HT-7470 TCGA-HT-7473 TCGA-HT-7476 
       16.41        28.54         7.43         8.81        16.54         6.54 
TCGA-HT-7479 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7688 TCGA-HT-7879 TCGA-HT-8106 
        7.10        60.03       154.19        31.69         3.68         0.10 
TCGA-HT-8111 TCGA-HT-8114 TCGA-HT-A74O TCGA-HW-7493 TCGA-IK-7675 TCGA-P5-A5EZ 
        0.23         3.88         0.10        35.90        19.00         2.30 
TCGA-P5-A5F1 TCGA-QH-A6XA TCGA-S9-A7IS TCGA-S9-A7J0 TCGA-S9-A89Z TCGA-TM-A7CA 
        5.88         0.23         7.92         9.37         5.00        34.78 
TCGA-TM-A84H TCGA-VM-A8C8 
       24.26        33.07 

$`10P GAIN WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
        0.10        21.01         9.96         6.38        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 
       17.95         8.48         8.02         7.40         6.61       122.73 
TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5278 TCGA-DB-5279 
       81.96        75.25        47.93        72.92        50.17        44.52 
TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC 
       36.56        78.28        30.08        10.29        12.72        27.62 
TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L 
       27.02        18.84        18.38        72.95        12.59        11.01 
TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U 
       18.84        16.80         5.98        16.08        15.42        27.81 
TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75O 
       14.73        13.64        10.92         7.40         6.44        30.74 
TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 
        3.81        19.96        31.82        30.31        14.40         8.02 
TCGA-DH-A669 TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       30.21        27.81        17.19        17.19        54.25        10.22 
TCGA-DH-A7UT TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 
        6.58        18.02        14.56        17.46         6.74        13.38 
TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 
        8.45         6.81       182.33        18.94        17.49        15.16 
TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6397 TCGA-DU-6399 
      211.17        52.11        22.42        49.02        46.06        65.75 
TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 
        1.22        87.45         7.04        11.64       133.74        19.89 
TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 
       16.83        94.52       114.08         7.96         7.73        11.47 
TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 
       62.96       156.23       138.28        14.99       105.21         6.54 
TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 
        8.84        90.77        30.67        10.36         7.96        94.32 
TCGA-DU-7298 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7306 TCGA-DU-7309 
       18.94        62.01        25.91        60.30        41.98         2.76 
TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 
        5.10        23.74         3.98        20.68        21.40        19.13 
TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TT TCGA-DU-A5TU 
       16.96        15.48        14.17        14.24         4.96         3.65 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
        5.65        12.20         8.65         2.70        77.98         7.23 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 
        5.98        11.41        26.76         7.13        21.30       124.50 
TCGA-DU-A7TG TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 
       44.42        50.14        67.46        79.99        57.93       134.27 
TCGA-E1-5318 TCGA-E1-5319 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 
       78.21        95.57        14.33         0.23         0.20        47.77 
TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 
       17.98        34.36        32.19        18.77        14.93        24.99 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 
       23.97        13.58        15.35        17.88        22.55        20.61 
TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 
       20.09        12.95        13.68        14.24        16.01        20.09 
TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW 
       14.96        22.52        15.52        38.27        10.72         5.26 
TCGA-FG-A4MX TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 
       18.71        14.76        17.82        15.02        16.44        10.59 
TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87Q TCGA-FN-7833 
       10.78        22.95        43.69         5.23         5.72         0.13 
TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7474 
        0.10         6.67         7.82         0.13         0.03         3.75 
TCGA-HT-7475 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7485 
       17.42        24.26         6.38        75.19        59.18         4.01 
TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 
        5.03        29.85        23.18       107.93         4.57        17.29 
TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 
        3.16        22.06        45.99        56.09        57.60         0.23 
TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 
       14.27         0.16        16.24         0.76        44.68         6.05 
TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 
       42.74         0.10        14.96         0.10         0.10         2.96 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 
       17.52         6.90        14.53        39.48        19.23        39.09 
TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 
        0.23        50.63         0.49        23.61        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 
        0.13         5.33         2.93         1.71        11.28        31.43 
TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 
        1.64        16.24         9.40        63.55         0.10        21.50 
TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 
       33.01        12.23         6.25         0.46         2.50         3.95 
TCGA-HT-8110 TCGA-HT-8113 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV 
        4.70        29.59        16.04        15.72         0.23        10.49 
TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC 
        0.13        14.01         0.07        14.70         0.10         5.33 
TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HW-7486 
        2.70        13.02         1.81        16.14         5.33        29.92 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 
       13.45         8.32        19.23        40.18         4.31        21.70 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
       21.60        19.59        17.82        20.35         7.89        20.81 
TCGA-HW-A5KM TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW 
       20.71        42.77         5.23         4.73         0.23         6.71 
TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5F0 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 
        1.64         2.37         4.11         7.63         0.76         1.28 
TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS 
        5.75         2.53         4.83         7.79         4.11         4.18 
TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
       14.83        14.53        12.23         2.20         3.16         0.59 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XC TCGA-QH-A86X 
        6.31         3.91         4.73         1.91         5.03         3.48 
TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TS 
        0.07        88.83        94.03        32.65        59.38        62.17 
TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ 
       69.07        18.77        37.84        34.49        31.33        21.63 
TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       16.37        17.62        23.64        32.61         9.86        94.62 
TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG 
       83.70         5.85       106.39        62.37        72.59        80.12 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO 
       32.45        84.99        10.88        19.86        15.91         7.59 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ 
       15.16        14.07        14.27        19.63        12.59         4.21 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY 
        8.19         2.04         8.12         3.58         4.04        28.37 
TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 
       13.02       164.38        10.39        99.06        17.42        83.80 
TCGA-S9-A7R8 TCGA-S9-A89V TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CF 
       31.59        18.71        49.45        48.33        49.32        48.39 
TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84I TCGA-TM-A84J 
       12.00        15.09        50.76        34.36        19.36        17.49 
TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S 
       40.83        16.50        29.92        18.90         9.44         4.57 
TCGA-TM-A84T TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE 
       12.00        30.08        13.51         0.10         7.89        26.79 
TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-W9-A837 
       10.95        27.06         7.04        23.21        45.07 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
              0.10               0.03 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
            154.19             211.17 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
            15.765             15.910 
[1] "0.1 - 154.2 (15.8)" "0.0 - 211.2 (15.9)"
[1] "hr=" "1.1"
D18V2, continuous
D18V3, binary
                    cls
clus                   0   1
  10P GAIN MUTATED    15  29
  10P GAIN WILD-TYPE 175 211
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     15   29
  10P GAIN WILD-TYPE  175  211
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE               15                175
  MALE                 29                211
[1] 2 2
[1] FALSE
D18V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  10P GAIN MUTATED            22               14                 8
  10P GAIN WILD-TYPE         137               93               156
D18V5, multiclass
                   clus
vv                  10P GAIN MUTATED 10P GAIN WILD-TYPE
  ASTROCYTOMA                     22                137
  OLIGOASTROCYTOMA                14                 93
  OLIGODENDROGLIOMA                8                156
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V6, binary
                    cls
clus                   0   1
  10P GAIN MUTATED    17  27
  10P GAIN WILD-TYPE  72 314
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     17   27
  10P GAIN WILD-TYPE   72  314
     clus
vv    10P GAIN MUTATED 10P GAIN WILD-TYPE
  NO                17                 72
  YES               27                314
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10P GAIN MUTATED                                  0     1
  10P GAIN WILD-TYPE                                1     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10P GAIN MUTATED                           1    42
  10P GAIN WILD-TYPE                        13   358
D18V7, multiclass
                                  clus
vv                                 10P GAIN MUTATED 10P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  5
  BLACK OR AFRICAN AMERICAN                       1                 13
  WHITE                                          42                358
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V8, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     4  38
  10P GAIN WILD-TYPE  12 349
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      4   38
  10P GAIN WILD-TYPE   12  349
                        clus
vv                       10P GAIN MUTATED 10P GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                 12
  NOT HISPANIC OR LATINO               38                349
[1] 2 2
[1] FALSE

Clustering(19) Variable = 10Q GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                  0   1
  10Q GAIN MUTATED     7   1
  10Q GAIN WILD-TYPE 345  74
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 8                419 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 1                 74 
$`10Q GAIN MUTATED`
TCGA-CS-5393 TCGA-DB-5277 TCGA-DU-A5TS TCGA-FG-A87N TCGA-HT-7476 TCGA-HT-8106 
       40.18        46.65        15.12         7.43         6.54         0.10 
TCGA-S9-A7J0 TCGA-S9-A89Z 
        9.37         5.00 

$`10Q GAIN WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
        0.10        21.01         9.96         6.38        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 
       17.95        12.43         8.48         7.56         8.02         7.40 
TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 
        6.61       122.73        81.96        75.25        47.93        72.92 
TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA 
       50.17        44.52        36.56        78.28        30.08        10.29 
TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG 
       12.72        27.62        27.02        18.84        18.38        72.95 
TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R 
       12.59        11.01        18.84        16.80         5.98        16.08 
TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K 
       15.42        27.81        14.73        13.64        10.92         7.40 
TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 
        6.44        10.29        30.74         3.81        19.96        31.82 
TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D 
       30.31        14.40         8.02        30.21        42.05        27.81 
TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU 
       17.19        17.19        54.25        10.22         6.58         3.45 
TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 
        6.21        18.02        14.56        17.46         6.74        13.38 
TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 
        8.45         6.81       182.33        18.94        17.49        15.16 
TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 
      211.17        52.11        22.42        49.02        75.16        46.06 
TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 
       65.75         1.22        87.45         7.04        11.64       133.74 
TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 
       19.89        16.83        94.52       114.08         7.96         7.73 
TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 
       11.47        62.96       156.23       138.28        14.99       105.21 
TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 
        6.54         8.84       117.40        90.77        30.67        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 
       10.36         7.96        94.32        18.94        44.02        62.01 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 
       25.91        60.30        23.31        41.98         2.76         5.10 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 
       23.74         3.98        20.68        21.40        19.13        16.96 
TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TT TCGA-DU-A5TU 
       15.48        14.17        14.24        12.59         4.96         3.65 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
        5.65        12.20         8.65         2.70        77.98         7.23 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 
        5.98        11.41        26.76         7.13        21.30       124.50 
TCGA-DU-A7TG TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 
       44.42        50.14        67.46        41.13        79.99        57.93 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 TCGA-F6-A8O3 
      134.27        78.21        95.57       130.78        14.33         0.23 
TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 
        0.20        47.77        17.98        34.36        32.19        18.77 
TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 
       14.93        24.99        23.97        13.58        15.35        17.88 
TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 
       22.55        20.61        20.09        12.95        13.68        14.24 
TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT 
       16.01        20.09        14.96        22.52        15.52        38.27 
TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K 
       10.72         5.26        18.71        23.70        14.76        17.82 
TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z 
       16.41        15.02        16.44        10.59        28.54        10.78 
TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 
       22.95        43.69         5.23         5.72         0.13         0.10 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 
        6.67         7.82         8.81         0.13         0.03        16.54 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 
        3.75        17.42        24.26         6.38         7.10        75.19 
TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 
       59.18        60.03       154.19         4.01         5.03        29.85 
TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 
       23.18       107.93         4.57        17.29         3.16        22.06 
TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 
       45.99        56.09        57.60         0.23        14.27         0.16 
TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 
       16.24         0.76        44.68         6.05        42.74         0.10 
TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 
       31.69        14.96         0.10         0.10         2.96        17.52 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 
        6.90        14.53        39.48        19.23        39.09         0.23 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
       50.63         0.49        23.61        37.15         0.33         0.13 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 
        3.68         5.33         2.93         1.71        11.28        31.43 
TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 
        1.64        16.24         9.40        63.55         0.10        21.50 
TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 
       33.01        12.23         6.25         0.46         2.50         3.95 
TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 
        4.70         0.23        29.59         3.88        16.04        15.72 
TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA 
        0.23        10.49         0.13        14.01         0.07        14.70 
TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 
        0.10         5.33         2.70        13.02         1.81        16.14 
TCGA-HT-A618 TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 
        5.33         0.10        29.92        13.45         8.32        19.23 
TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 
       40.18        35.90         4.31        21.70        21.60        19.59 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 
       17.82        20.35         7.89        20.81        20.71        19.00 
TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX 
       42.77         5.23         4.73         0.23         6.71         1.64 
TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 
        2.37         2.30         4.11         5.88         7.63         0.76 
TCGA-P5-A5F6 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z 
        1.28         5.75         2.53         4.83         7.79         4.11 
TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ 
        4.18        14.83        14.53        12.23         2.20         3.16 
TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA 
        0.59         6.31         3.91         4.73         1.91         0.23 
TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO 
        5.03         3.48         0.07        88.83        94.03        32.65 
TCGA-R8-A73M TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX 
       59.38        62.17        69.07        18.77        37.84        34.49 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       31.33        21.63        16.37        17.62        23.64        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
        9.86        94.62        83.70         5.85       106.39        62.37 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM 
       72.59        80.12        32.45        84.99        10.88        19.86 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
       15.91         7.59        15.16        14.07        14.27         7.92 
TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       19.63        12.59         4.21         8.19         2.04         8.12 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 
        3.58         4.04        28.37        13.02       164.38        10.39 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-TM-A7C3 
       99.06        17.42        83.80        31.59        18.71        49.45 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
       48.33        49.32        34.78        48.39        12.00        15.09 
TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L 
       50.76        34.36        24.26        19.36        17.49        40.83 
TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T 
       16.50        29.92        18.90         9.44         4.57        12.00 
TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE 
       33.07        30.08        13.51         0.10         7.89        26.79 
TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-W9-A837 
       10.95        27.06         7.04        23.21        45.07 

  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
              0.10               0.03 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
             46.65             211.17 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
              8.40              16.04 
[1] "0.1 - 46.6 (8.4)"   "0.0 - 211.2 (16.0)"
[1] "hr=" "1.3"
D19V2, continuous
D19V3, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     2   6
  10Q GAIN WILD-TYPE 188 234
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      2    6
  10Q GAIN WILD-TYPE  188  234
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  FEMALE                2                188
  MALE                  6                234
[1] 2 2
[1] FALSE
D19V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  10Q GAIN MUTATED             6                0                 2
  10Q GAIN WILD-TYPE         153              107               162
D19V5, multiclass
                   clus
vv                  10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  ASTROCYTOMA                      6                153
  OLIGOASTROCYTOMA                 0                107
  OLIGODENDROGLIOMA                2                162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V6, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     3   5
  10Q GAIN WILD-TYPE  86 336
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      3    5
  10Q GAIN WILD-TYPE   86  336
     clus
vv    10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  NO                 3                 86
  YES                5                336
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10Q GAIN MUTATED                                  0     1
  10Q GAIN WILD-TYPE                                1     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10Q GAIN MUTATED                           1     6
  10Q GAIN WILD-TYPE                        13   394
D19V7, multiclass
                                  clus
vv                                 10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  5
  BLACK OR AFRICAN AMERICAN                       1                 13
  WHITE                                           6                394
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V8, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     1   6
  10Q GAIN WILD-TYPE  15 381
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      1    6
  10Q GAIN WILD-TYPE   15  381
                        clus
vv                       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 15
  NOT HISPANIC OR LATINO                6                381
[1] 2 2
[1] FALSE

Clustering(20) Variable = 11P GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                  0   1
  11P GAIN MUTATED    24   3
  11P GAIN WILD-TYPE 328  72
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                27                400 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 3                 72 
$`11P GAIN MUTATED`
TCGA-CS-5396 TCGA-CS-6666 TCGA-DB-A4X9 TCGA-DB-A64L TCGA-DH-5144 TCGA-DH-A66D 
        9.96         8.48        30.08        11.01         8.02        27.81 
TCGA-DU-5871 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6400 TCGA-DU-7018 TCGA-DU-7306 
       18.94       211.17        52.11         1.22        30.67        41.98 
TCGA-DU-8168 TCGA-DU-A5TW TCGA-DU-A6S8 TCGA-FG-5962 TCGA-FG-7634 TCGA-HT-7474 
       14.17         5.65         5.98        47.77        15.35         3.75 
TCGA-HT-7684 TCGA-HT-8109 TCGA-QH-A65X TCGA-QH-A6CZ TCGA-S9-A6TW TCGA-S9-A6TY 
        6.05         3.95         7.79         3.16        37.84        31.33 
TCGA-S9-A6WH TCGA-S9-A7QY TCGA-VM-A8CA 
       32.45        28.37        13.51 

$`11P GAIN WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
       40.18         0.10        21.01         6.38        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 
       17.95        12.43         7.56         8.02         7.40         6.61 
TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 
      122.73        81.96        75.25        47.93        72.92        46.65 
TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4XA TCGA-DB-A4XB 
       50.17        44.52        36.56        78.28        10.29        12.72 
TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH 
       27.62        27.02        18.84        18.38        72.95        12.59 
TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U 
       18.84        16.80         5.98        16.08        15.42        27.81 
TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M 
       14.73        13.64        10.92         7.40         6.44        10.29 
TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 
       30.74         3.81        19.96        31.82        30.31        14.40 
TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       30.21        42.05        17.19        17.19        54.25        10.22 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
        6.58         3.45         6.21        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5872 
        6.74        13.38         8.45         6.81       182.33        17.49 
TCGA-DU-5874 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 
       15.16        22.42        49.02        75.16        46.06        65.75 
TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 
       87.45         7.04        11.64       133.74        19.89        16.83 
TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 
       94.52       114.08         7.96         7.73        11.47        62.96 
TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 
      156.23       138.28        14.99       105.21         6.54         8.84 
TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 
      117.40        90.77        26.30        10.36         7.96        94.32 
TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 
       18.94        44.02        62.01        25.91        60.30        23.31 
TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 
        2.76         5.10        23.74         3.98        20.68        21.40 
TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS 
       19.13        16.96        15.48        14.24        12.59        15.12 
TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
        4.96         3.65        12.20         8.65         2.70        77.98 
TCGA-DU-A6S7 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 
        7.23        11.41        26.76         7.13        21.30       124.50 
TCGA-DU-A7TG TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 
       44.42        50.14        67.46        41.13        79.99        57.93 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 TCGA-F6-A8O3 
      134.27        78.21        95.57       130.78        14.33         0.23 
TCGA-F6-A8O4 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 
        0.20        17.98        34.36        32.19        18.77        14.93 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 
       24.99        23.97        13.58        17.88        22.55        20.61 
TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 
       20.09        12.95        13.68        14.24        16.01        20.09 
TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW 
       14.96        22.52        15.52        38.27        10.72         5.26 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ 
       18.71        23.70        14.76        17.82        16.41        15.02 
TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 
       16.44        10.59        28.54        10.78        22.95        43.69 
TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 
        5.23         7.43         5.72         0.13         0.10         6.67 
TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7475 
        7.82         8.81         0.13         0.03        16.54        17.42 
TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 
        6.54        24.26         6.38         7.10        75.19        59.18 
TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 
       60.03       154.19         4.01         5.03        29.85        23.18 
TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 
      107.93         4.57        17.29         3.16        22.06        45.99 
TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 
       56.09        57.60         0.23        14.27         0.16        16.24 
TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 
        0.76        44.68        42.74         0.10        31.69        14.96 
TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 
        0.10         0.10         2.96        17.52         6.90        14.53 
TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 
       39.48        19.23        39.09         0.23        50.63         0.49 
TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 
       23.61        37.15         0.33         0.13         3.68         5.33 
TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 
        2.93         1.71        11.28        31.43         1.64        16.24 
TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 
        9.40        63.55         0.10        21.50        33.01        12.23 
TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8110 TCGA-HT-8111 
        6.25         0.10         0.46         2.50         4.70         0.23 
TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV 
       29.59         3.88        16.04        15.72         0.23        10.49 
TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC 
        0.13        14.01         0.07        14.70         0.10         5.33 
TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A74O 
        2.70        13.02         1.81        16.14         5.33         0.10 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 
       29.92        13.45         8.32        19.23        40.18        35.90 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
        4.31        21.70        21.60        19.59        17.82        20.35 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X 
        7.89        20.81        20.71        19.00        42.77         5.23 
TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ 
        4.73         0.23         6.71         1.64         2.37         2.30 
TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-QH-A65R 
        4.11         5.88         7.63         0.76         1.28         5.75 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV 
        2.53         4.83         4.11         4.18        14.83        14.53 
TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 
       12.23         2.20         0.59         6.31         3.91         4.73 
TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK 
        1.91         0.23         5.03         3.48         0.07        88.83 
TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV 
       94.03        32.65        59.38        62.17        69.07        18.77 
TCGA-S9-A6TX TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       34.49        21.63        16.37        17.62        23.64        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
        9.86        94.62        83.70         5.85       106.39        62.37 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN 
       72.59        80.12        84.99        10.88        19.86        15.91 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX 
        7.59        15.16        14.07        14.27         7.92        19.63 
TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       12.59         4.21         9.37         8.19         2.04         8.12 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 
        3.58         4.04        13.02       164.38        10.39        99.06 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 
       17.42        83.80        31.59        18.71         5.00        49.45 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
       48.33        49.32        34.78        48.39        12.00        15.09 
TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L 
       50.76        34.36        24.26        19.36        17.49        40.83 
TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T 
       16.50        29.92        18.90         9.44         4.57        12.00 
TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH 
       33.07        30.08         0.10         7.89        26.79        10.95 
TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-W9-A837 
       27.06         7.04        23.21        45.07 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              1.22               0.03 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
            211.17             182.33 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
            14.170             16.025 
[1] "1.2 - 211.2 (14.2)" "0.0 - 182.3 (16.0)"
[1] "hr=" "1.5"
D20V2, continuous
D20V3, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    15  12
  11P GAIN WILD-TYPE 175 228
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     15   12
  11P GAIN WILD-TYPE  175  228
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE               15                175
  MALE                 12                228
[1] 2 2
[1] FALSE
D20V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  11P GAIN MUTATED             4                9                14
  11P GAIN WILD-TYPE         155               98               150
D20V5, multiclass
                   clus
vv                  11P GAIN MUTATED 11P GAIN WILD-TYPE
  ASTROCYTOMA                      4                155
  OLIGOASTROCYTOMA                 9                 98
  OLIGODENDROGLIOMA               14                150
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V6, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     6  21
  11P GAIN WILD-TYPE  83 320
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      6   21
  11P GAIN WILD-TYPE   83  320
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  NO                 6                 83
  YES               21                320
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11P GAIN MUTATED                                  0     0
  11P GAIN WILD-TYPE                                1     6
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11P GAIN MUTATED                           1    25
  11P GAIN WILD-TYPE                        13   375
D20V7, multiclass
                                  clus
vv                                 11P GAIN MUTATED 11P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  6
  BLACK OR AFRICAN AMERICAN                       1                 13
  WHITE                                          25                375
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V8, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     1  25
  11P GAIN WILD-TYPE  15 362
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      1   25
  11P GAIN WILD-TYPE   15  362
                        clus
vv                       11P GAIN MUTATED 11P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 15
  NOT HISPANIC OR LATINO               25                362
[1] 2 2
[1] FALSE

Clustering(21) Variable = 11Q GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                  0   1
  11Q GAIN MUTATED    42   7
  11Q GAIN WILD-TYPE 310  68
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                49                378 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 7                 68 
$`11Q GAIN MUTATED`
TCGA-CS-5396 TCGA-DB-5277 TCGA-DB-A4X9 TCGA-DB-A64L TCGA-DB-A64Q TCGA-DB-A75L 
        9.96        46.65        30.08        11.01         5.98         6.44 
TCGA-DH-5144 TCGA-DH-A66D TCGA-DH-A66G TCGA-DH-A7UT TCGA-DU-5870 TCGA-DU-5871 
        8.02        27.81        17.19         6.58       182.33        18.94 
TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6397 TCGA-DU-6400 TCGA-DU-7018 TCGA-DU-7304 
      211.17        52.11        46.06         1.22        30.67        23.31 
TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-A5TT TCGA-DU-A5TW TCGA-DU-A6S8 TCGA-FG-5962 
       41.98         2.76         4.96         5.65         5.98        47.77 
TCGA-FG-7634 TCGA-FG-A60L TCGA-HT-7474 TCGA-HT-7601 TCGA-HT-7604 TCGA-HT-7607 
       15.35        16.41         3.75         5.03       107.93         3.16 
TCGA-HT-7684 TCGA-HT-7688 TCGA-HT-7693 TCGA-HT-8109 TCGA-HW-7490 TCGA-HW-8319 
        6.05        31.69        17.52         3.95        19.23        21.70 
TCGA-QH-A65S TCGA-QH-A65X TCGA-QH-A6CZ TCGA-S9-A6TW TCGA-S9-A6TY TCGA-S9-A6WD 
        2.53         7.79         3.16        37.84        31.33        62.37 
TCGA-S9-A6WH TCGA-S9-A7IZ TCGA-S9-A7QY TCGA-S9-A89Z TCGA-TM-A84J TCGA-VM-A8C8 
       32.45         4.21        28.37         5.00        17.49        33.07 
TCGA-VM-A8CA 
       13.51 

$`11Q GAIN WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
       40.18         0.10        21.01         6.38        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 
       17.95        12.43         8.48         7.56         8.02         7.40 
TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 
        6.61       122.73        81.96        75.25        47.93        72.92 
TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4XA TCGA-DB-A4XB 
       50.17        44.52        36.56        78.28        10.29        12.72 
TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH 
       27.62        27.02        18.84        18.38        72.95        12.59 
TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V 
       18.84        16.80        16.08        15.42        27.81        14.73 
TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       13.64        10.92         7.40        10.29        30.74         3.81 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-A669 TCGA-DH-A66B 
       19.96        31.82        30.31        14.40        30.21        42.05 
TCGA-DH-A66F TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 
       17.19        54.25        10.22         3.45         6.21        18.02 
TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 
       14.56        17.46         6.74        13.38         8.45         6.81 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6399 
       17.49        15.16        22.42        49.02        75.16        65.75 
TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 
       87.45         7.04        11.64       133.74        19.89        16.83 
TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 
       94.52       114.08         7.96         7.73        11.47        62.96 
TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 
      156.23       138.28        14.99       105.21         6.54         8.84 
TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 
      117.40        90.77        26.30        10.36         7.96        94.32 
TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-8158 
       18.94        44.02        62.01        25.91        60.30         5.10 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 
       23.74         3.98        20.68        21.40        19.13        16.96 
TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TU 
       15.48        14.17        14.24        12.59        15.12         3.65 
TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A76K 
       12.20         8.65         2.70        77.98         7.23        11.41 
TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 TCGA-DU-A7TG TCGA-E1-5302 
       26.76         7.13        21.30       124.50        44.42        50.14 
TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 
       67.46        41.13        79.99        57.93       134.27        78.21 
TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5963 
       95.57       130.78        14.33         0.23         0.20        17.98 
TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 
       34.36        32.19        18.77        14.93        24.99        23.97 
TCGA-FG-6692 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 
       13.58        17.88        22.55        20.61        20.09        12.95 
TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 
       13.68        14.24        16.01        20.09        14.96        22.52 
TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY 
       15.52        38.27        10.72         5.26        18.71        23.70 
TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y 
       14.76        17.82        15.02        16.44        10.59        28.54 
TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q 
       10.78        22.95        43.69         5.23         7.43         5.72 
TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 
        0.13         0.10         6.67         7.82         8.81         0.13 
TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 
        0.03        16.54        17.42         6.54        24.26         6.38 
TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 
        7.10        75.19        59.18        60.03       154.19         4.01 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7608 TCGA-HT-7609 
       29.85        23.18         4.57        17.29        22.06        45.99 
TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 
       56.09        57.60         0.23        14.27         0.16        16.24 
TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7689 TCGA-HT-7690 
        0.76        44.68        42.74         0.10        14.96         0.10 
TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 
        0.10         2.96         6.90        14.53        39.48        19.23 
TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 
       39.09         0.23        50.63         0.49        23.61        37.15 
TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 
        0.33         0.13         3.68         5.33         2.93         1.71 
TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 
       11.28        31.43         1.64        16.24         9.40        63.55 
TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 
        0.10        21.50        33.01        12.23         6.25         0.10 
TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 
        0.46         2.50         4.70         0.23        29.59         3.88 
TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 
       16.04        15.72         0.23        10.49         0.13        14.01 
TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 
        0.07        14.70         0.10         5.33         2.70        13.02 
TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 
        1.81        16.14         5.33         0.10        29.92        13.45 
TCGA-HW-7489 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8320 TCGA-HW-8321 
        8.32        40.18        35.90         4.31        21.60        19.59 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 
       17.82        20.35         7.89        20.81        20.71        19.00 
TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX 
       42.77         5.23         4.73         0.23         6.71         1.64 
TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 
        2.37         2.30         4.11         5.88         7.63         0.76 
TCGA-P5-A5F6 TCGA-QH-A65R TCGA-QH-A65V TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU 
        1.28         5.75         4.83         4.11         4.18        14.83 
TCGA-QH-A6CV TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 
       14.53        12.23         2.20         0.59         6.31         3.91 
TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 
        4.73         1.91         0.23         5.03         3.48         0.07 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TS TCGA-S9-A6TU 
       88.83        94.03        32.65        59.38        62.17        69.07 
TCGA-S9-A6TV TCGA-S9-A6TX TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 
       18.77        34.49        21.63        16.37        17.62        23.64 
TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB 
       32.61         9.86        94.62        83.70         5.85       106.39 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN 
       72.59        80.12        84.99        10.88        19.86        15.91 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX 
        7.59        15.16        14.07        14.27         7.92        19.63 
TCGA-S9-A7IY TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW 
       12.59         9.37         8.19         2.04         8.12         3.58 
TCGA-S9-A7QX TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 
        4.04        13.02       164.38        10.39        99.06        17.42 
TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 
       83.80        31.59        18.71        49.45        48.33        49.32 
TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G 
       34.78        48.39        12.00        15.09        50.76        34.36 
TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q 
       24.26        19.36        40.83        16.50        29.92        18.90 
TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-VM-A8C9 TCGA-VM-A8CB TCGA-VM-A8CD 
        9.44         4.57        12.00        30.08         0.10         7.89 
TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-W9-A837 
       26.79        10.95        27.06         7.04        23.21        45.07 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              1.22               0.03 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            211.17             164.38 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             17.19              15.62 
[1] "1.2 - 211.2 (17.2)" "0.0 - 164.4 (15.6)"
[1] "hr=" "1.3"
D21V2, continuous
D21V3, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    27  22
  11Q GAIN WILD-TYPE 163 218
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     27   22
  11Q GAIN WILD-TYPE  163  218
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE               27                163
  MALE                 22                218
[1] 2 2
[1] FALSE
D21V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  11Q GAIN MUTATED            14               12                23
  11Q GAIN WILD-TYPE         145               95               141
D21V5, multiclass
                   clus
vv                  11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  ASTROCYTOMA                     14                145
  OLIGOASTROCYTOMA                12                 95
  OLIGODENDROGLIOMA               23                141
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V6, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    10  39
  11Q GAIN WILD-TYPE  79 302
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     10   39
  11Q GAIN WILD-TYPE   79  302
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  NO                10                 79
  YES               39                302
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11Q GAIN MUTATED                                  0     0
  11Q GAIN WILD-TYPE                                1     6
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11Q GAIN MUTATED                           2    45
  11Q GAIN WILD-TYPE                        12   355
D21V7, multiclass
                                  clus
vv                                 11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  6
  BLACK OR AFRICAN AMERICAN                       2                 12
  WHITE                                          45                355
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V8, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     1  45
  11Q GAIN WILD-TYPE  15 342
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      1   45
  11Q GAIN WILD-TYPE   15  342
                        clus
vv                       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 15
  NOT HISPANIC OR LATINO               45                342
[1] 2 2
[1] FALSE

Clustering(22) Variable = 12P GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                  0   1
  12P GAIN MUTATED    21   6
  12P GAIN WILD-TYPE 331  69
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                27                400 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 6                 69 
$`12P GAIN MUTATED`
TCGA-DB-5273 TCGA-DB-5275 TCGA-DB-A4XE TCGA-DB-A64P TCGA-DH-A669 TCGA-DU-6395 
       81.96        47.93        18.84        16.80        30.21        49.02 
TCGA-DU-6400 TCGA-DU-7007 TCGA-DU-8165 TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TY 
        1.22        62.96        19.13         4.96         3.65        12.20 
TCGA-DU-A7T8 TCGA-E1-5304 TCGA-FG-7634 TCGA-FG-8182 TCGA-FG-8191 TCGA-HT-7469 
      124.50        41.13        15.35        13.68        15.52         7.82 
TCGA-HT-7473 TCGA-HT-7604 TCGA-HT-7873 TCGA-HT-7884 TCGA-HT-8018 TCGA-HT-A614 
       16.54       107.93        23.61        11.28        21.50         2.70 
TCGA-QH-A6CV TCGA-S9-A7IZ TCGA-TM-A84I 
       14.53         4.21        19.36 

$`12P GAIN WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5274 TCGA-DB-5276 TCGA-DB-5277 
        7.40         6.61       122.73        75.25        72.92        46.65 
TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA 
       50.17        44.52        36.56        78.28        30.08        10.29 
TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH 
       12.72        27.62        27.02        18.38        72.95        12.59 
TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U 
       11.01        18.84         5.98        16.08        15.42        27.81 
TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M 
       14.73        13.64        10.92         7.40         6.44        10.29 
TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 
       30.74         3.81        19.96        31.82        30.31        14.40 
TCGA-DH-5144 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR 
        8.02        42.05        27.81        17.19        17.19        54.25 
TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 
       10.22         6.58         3.45         6.21        18.02        14.56 
TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 
       17.46         6.74        13.38         8.45         6.81       182.33 
TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 
       18.94        17.49        15.16       211.17        52.11        22.42 
TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       75.16        46.06        65.75        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 
      133.74        19.89        16.83        94.52       114.08         7.96 
TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 
        7.73        11.47       156.23       138.28        14.99       105.21 
TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 
        6.54         8.84       117.40        90.77        30.67        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 
       10.36         7.96        94.32        18.94        44.02        62.01 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 
       25.91        60.30        23.31        41.98         2.76         5.10 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-8167 
       23.74         3.98        20.68        21.40        16.96        15.48 
TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TW TCGA-DU-A6S2 
       14.17        14.24        12.59        15.12         5.65         8.65 
TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L 
        2.70        77.98         7.23         5.98        11.41        26.76 
TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7TG TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5305 
        7.13        21.30        44.42        50.14        67.46        79.99 
TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 
       57.93       134.27        78.21        95.57       130.78        14.33 
TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 
        0.23         0.20        47.77        17.98        34.36        32.19 
TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7636 
       18.77        14.93        24.99        23.97        13.58        17.88 
TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8185 TCGA-FG-8186 
       22.55        20.61        20.09        12.95        14.24        16.01 
TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW 
       20.09        14.96        22.52        38.27        10.72         5.26 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ 
       18.71        23.70        14.76        17.82        16.41        15.02 
TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 
       16.44        10.59        28.54        10.78        22.95        43.69 
TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 
        5.23         7.43         5.72         0.13         0.10         6.67 
TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 
        8.81         0.13         0.03         3.75        17.42         6.54 
TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 
       24.26         6.38         7.10        75.19        59.18        60.03 
TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7605 
      154.19         4.01         5.03        29.85        23.18         4.57 
TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 
       17.29         3.16        22.06        45.99        56.09        57.60 
TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 
        0.23        14.27         0.16        16.24         0.76        44.68 
TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 
        6.05        42.74         0.10        31.69        14.96         0.10 
TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 
        0.10         2.96        17.52         6.90        14.53        39.48 
TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7874 
       19.23        39.09         0.23        50.63         0.49        37.15 
TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 
        0.33         0.13         3.68         5.33         2.93         1.71 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 
       31.43         1.64        16.24         9.40        63.55         0.10 
TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 
       33.01        12.23         6.25         0.10         0.46         2.50 
TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 
        3.95         4.70         0.23        29.59         3.88        16.04 
TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 
       15.72         0.23        10.49         0.13        14.01         0.07 
TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 
       14.70         0.10         5.33        13.02         1.81        16.14 
TCGA-HT-A618 TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 
        5.33         0.10        29.92        13.45         8.32        19.23 
TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 
       40.18        35.90         4.31        21.70        21.60        19.59 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 
       17.82        20.35         7.89        20.81        20.71        19.00 
TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX 
       42.77         5.23         4.73         0.23         6.71         1.64 
TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 
        2.37         2.30         4.11         5.88         7.63         0.76 
TCGA-P5-A5F6 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z 
        1.28         5.75         2.53         4.83         7.79         4.11 
TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
        4.18        14.83        12.23         2.20         3.16         0.59 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC 
        6.31         3.91         4.73         1.91         0.23         5.03 
TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
        3.48         0.07        88.83        94.03        32.65        59.38 
TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY 
       62.17        69.07        18.77        37.84        34.49        31.33 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       21.63        16.37        17.62        23.64        32.61         9.86 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE 
       94.62        83.70         5.85       106.39        62.37        72.59 
TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN 
       80.12        32.45        84.99        10.88        19.86        15.91 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX 
        7.59        15.16        14.07        14.27         7.92        19.63 
TCGA-S9-A7IY TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW 
       12.59         9.37         8.19         2.04         8.12         3.58 
TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 
        4.04        28.37        13.02       164.38        10.39        99.06 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 
       17.42        83.80        31.59        18.71         5.00        49.45 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
       48.33        49.32        34.78        48.39        12.00        15.09 
TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M 
       50.76        34.36        24.26        17.49        40.83        16.50 
TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-VM-A8C8 
       29.92        18.90         9.44         4.57        12.00        33.07 
TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH 
       30.08        13.51         0.10         7.89        26.79        10.95 
TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-W9-A837 
       27.06         7.04        23.21        45.07 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              1.22               0.03 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            124.50             211.17 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              16.8               15.6 
[1] "1.2 - 124.5 (16.8)" "0.0 - 211.2 (15.6)"
[1] "hr=" "1.1"
D22V2, continuous
D22V3, binary
                    cls
clus                   0   1
  12P GAIN MUTATED     8  19
  12P GAIN WILD-TYPE 182 221
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      8   19
  12P GAIN WILD-TYPE  182  221
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE                8                182
  MALE                 19                221
[1] 2 2
[1] FALSE
D22V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  12P GAIN MUTATED             9                9                 9
  12P GAIN WILD-TYPE         150               98               155
D22V5, multiclass
                   clus
vv                  12P GAIN MUTATED 12P GAIN WILD-TYPE
  ASTROCYTOMA                      9                150
  OLIGOASTROCYTOMA                 9                 98
  OLIGODENDROGLIOMA                9                155
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V6, binary
                    cls
clus                   0   1
  12P GAIN MUTATED     6  21
  12P GAIN WILD-TYPE  83 320
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      6   21
  12P GAIN WILD-TYPE   83  320
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  NO                 6                 83
  YES               21                320
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12P GAIN MUTATED                                  0     1
  12P GAIN WILD-TYPE                                1     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12P GAIN MUTATED                           1    25
  12P GAIN WILD-TYPE                        13   375
D22V7, multiclass
                                  clus
vv                                 12P GAIN MUTATED 12P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  5
  BLACK OR AFRICAN AMERICAN                       1                 13
  WHITE                                          25                375
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V8, binary
                    cls
clus                   0   1
  12P GAIN MUTATED     1  26
  12P GAIN WILD-TYPE  15 361
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      1   26
  12P GAIN WILD-TYPE   15  361
                        clus
vv                       12P GAIN MUTATED 12P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 15
  NOT HISPANIC OR LATINO               26                361
[1] 2 2
[1] FALSE

Clustering(23) Variable = 12Q GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                  0   1
  12Q GAIN MUTATED     7   6
  12Q GAIN WILD-TYPE 345  69
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                13                414 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 6                 69 
$`12Q GAIN MUTATED`
TCGA-DH-A669 TCGA-DU-6395 TCGA-DU-6400 TCGA-DU-7007 TCGA-DU-8165 TCGA-DU-A5TT 
       30.21        49.02         1.22        62.96        19.13         4.96 
TCGA-DU-A5TY TCGA-E1-5304 TCGA-FG-7634 TCGA-HT-7873 TCGA-HT-7884 TCGA-QH-A6CV 
       12.20        41.13        15.35        23.61        11.28        14.53 
TCGA-S9-A6UA 
        5.85 

$`12Q GAIN WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        46.65        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       30.08        10.29        12.72        27.62        27.02        18.84 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       18.38        72.95        12.59        11.01        18.84        16.80 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        16.08        15.42        27.81        14.73        13.64 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       10.92         7.40         6.44        10.29        30.74         3.81 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A66B 
       19.96        31.82        30.31        14.40         8.02        42.05 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT 
       27.81        17.19        17.19        54.25        10.22         6.58 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
        3.45         6.21        18.02        14.56        17.46         6.74 
TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 
       13.38         8.45         6.81       182.33        18.94        17.49 
TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6396 TCGA-DU-6397 
       15.16       211.17        52.11        22.42        75.16        46.06 
TCGA-DU-6399 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 
       65.75        87.45         7.04        11.64       133.74        19.89 
TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 
       16.83        94.52       114.08         7.96         7.73        11.47 
TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 
      156.23       138.28        14.99       105.21         6.54         8.84 
TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 
      117.40        90.77        30.67        26.30        10.36         7.96 
TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 
       94.32        18.94        44.02        62.01        25.91        60.30 
TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 
       23.31        41.98         2.76         5.10        23.74         3.98 
TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP 
       20.68        21.40        16.96        15.48        14.17        14.24 
TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A6S2 TCGA-DU-A6S3 
       12.59        15.12         3.65         5.65         8.65         2.70 
TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O 
       77.98         7.23         5.98        11.41        26.76         7.13 
TCGA-DU-A76R TCGA-DU-A7T8 TCGA-DU-A7TG TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5305 
       21.30       124.50        44.42        50.14        67.46        79.99 
TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 
       57.93       134.27        78.21        95.57       130.78        14.33 
TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 
        0.23         0.20        47.77        17.98        34.36        32.19 
TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7636 
       18.77        14.93        24.99        23.97        13.58        17.88 
TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 
       22.55        20.61        20.09        12.95        13.68        14.24 
TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT 
       16.01        20.09        14.96        22.52        15.52        38.27 
TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K 
       10.72         5.26        18.71        23.70        14.76        17.82 
TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z 
       16.41        15.02        16.44        10.59        28.54        10.78 
TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 
       22.95        43.69         5.23         7.43         5.72         0.13 
TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 
        0.10         6.67         7.82         8.81         0.13         0.03 
TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 
       16.54         3.75        17.42         6.54        24.26         6.38 
TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 
        7.10        75.19        59.18        60.03       154.19         4.01 
TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 
        5.03        29.85        23.18       107.93         4.57        17.29 
TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 
        3.16        22.06        45.99        56.09        57.60         0.23 
TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 
       14.27         0.16        16.24         0.76        44.68         6.05 
TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 
       42.74         0.10        31.69        14.96         0.10         0.10 
TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 
        2.96        17.52         6.90        14.53        39.48        19.23 
TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7874 TCGA-HT-7875 
       39.09         0.23        50.63         0.49        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7902 
        0.13         3.68         5.33         2.93         1.71        31.43 
TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 
        1.64        16.24         9.40        63.55         0.10        21.50 
TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 
       33.01        12.23         6.25         0.10         0.46         2.50 
TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 
        3.95         4.70         0.23        29.59         3.88        16.04 
TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 
       15.72         0.23        10.49         0.13        14.01         0.07 
TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 
       14.70         0.10         5.33         2.70        13.02         1.81 
TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 
       16.14         5.33         0.10        29.92        13.45         8.32 
TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 
       19.23        40.18        35.90         4.31        21.70        21.60 
TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM 
       19.59        17.82        20.35         7.89        20.81        20.71 
TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW 
       19.00        42.77         5.23         4.73         0.23         6.71 
TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 
        1.64         2.37         2.30         4.11         5.88         7.63 
TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X 
        0.76         1.28         5.75         2.53         4.83         7.79 
TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ 
        4.11         4.18        14.83        12.23         2.20         3.16 
TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA 
        0.59         6.31         3.91         4.73         1.91         0.23 
TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO 
        5.03         3.48         0.07        88.83        94.03        32.65 
TCGA-R8-A73M TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX 
       59.38        62.17        69.07        18.77        37.84        34.49 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       31.33        21.63        16.37        17.62        23.64        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE 
        9.86        94.62        83.70       106.39        62.37        72.59 
TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN 
       80.12        32.45        84.99        10.88        19.86        15.91 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX 
        7.59        15.16        14.07        14.27         7.92        19.63 
TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       12.59         4.21         9.37         8.19         2.04         8.12 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 
        3.58         4.04        28.37        13.02       164.38        10.39 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z 
       99.06        17.42        83.80        31.59        18.71         5.00 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B 
       49.45        48.33        49.32        34.78        48.39        12.00 
TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J 
       15.09        50.76        34.36        24.26        19.36        17.49 
TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S 
       40.83        16.50        29.92        18.90         9.44         4.57 
TCGA-TM-A84T TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD 
       12.00        33.07        30.08        13.51         0.10         7.89 
TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-W9-A837 
       26.79        10.95        27.06         7.04        23.21        45.07 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              1.22               0.03 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             62.96             211.17 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             15.35              15.96 
[1] "1.2 - 63.0 (15.3)"  "0.0 - 211.2 (16.0)"
[1] "hr=" "3.5"
D23V2, continuous
D23V3, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED     4   9
  12Q GAIN WILD-TYPE 186 231
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      4    9
  12Q GAIN WILD-TYPE  186  231
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE                4                186
  MALE                  9                231
[1] 2 2
[1] FALSE
D23V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  12Q GAIN MUTATED             5                3                 5
  12Q GAIN WILD-TYPE         154              104               159
D23V5, multiclass
                   clus
vv                  12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  ASTROCYTOMA                      5                154
  OLIGOASTROCYTOMA                 3                104
  OLIGODENDROGLIOMA                5                159
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V6, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED     2  11
  12Q GAIN WILD-TYPE  87 330
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      2   11
  12Q GAIN WILD-TYPE   87  330
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  NO                 2                 87
  YES               11                330
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12Q GAIN MUTATED                                  0     1
  12Q GAIN WILD-TYPE                                1     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12Q GAIN MUTATED                           0    12
  12Q GAIN WILD-TYPE                        14   388
D23V7, multiclass
                                  clus
vv                                 12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  5
  BLACK OR AFRICAN AMERICAN                       0                 14
  WHITE                                          12                388
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V8, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED     0  13
  12Q GAIN WILD-TYPE  16 374
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      0   13
  12Q GAIN WILD-TYPE   16  374
                        clus
vv                       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 16
  NOT HISPANIC OR LATINO               13                374
[1] 2 2
[1] FALSE

Clustering(24) Variable = 13Q GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                  0   1
  13Q GAIN MUTATED     5   0
  13Q GAIN WILD-TYPE 347  75
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 5                422 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 0                 75 
$`13Q GAIN MUTATED`
TCGA-HT-7611 TCGA-HT-A5R7 TCGA-QH-A65S TCGA-QH-A6X9 TCGA-VM-A8CA 
       57.60        14.01         2.53         1.91        13.51 

$`13Q GAIN WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        46.65        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       30.08        10.29        12.72        27.62        27.02        18.84 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       18.38        72.95        12.59        11.01        18.84        16.80 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        16.08        15.42        27.81        14.73        13.64 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       10.92         7.40         6.44        10.29        30.74         3.81 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       42.05        27.81        17.19        17.19        54.25        10.22 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
        6.58         3.45         6.21        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
        6.74        13.38         8.45         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 
       17.49        15.16       211.17        52.11        22.42        49.02 
TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 
       75.16        46.06        65.75         1.22        87.45         7.04 
TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 
       11.64       133.74        19.89        16.83        94.52       114.08 
TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 
        7.96         7.73        11.47        62.96       156.23       138.28 
TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 
       14.99       105.21         6.54         8.84       117.40        90.77 
TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 
       30.67        26.30        10.36         7.96        94.32        18.94 
TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 
       44.02        62.01        25.91        60.30        23.31        41.98 
TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 
        2.76         5.10        23.74         3.98        20.68        21.40 
TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR 
       19.13        16.96        15.48        14.17        14.24        12.59 
TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 
       15.12         4.96         3.65         5.65        12.20         8.65 
TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L 
        2.70        77.98         7.23         5.98        11.41        26.76 
TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 TCGA-DU-A7TG TCGA-E1-5302 TCGA-E1-5303 
        7.13        21.30       124.50        44.42        50.14        67.46 
TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 
       41.13        79.99        57.93       134.27        78.21        95.57 
TCGA-E1-5322 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 
      130.78        14.33         0.23         0.20        47.77        17.98 
TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 
       34.36        32.19        18.77        14.93        24.99        23.97 
TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 
       13.58        15.35        17.88        22.55        20.61        20.09 
TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 
       12.95        13.68        14.24        16.01        20.09        14.96 
TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX 
       22.52        15.52        38.27        10.72         5.26        18.71 
TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 
       23.70        14.76        17.82        16.41        15.02        16.44 
TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 
       10.59        28.54        10.78        22.95        43.69         5.23 
TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 
        7.43         5.72         0.13         0.10         6.67         7.82 
TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 
        8.81         0.13         0.03        16.54         3.75        17.42 
TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 
        6.54        24.26         6.38         7.10        75.19        59.18 
TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 
       60.03       154.19         4.01         5.03        29.85        23.18 
TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 
      107.93         4.57        17.29         3.16        22.06        45.99 
TCGA-HT-7610 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 
       56.09         0.23        14.27         0.16        16.24         0.76 
TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 
       44.68         6.05        42.74         0.10        31.69        14.96 
TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 
        0.10         0.10         2.96        17.52         6.90        14.53 
TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 
       39.48        19.23        39.09         0.23        50.63         0.49 
TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 
       23.61        37.15         0.33         0.13         3.68         5.33 
TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 
        2.93         1.71        11.28        31.43         1.64        16.24 
TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 
        9.40        63.55         0.10        21.50        33.01        12.23 
TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 
        6.25         0.10         0.46         2.50         3.95         4.70 
TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS 
        0.23        29.59         3.88        16.04        15.72         0.23 
TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC 
       10.49         0.13         0.07        14.70         0.10         5.33 
TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A74O 
        2.70        13.02         1.81        16.14         5.33         0.10 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 
       29.92        13.45         8.32        19.23        40.18        35.90 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
        4.31        21.70        21.60        19.59        17.82        20.35 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X 
        7.89        20.81        20.71        19.00        42.77         5.23 
TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ 
        4.73         0.23         6.71         1.64         2.37         2.30 
TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-QH-A65R 
        4.11         5.88         7.63         0.76         1.28         5.75 
TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV 
        4.83         7.79         4.11         4.18        14.83        14.53 
TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 
       12.23         2.20         3.16         0.59         6.31         3.91 
TCGA-QH-A6X8 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK 
        4.73         0.23         5.03         3.48         0.07        88.83 
TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV 
       94.03        32.65        59.38        62.17        69.07        18.77 
TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 
       37.84        34.49        31.33        21.63        16.37        17.62 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA 
       23.64        32.61         9.86        94.62        83.70         5.85 
TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI 
      106.39        62.37        72.59        80.12        32.45        84.99 
TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ 
       10.88        19.86        15.91         7.59        15.16        14.07 
TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 
       14.27         7.92        19.63        12.59         4.21         9.37 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY 
        8.19         2.04         8.12         3.58         4.04        28.37 
TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 
       13.02       164.38        10.39        99.06        17.42        83.80 
TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 
       31.59        18.71         5.00        49.45        48.33        49.32 
TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G 
       34.78        48.39        12.00        15.09        50.76        34.36 
TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O 
       24.26        19.36        17.49        40.83        16.50        29.92 
TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-VM-A8C8 TCGA-VM-A8C9 
       18.90         9.44         4.57        12.00        33.07        30.08 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M 
        0.10         7.89        26.79        10.95        27.06         7.04 
TCGA-VW-A7QS TCGA-W9-A837 
       23.21        45.07 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              1.91               0.03 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             57.60             211.17 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
            13.510             16.025 
[1] "1.9 - 57.6 (13.5)"  "0.0 - 211.2 (16.0)"
[1] "hr="     "3300000"
D24V2, continuous
D24V3, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     3   3
  13Q GAIN WILD-TYPE 187 237
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      3    3
  13Q GAIN WILD-TYPE  187  237
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE                3                187
  MALE                  3                237
[1] 2 2
[1] FALSE
D24V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  13Q GAIN MUTATED             2                2                 2
  13Q GAIN WILD-TYPE         157              105               162
D24V5, multiclass
                   clus
vv                  13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  ASTROCYTOMA                      2                157
  OLIGOASTROCYTOMA                 2                105
  OLIGODENDROGLIOMA                2                162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V6, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     0   6
  13Q GAIN WILD-TYPE  89 335
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      0    6
  13Q GAIN WILD-TYPE   89  335
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  NO                 0                 89
  YES                6                335
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  13Q GAIN MUTATED                                  0     0
  13Q GAIN WILD-TYPE                                1     6
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  13Q GAIN MUTATED                           0     5
  13Q GAIN WILD-TYPE                        14   395
D24V7, multiclass
                                  clus
vv                                 13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  6
  BLACK OR AFRICAN AMERICAN                       0                 14
  WHITE                                           5                395
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V8, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     0   5
  13Q GAIN WILD-TYPE  16 382
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      0    5
  13Q GAIN WILD-TYPE   16  382
                        clus
vv                       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 16
  NOT HISPANIC OR LATINO                5                382
[1] 2 2
[1] FALSE

Clustering(25) Variable = 14Q GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                  0   1
  14Q GAIN MUTATED     2   1
  14Q GAIN WILD-TYPE 350  74
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 3                424 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 1                 74 
$`14Q GAIN MUTATED`
TCGA-CS-6665 TCGA-DH-A669 TCGA-DU-7019 
       12.43        30.21        26.30 

$`14Q GAIN WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 
       23.84        17.95         8.48         7.56         8.02         7.40 
TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 
        6.61       122.73        81.96        75.25        47.93        72.92 
TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 
       46.65        50.17        44.52        36.56        78.28        30.08 
TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF 
       10.29        12.72        27.62        27.02        18.84        18.38 
TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q 
       72.95        12.59        11.01        18.84        16.80         5.98 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X 
       16.08        15.42        27.81        14.73        13.64        10.92 
TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 
        7.40         6.44        10.29        30.74         3.81        19.96 
TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A66B TCGA-DH-A66D 
       31.82        30.31        14.40         8.02        42.05        27.81 
TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU 
       17.19        17.19        54.25        10.22         6.58         3.45 
TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 
        6.21        18.02        14.56        17.46         6.74        13.38 
TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 
        8.45         6.81       182.33        18.94        17.49        15.16 
TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 
      211.17        52.11        22.42        49.02        75.16        46.06 
TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 
       65.75         1.22        87.45         7.04        11.64       133.74 
TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 
       19.89        16.83        94.52       114.08         7.96         7.73 
TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 
       11.47        62.96       156.23       138.28        14.99       105.21 
TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7290 
        6.54         8.84       117.40        90.77        30.67        10.36 
TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 
        7.96        94.32        18.94        44.02        62.01        25.91 
TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 
       60.30        23.31        41.98         2.76         5.10        23.74 
TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 
        3.98        20.68        21.40        19.13        16.96        15.48 
TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU 
       14.17        14.24        12.59        15.12         4.96         3.65 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
        5.65        12.20         8.65         2.70        77.98         7.23 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 
        5.98        11.41        26.76         7.13        21.30       124.50 
TCGA-DU-A7TG TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 
       44.42        50.14        67.46        41.13        79.99        57.93 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 TCGA-F6-A8O3 
      134.27        78.21        95.57       130.78        14.33         0.23 
TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 
        0.20        47.77        17.98        34.36        32.19        18.77 
TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 
       14.93        24.99        23.97        13.58        15.35        17.88 
TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 
       22.55        20.61        20.09        12.95        13.68        14.24 
TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT 
       16.01        20.09        14.96        22.52        15.52        38.27 
TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K 
       10.72         5.26        18.71        23.70        14.76        17.82 
TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z 
       16.41        15.02        16.44        10.59        28.54        10.78 
TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 
       22.95        43.69         5.23         7.43         5.72         0.13 
TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 
        0.10         6.67         7.82         8.81         0.13         0.03 
TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 
       16.54         3.75        17.42         6.54        24.26         6.38 
TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 
        7.10        75.19        59.18        60.03       154.19         4.01 
TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 
        5.03        29.85        23.18       107.93         4.57        17.29 
TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 
        3.16        22.06        45.99        56.09        57.60         0.23 
TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 
       14.27         0.16        16.24         0.76        44.68         6.05 
TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 
       42.74         0.10        31.69        14.96         0.10         0.10 
TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 
        2.96        17.52         6.90        14.53        39.48        19.23 
TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 
       39.09         0.23        50.63         0.49        23.61        37.15 
TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 
        0.33         0.13         3.68         5.33         2.93         1.71 
TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 
       11.28        31.43         1.64        16.24         9.40        63.55 
TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 
        0.10        21.50        33.01        12.23         6.25         0.10 
TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 
        0.46         2.50         3.95         4.70         0.23        29.59 
TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
        3.88        16.04        15.72         0.23        10.49         0.13 
TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 
       14.01         0.07        14.70         0.10         5.33         2.70 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A74O TCGA-HW-7486 
       13.02         1.81        16.14         5.33         0.10        29.92 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 
       13.45         8.32        19.23        40.18        35.90         4.31 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
       21.70        21.60        19.59        17.82        20.35         7.89 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 
       20.81        20.71        19.00        42.77         5.23         4.73 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 
        0.23         6.71         1.64         2.37         2.30         4.11 
TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-QH-A65R TCGA-QH-A65S 
        5.88         7.63         0.76         1.28         5.75         2.53 
TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV 
        4.83         7.79         4.11         4.18        14.83        14.53 
TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 
       12.23         2.20         3.16         0.59         6.31         3.91 
TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 
        4.73         1.91         0.23         5.03         3.48         0.07 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TS TCGA-S9-A6TU 
       88.83        94.03        32.65        59.38        62.17        69.07 
TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 
       18.77        37.84        34.49        31.33        21.63        16.37 
TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
       17.62        23.64        32.61         9.86        94.62        83.70 
TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH 
        5.85       106.39        62.37        72.59        80.12        32.45 
TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP 
       84.99        10.88        19.86        15.91         7.59        15.16 
TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ 
       14.07        14.27         7.92        19.63        12.59         4.21 
TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX 
        9.37         8.19         2.04         8.12         3.58         4.04 
TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 
       28.37        13.02       164.38        10.39        99.06        17.42 
TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 
       83.80        31.59        18.71         5.00        49.45        48.33 
TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F 
       49.32        34.78        48.39        12.00        15.09        50.76 
TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M 
       34.36        24.26        19.36        17.49        40.83        16.50 
TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-VM-A8C8 
       29.92        18.90         9.44         4.57        12.00        33.07 
TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH 
       30.08        13.51         0.10         7.89        26.79        10.95 
TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-W9-A837 
       27.06         7.04        23.21        45.07 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             12.43               0.03 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             30.21             211.17 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
            26.300             15.815 
[1] "12.4 - 30.2 (26.3)" "0.0 - 211.2 (15.8)"
[1] "hr=" "2.3"
D25V2, continuous
D25V3, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     1   2
  14Q GAIN WILD-TYPE 189 238
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      1    2
  14Q GAIN WILD-TYPE  189  238
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE                1                189
  MALE                  2                238
[1] 2 2
[1] FALSE
D25V4, continuous
[1] "Remove cluster labels:" "14Q GAIN MUTATED"      
clus
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 2                247 
        TCGA-CS-4938         TCGA-CS-4941         TCGA-CS-4942 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CS-4943         TCGA-CS-4944         TCGA-CS-5390 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CS-5393         TCGA-CS-5395         TCGA-CS-5396 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CS-5397         TCGA-CS-6186         TCGA-CS-6188 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CS-6290         TCGA-CS-6666         TCGA-CS-6667 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CS-6668         TCGA-CS-6669         TCGA-DB-5274 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DB-A4XE         TCGA-DB-A64L         TCGA-DB-A64Q 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DB-A64R         TCGA-DB-A64S         TCGA-DB-A64U 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DB-A64V         TCGA-DB-A64W         TCGA-DB-A64X 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DB-A75L         TCGA-DB-A75O         TCGA-DH-5140 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DH-5142         TCGA-DH-5143         TCGA-DH-5144 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DH-A66B         TCGA-DH-A66D         TCGA-DH-A66F 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DH-A66G         TCGA-DH-A7UR         TCGA-DH-A7UU 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DH-A7UV         TCGA-DU-5851         TCGA-DU-5852 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-5853         TCGA-DU-5854         TCGA-DU-5855 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-5870         TCGA-DU-5871         TCGA-DU-5874 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-6396         TCGA-DU-6403         TCGA-DU-6404 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-6405         TCGA-DU-6407         TCGA-DU-6408 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-6410         TCGA-DU-7011         TCGA-DU-7013 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-7014         TCGA-DU-7015         TCGA-DU-7018 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-7294         TCGA-DU-7298         TCGA-DU-7299 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-7300         TCGA-DU-7301         TCGA-DU-7302 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-7304         TCGA-DU-7306         TCGA-DU-7309 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-8158         TCGA-DU-8161         TCGA-DU-8162 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-8163         TCGA-DU-8165         TCGA-DU-8167 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-8168         TCGA-DU-A5TP         TCGA-DU-A5TR 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-A5TS         TCGA-DU-A5TU         TCGA-DU-A5TW 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-A6S2         TCGA-DU-A6S6         TCGA-DU-A6S7 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-A6S8         TCGA-DU-A76R         TCGA-DU-A7T8 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-A7TG         TCGA-E1-5302         TCGA-E1-5303 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-E1-5304         TCGA-E1-5305         TCGA-E1-5307 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-E1-5311         TCGA-E1-5318         TCGA-E1-5319 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-E1-5322         TCGA-FG-5963         TCGA-FG-5965 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FG-6688         TCGA-FG-6689         TCGA-FG-6690 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FG-6691         TCGA-FG-7636         TCGA-FG-7638 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FG-8181         TCGA-FG-8185         TCGA-FG-8186 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FG-8187         TCGA-FG-8188         TCGA-FG-8189 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FG-A4MT         TCGA-FG-A4MW         TCGA-FG-A4MX 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FG-A60J         TCGA-FG-A60L         TCGA-FG-A6J1 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FG-A6J3         TCGA-FG-A711         TCGA-FG-A713 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FG-A87Q         TCGA-HT-7468         TCGA-HT-7470 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HT-7475         TCGA-HT-7477         TCGA-HT-7485 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HT-7607         TCGA-HT-7609         TCGA-HT-7611 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HT-7689         TCGA-HT-7692         TCGA-HT-7693 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HT-7694         TCGA-HT-7854         TCGA-HT-7875 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HT-7884         TCGA-HT-8564         TCGA-HT-A4DV 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HT-A5R7         TCGA-HT-A5RA         TCGA-HT-A5RC 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HT-A615         TCGA-HT-A617         TCGA-HT-A618 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-IK-7675         TCGA-KT-A74X         TCGA-KT-A7W1 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-P5-A5EU         TCGA-P5-A5EV         TCGA-P5-A5EW 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-P5-A5EX         TCGA-P5-A5F0         TCGA-P5-A5F2 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-P5-A5F4         TCGA-P5-A5F6         TCGA-QH-A65R 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-QH-A65S         TCGA-QH-A65V         TCGA-QH-A65X 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-QH-A65Z         TCGA-QH-A6CS         TCGA-QH-A6CU 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-QH-A6CV         TCGA-QH-A6CW         TCGA-QH-A6CX 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-QH-A6CY         TCGA-QH-A6CZ         TCGA-QH-A6X3 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-QH-A6X4         TCGA-QH-A6X5         TCGA-QH-A6X8 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-QH-A6X9         TCGA-QH-A6XA         TCGA-QH-A6XC 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-QH-A86X         TCGA-QH-A870         TCGA-S9-A6TS 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-S9-A6TU         TCGA-S9-A6TV         TCGA-S9-A6TW 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-S9-A6TX         TCGA-S9-A6TY         TCGA-S9-A6TZ 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-S9-A6U0         TCGA-S9-A6U1         TCGA-S9-A6U2 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-S9-A6U5         TCGA-S9-A6U6         TCGA-S9-A6U8 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-S9-A6UA         TCGA-S9-A6UB         TCGA-S9-A6WD 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-S9-A6WE         TCGA-S9-A6WG         TCGA-S9-A6WH 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-S9-A6WI         TCGA-S9-A6WL         TCGA-S9-A6WM 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-S9-A6WN         TCGA-S9-A6WO         TCGA-S9-A6WP 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-S9-A6WQ         TCGA-S9-A7IQ         TCGA-S9-A7IS 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-S9-A7IX         TCGA-S9-A7IY         TCGA-S9-A7IZ 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-S9-A7J0         TCGA-S9-A7J1         TCGA-S9-A7J2 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-S9-A7J3         TCGA-S9-A7QW         TCGA-S9-A7QX 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-S9-A7QY         TCGA-S9-A7QZ         TCGA-S9-A7R1 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-S9-A7R2         TCGA-S9-A7R3         TCGA-S9-A7R4 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-S9-A7R7         TCGA-S9-A7R8         TCGA-S9-A89V 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-S9-A89Z         TCGA-TM-A7C3         TCGA-TM-A7C4 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-TM-A7C5         TCGA-TM-A7CA         TCGA-TM-A7CF 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-TM-A84B         TCGA-TM-A84C         TCGA-TM-A84F 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-TM-A84G         TCGA-TM-A84H         TCGA-TM-A84I 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-TM-A84J         TCGA-TM-A84L         TCGA-TM-A84M 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-TM-A84O         TCGA-TM-A84Q         TCGA-TM-A84R 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-TM-A84S         TCGA-TM-A84T         TCGA-VM-A8C8 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-VM-A8CA         TCGA-VM-A8CD         TCGA-VM-A8CE 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-VM-A8CH 
"14Q GAIN WILD-TYPE" 
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  14Q GAIN MUTATED             1                1                 1
  14Q GAIN WILD-TYPE         158              106               163
D25V5, multiclass
                   clus
vv                  14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  ASTROCYTOMA                      1                158
  OLIGOASTROCYTOMA                 1                106
  OLIGODENDROGLIOMA                1                163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V6, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     2   1
  14Q GAIN WILD-TYPE  87 340
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      2    1
  14Q GAIN WILD-TYPE   87  340
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  NO                 2                 87
  YES                1                340
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  14Q GAIN MUTATED                                  0     0
  14Q GAIN WILD-TYPE                                1     6
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  14Q GAIN MUTATED                           0     3
  14Q GAIN WILD-TYPE                        14   397
D25V7, multiclass
                                  clus
vv                                 14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  6
  BLACK OR AFRICAN AMERICAN                       0                 14
  WHITE                                           3                397
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V8, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     0   3
  14Q GAIN WILD-TYPE  16 384
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      0    3
  14Q GAIN WILD-TYPE   16  384
                        clus
vv                       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 16
  NOT HISPANIC OR LATINO                3                384
[1] 2 2
[1] FALSE

Clustering(26) Variable = 15Q GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                  0   1
  15Q GAIN MUTATED     4   4
  15Q GAIN WILD-TYPE 348  71
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 8                419 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 4                 71 
$`15Q GAIN MUTATED`
TCGA-CS-4943 TCGA-DU-5852 TCGA-DU-7014 TCGA-DU-7306 TCGA-E1-5304 TCGA-HT-7477 
       18.15         6.74       117.40        41.98        41.13        24.26 
TCGA-S9-A6UA TCGA-S9-A7IZ 
        5.85         4.21 

$`15Q GAIN WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5393 
        4.70         7.69        43.89        10.62        64.64        40.18 
TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
        0.10        21.01         9.96         6.38        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 
       17.95        12.43         8.48         7.56         8.02         7.40 
TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 
        6.61       122.73        81.96        75.25        47.93        72.92 
TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 
       46.65        50.17        44.52        36.56        78.28        30.08 
TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF 
       10.29        12.72        27.62        27.02        18.84        18.38 
TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q 
       72.95        12.59        11.01        18.84        16.80         5.98 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X 
       16.08        15.42        27.81        14.73        13.64        10.92 
TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 
        7.40         6.44        10.29        30.74         3.81        19.96 
TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B 
       31.82        30.31        14.40         8.02        30.21        42.05 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT 
       27.81        17.19        17.19        54.25        10.22         6.58 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5853 
        3.45         6.21        18.02        14.56        17.46        13.38 
TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 
        8.45         6.81       182.33        18.94        17.49        15.16 
TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 
      211.17        52.11        22.42        49.02        75.16        46.06 
TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 
       65.75         1.22        87.45         7.04        11.64       133.74 
TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 
       19.89        16.83        94.52       114.08         7.96         7.73 
TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 
       11.47        62.96       156.23       138.28        14.99       105.21 
TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 
        6.54         8.84        90.77        30.67        26.30        10.36 
TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 
        7.96        94.32        18.94        44.02        62.01        25.91 
TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 
       60.30        23.31         2.76         5.10        23.74         3.98 
TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 
       20.68        21.40        19.13        16.96        15.48        14.17 
TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW 
       14.24        12.59        15.12         4.96         3.65         5.65 
TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 
       12.20         8.65         2.70        77.98         7.23         5.98 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 TCGA-DU-A7TG 
       11.41        26.76         7.13        21.30       124.50        44.42 
TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 
       50.14        67.46        79.99        57.93       134.27        78.21 
TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 
       95.57       130.78        14.33         0.23         0.20        47.77 
TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 
       17.98        34.36        32.19        18.77        14.93        24.99 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 
       23.97        13.58        15.35        17.88        22.55        20.61 
TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 
       20.09        12.95        13.68        14.24        16.01        20.09 
TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW 
       14.96        22.52        15.52        38.27        10.72         5.26 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ 
       18.71        23.70        14.76        17.82        16.41        15.02 
TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 
       16.44        10.59        28.54        10.78        22.95        43.69 
TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 
        5.23         7.43         5.72         0.13         0.10         6.67 
TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 
        7.82         8.81         0.13         0.03        16.54         3.75 
TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 
       17.42         6.54         6.38         7.10        75.19        59.18 
TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 
       60.03       154.19         4.01         5.03        29.85        23.18 
TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 
      107.93         4.57        17.29         3.16        22.06        45.99 
TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 
       56.09        57.60         0.23        14.27         0.16        16.24 
TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 
        0.76        44.68         6.05        42.74         0.10        31.69 
TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 
       14.96         0.10         0.10         2.96        17.52         6.90 
TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 
       14.53        39.48        19.23        39.09         0.23        50.63 
TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 
        0.49        23.61        37.15         0.33         0.13         3.68 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 
        5.33         2.93         1.71        11.28        31.43         1.64 
TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 
       16.24         9.40        63.55         0.10        21.50        33.01 
TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 
       12.23         6.25         0.10         0.46         2.50         3.95 
TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 
        4.70         0.23        29.59         3.88        16.04        15.72 
TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA 
        0.23        10.49         0.13        14.01         0.07        14.70 
TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 
        0.10         5.33         2.70        13.02         1.81        16.14 
TCGA-HT-A618 TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 
        5.33         0.10        29.92        13.45         8.32        19.23 
TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 
       40.18        35.90         4.31        21.70        21.60        19.59 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 
       17.82        20.35         7.89        20.81        20.71        19.00 
TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX 
       42.77         5.23         4.73         0.23         6.71         1.64 
TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 
        2.37         2.30         4.11         5.88         7.63         0.76 
TCGA-P5-A5F6 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z 
        1.28         5.75         2.53         4.83         7.79         4.11 
TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ 
        4.18        14.83        14.53        12.23         2.20         3.16 
TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA 
        0.59         6.31         3.91         4.73         1.91         0.23 
TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO 
        5.03         3.48         0.07        88.83        94.03        32.65 
TCGA-R8-A73M TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX 
       59.38        62.17        69.07        18.77        37.84        34.49 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       31.33        21.63        16.37        17.62        23.64        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE 
        9.86        94.62        83.70       106.39        62.37        72.59 
TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN 
       80.12        32.45        84.99        10.88        19.86        15.91 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX 
        7.59        15.16        14.07        14.27         7.92        19.63 
TCGA-S9-A7IY TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW 
       12.59         9.37         8.19         2.04         8.12         3.58 
TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 
        4.04        28.37        13.02       164.38        10.39        99.06 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 
       17.42        83.80        31.59        18.71         5.00        49.45 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
       48.33        49.32        34.78        48.39        12.00        15.09 
TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L 
       50.76        34.36        24.26        19.36        17.49        40.83 
TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T 
       16.50        29.92        18.90         9.44         4.57        12.00 
TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE 
       33.07        30.08        13.51         0.10         7.89        26.79 
TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-W9-A837 
       10.95        27.06         7.04        23.21        45.07 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              4.21               0.03 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            117.40             211.17 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            21.205             15.720 
[1] "4.2 - 117.4 (21.2)" "0.0 - 211.2 (15.7)"
[1] "hr=" "2.3"
D26V2, continuous
D26V3, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     2   6
  15Q GAIN WILD-TYPE 188 234
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      2    6
  15Q GAIN WILD-TYPE  188  234
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE                2                188
  MALE                  6                234
[1] 2 2
[1] FALSE
D26V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  15Q GAIN MUTATED             5                2                 1
  15Q GAIN WILD-TYPE         154              105               163
D26V5, multiclass
                   clus
vv                  15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  ASTROCYTOMA                      5                154
  OLIGOASTROCYTOMA                 2                105
  OLIGODENDROGLIOMA                1                163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V6, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     2   6
  15Q GAIN WILD-TYPE  87 335
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      2    6
  15Q GAIN WILD-TYPE   87  335
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  NO                 2                 87
  YES                6                335
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  15Q GAIN MUTATED                                  0     0
  15Q GAIN WILD-TYPE                                1     6
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  15Q GAIN MUTATED                           0     8
  15Q GAIN WILD-TYPE                        14   392
D26V7, multiclass
                                  clus
vv                                 15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  6
  BLACK OR AFRICAN AMERICAN                       0                 14
  WHITE                                           8                392
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V8, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     0   7
  15Q GAIN WILD-TYPE  16 380
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      0    7
  15Q GAIN WILD-TYPE   16  380
                        clus
vv                       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 16
  NOT HISPANIC OR LATINO                7                380
[1] 2 2
[1] FALSE

Clustering(27) Variable = 16P GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                  0   1
  16P GAIN MUTATED    11   5
  16P GAIN WILD-TYPE 341  70
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                16                411 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 5                 70 
$`16P GAIN MUTATED`
TCGA-CS-5397 TCGA-DB-A4XH TCGA-DH-A66B TCGA-DU-6392 TCGA-DU-6400 TCGA-DU-7007 
        6.38        12.59        42.05       211.17         1.22        62.96 
TCGA-DU-7010 TCGA-DU-A5TS TCGA-E1-5304 TCGA-FG-5962 TCGA-HT-A5R7 TCGA-HT-A618 
       14.99        15.12        41.13        47.77        14.01         5.33 
TCGA-S9-A6WH TCGA-S9-A7QW TCGA-TM-A84I TCGA-VM-A8CA 
       32.45         3.58        19.36        13.51 

$`16P GAIN WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-6186 TCGA-CS-6188 
       40.18         0.10        21.01         9.96        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 
       17.95        12.43         8.48         7.56         8.02         7.40 
TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 
        6.61       122.73        81.96        75.25        47.93        72.92 
TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 
       46.65        50.17        44.52        36.56        78.28        30.08 
TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF 
       10.29        12.72        27.62        27.02        18.84        18.38 
TCGA-DB-A4XG TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R 
       72.95        11.01        18.84        16.80         5.98        16.08 
TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K 
       15.42        27.81        14.73        13.64        10.92         7.40 
TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 
        6.44        10.29        30.74         3.81        19.96        31.82 
TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66D TCGA-DH-A66F 
       30.31        14.40         8.02        30.21        27.81        17.19 
TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV 
       17.19        54.25        10.22         6.58         3.45         6.21 
TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 
       18.02        14.56        17.46         6.74        13.38         8.45 
TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6393 
        6.81       182.33        18.94        17.49        15.16        52.11 
TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6401 
       22.42        49.02        75.16        46.06        65.75        87.45 
TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 
        7.04        11.64       133.74        19.89        16.83        94.52 
TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7008 TCGA-DU-7009 
      114.08         7.96         7.73        11.47       156.23       138.28 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 
      105.21         6.54         8.84       117.40        90.77        30.67 
TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 
       26.30        10.36         7.96        94.32        18.94        44.02 
TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 
       62.01        25.91        60.30        23.31        41.98         2.76 
TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 
        5.10        23.74         3.98        20.68        21.40        19.13 
TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TT 
       16.96        15.48        14.17        14.24        12.59         4.96 
TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
        3.65         5.65        12.20         8.65         2.70        77.98 
TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R 
        7.23         5.98        11.41        26.76         7.13        21.30 
TCGA-DU-A7T8 TCGA-DU-A7TG TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5307 
      124.50        44.42        50.14        67.46        79.99        57.93 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 TCGA-F6-A8O3 
      134.27        78.21        95.57       130.78        14.33         0.23 
TCGA-F6-A8O4 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 
        0.20        17.98        34.36        32.19        18.77        14.93 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 
       24.99        23.97        13.58        15.35        17.88        22.55 
TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 
       20.61        20.09        12.95        13.68        14.24        16.01 
TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU 
       20.09        14.96        22.52        15.52        38.27        10.72 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
        5.26        18.71        23.70        14.76        17.82        16.41 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 
       15.02        16.44        10.59        28.54        10.78        22.95 
TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 
       43.69         5.23         7.43         5.72         0.13         0.10 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 
        6.67         7.82         8.81         0.13         0.03        16.54 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 
        3.75        17.42         6.54        24.26         6.38         7.10 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
       75.19        59.18        60.03       154.19         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 
       29.85        23.18       107.93         4.57        17.29         3.16 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
       22.06        45.99        56.09        57.60         0.23        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 
        0.16        16.24         0.76        44.68         6.05        42.74 
TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 
        0.10        31.69        14.96         0.10         0.10         2.96 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 
       17.52         6.90        14.53        39.48        19.23        39.09 
TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 
        0.23        50.63         0.49        23.61        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 
        0.13         3.68         5.33         2.93         1.71        11.28 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 
       31.43         1.64        16.24         9.40        63.55         0.10 
TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 
       21.50        33.01        12.23         6.25         0.10         0.46 
TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 
        2.50         3.95         4.70         0.23        29.59         3.88 
TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R9 
       16.04        15.72         0.23        10.49         0.13         0.07 
TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 
       14.70         0.10         5.33         2.70        13.02         1.81 
TCGA-HT-A617 TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 
       16.14         0.10        29.92        13.45         8.32        19.23 
TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 
       40.18        35.90         4.31        21.70        21.60        19.59 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 
       17.82        20.35         7.89        20.81        20.71        19.00 
TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX 
       42.77         5.23         4.73         0.23         6.71         1.64 
TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 
        2.37         2.30         4.11         5.88         7.63         0.76 
TCGA-P5-A5F6 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z 
        1.28         5.75         2.53         4.83         7.79         4.11 
TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ 
        4.18        14.83        14.53        12.23         2.20         3.16 
TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA 
        0.59         6.31         3.91         4.73         1.91         0.23 
TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO 
        5.03         3.48         0.07        88.83        94.03        32.65 
TCGA-R8-A73M TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX 
       59.38        62.17        69.07        18.77        37.84        34.49 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       31.33        21.63        16.37        17.62        23.64        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
        9.86        94.62        83.70         5.85       106.39        62.37 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN 
       72.59        80.12        84.99        10.88        19.86        15.91 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX 
        7.59        15.16        14.07        14.27         7.92        19.63 
TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       12.59         4.21         9.37         8.19         2.04         8.12 
TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 
        4.04        28.37        13.02       164.38        10.39        99.06 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 
       17.42        83.80        31.59        18.71         5.00        49.45 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
       48.33        49.32        34.78        48.39        12.00        15.09 
TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M 
       50.76        34.36        24.26        17.49        40.83        16.50 
TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-VM-A8C8 
       29.92        18.90         9.44         4.57        12.00        33.07 
TCGA-VM-A8C9 TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 
       30.08         0.10         7.89        26.79        10.95        27.06 
TCGA-VV-A86M TCGA-VW-A7QS TCGA-W9-A837 
        7.04        23.21        45.07 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              1.22               0.03 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
            211.17             182.33 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
            15.055             16.010 
[1] "1.2 - 211.2 (15.1)" "0.0 - 182.3 (16.0)"
[1] "hr=" "1.5"
D27V2, continuous
D27V3, binary
                    cls
clus                   0   1
  16P GAIN MUTATED     9   7
  16P GAIN WILD-TYPE 181 233
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      9    7
  16P GAIN WILD-TYPE  181  233
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE                9                181
  MALE                  7                233
[1] 2 2
[1] FALSE
D27V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  16P GAIN MUTATED            10                2                 4
  16P GAIN WILD-TYPE         149              105               160
D27V5, multiclass
                   clus
vv                  16P GAIN MUTATED 16P GAIN WILD-TYPE
  ASTROCYTOMA                     10                149
  OLIGOASTROCYTOMA                 2                105
  OLIGODENDROGLIOMA                4                160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V6, binary
                    cls
clus                   0   1
  16P GAIN MUTATED     4  12
  16P GAIN WILD-TYPE  85 329
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      4   12
  16P GAIN WILD-TYPE   85  329
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  NO                 4                 85
  YES               12                329
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16P GAIN MUTATED                                  0     0
  16P GAIN WILD-TYPE                                1     6
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16P GAIN MUTATED                           1    14
  16P GAIN WILD-TYPE                        13   386
D27V7, multiclass
                                  clus
vv                                 16P GAIN MUTATED 16P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  6
  BLACK OR AFRICAN AMERICAN                       1                 13
  WHITE                                          14                386
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V8, binary
                    cls
clus                   0   1
  16P GAIN MUTATED     0  15
  16P GAIN WILD-TYPE  16 372
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      0   15
  16P GAIN WILD-TYPE   16  372
                        clus
vv                       16P GAIN MUTATED 16P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 16
  NOT HISPANIC OR LATINO               15                372
[1] 2 2
[1] FALSE

Clustering(28) Variable = 16Q GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                  0   1
  16Q GAIN MUTATED    12   6
  16Q GAIN WILD-TYPE 340  69
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                18                409 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 6                 69 
$`16Q GAIN MUTATED`
TCGA-CS-5397 TCGA-DB-A4XH TCGA-DU-6392 TCGA-DU-6400 TCGA-DU-7007 TCGA-DU-7010 
        6.38        12.59       211.17         1.22        62.96        14.99 
TCGA-DU-A5TS TCGA-E1-5302 TCGA-E1-5304 TCGA-FG-5962 TCGA-HT-A5R7 TCGA-HT-A616 
       15.12        50.14        41.13        47.77        14.01         1.81 
TCGA-HT-A618 TCGA-S9-A7J0 TCGA-S9-A7QW TCGA-TM-A84I TCGA-TM-A84Q TCGA-VM-A8CA 
        5.33         9.37         3.58        19.36        18.90        13.51 

$`16Q GAIN WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-6186 TCGA-CS-6188 
       40.18         0.10        21.01         9.96        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 
       17.95        12.43         8.48         7.56         8.02         7.40 
TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 
        6.61       122.73        81.96        75.25        47.93        72.92 
TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 
       46.65        50.17        44.52        36.56        78.28        30.08 
TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF 
       10.29        12.72        27.62        27.02        18.84        18.38 
TCGA-DB-A4XG TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R 
       72.95        11.01        18.84        16.80         5.98        16.08 
TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K 
       15.42        27.81        14.73        13.64        10.92         7.40 
TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 
        6.44        10.29        30.74         3.81        19.96        31.82 
TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D 
       30.31        14.40         8.02        30.21        42.05        27.81 
TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU 
       17.19        17.19        54.25        10.22         6.58         3.45 
TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 
        6.21        18.02        14.56        17.46         6.74        13.38 
TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 
        8.45         6.81       182.33        18.94        17.49        15.16 
TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 
       52.11        22.42        49.02        75.16        46.06        65.75 
TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 
       87.45         7.04        11.64       133.74        19.89        16.83 
TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7008 
       94.52       114.08         7.96         7.73        11.47       156.23 
TCGA-DU-7009 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 
      138.28       105.21         6.54         8.84       117.40        90.77 
TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 
       30.67        26.30        10.36         7.96        94.32        18.94 
TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 
       44.02        62.01        25.91        60.30        23.31        41.98 
TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 
        2.76         5.10        23.74         3.98        20.68        21.40 
TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR 
       19.13        16.96        15.48        14.17        14.24        12.59 
TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 
        4.96         3.65         5.65        12.20         8.65         2.70 
TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O 
       77.98         7.23         5.98        11.41        26.76         7.13 
TCGA-DU-A76R TCGA-DU-A7T8 TCGA-DU-A7TG TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5307 
       21.30       124.50        44.42        67.46        79.99        57.93 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 TCGA-F6-A8O3 
      134.27        78.21        95.57       130.78        14.33         0.23 
TCGA-F6-A8O4 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 
        0.20        17.98        34.36        32.19        18.77        14.93 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 
       24.99        23.97        13.58        15.35        17.88        22.55 
TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 
       20.61        20.09        12.95        13.68        14.24        16.01 
TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU 
       20.09        14.96        22.52        15.52        38.27        10.72 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
        5.26        18.71        23.70        14.76        17.82        16.41 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 
       15.02        16.44        10.59        28.54        10.78        22.95 
TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 
       43.69         5.23         7.43         5.72         0.13         0.10 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 
        6.67         7.82         8.81         0.13         0.03        16.54 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 
        3.75        17.42         6.54        24.26         6.38         7.10 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
       75.19        59.18        60.03       154.19         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 
       29.85        23.18       107.93         4.57        17.29         3.16 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
       22.06        45.99        56.09        57.60         0.23        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 
        0.16        16.24         0.76        44.68         6.05        42.74 
TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 
        0.10        31.69        14.96         0.10         0.10         2.96 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 
       17.52         6.90        14.53        39.48        19.23        39.09 
TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 
        0.23        50.63         0.49        23.61        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 
        0.13         3.68         5.33         2.93         1.71        11.28 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 
       31.43         1.64        16.24         9.40        63.55         0.10 
TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 
       21.50        33.01        12.23         6.25         0.10         0.46 
TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 
        2.50         3.95         4.70         0.23        29.59         3.88 
TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R9 
       16.04        15.72         0.23        10.49         0.13         0.07 
TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A617 
       14.70         0.10         5.33         2.70        13.02        16.14 
TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 
        0.10        29.92        13.45         8.32        19.23        40.18 
TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 
       35.90         4.31        21.70        21.60        19.59        17.82 
TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 
       20.35         7.89        20.81        20.71        19.00        42.77 
TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY 
        5.23         4.73         0.23         6.71         1.64         2.37 
TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 
        2.30         4.11         5.88         7.63         0.76         1.28 
TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS 
        5.75         2.53         4.83         7.79         4.11         4.18 
TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
       14.83        14.53        12.23         2.20         3.16         0.59 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC 
        6.31         3.91         4.73         1.91         0.23         5.03 
TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
        3.48         0.07        88.83        94.03        32.65        59.38 
TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY 
       62.17        69.07        18.77        37.84        34.49        31.33 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       21.63        16.37        17.62        23.64        32.61         9.86 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE 
       94.62        83.70         5.85       106.39        62.37        72.59 
TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN 
       80.12        32.45        84.99        10.88        19.86        15.91 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX 
        7.59        15.16        14.07        14.27         7.92        19.63 
TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QX 
       12.59         4.21         8.19         2.04         8.12         4.04 
TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 
       28.37        13.02       164.38        10.39        99.06        17.42 
TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 
       83.80        31.59        18.71         5.00        49.45        48.33 
TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F 
       49.32        34.78        48.39        12.00        15.09        50.76 
TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O 
       34.36        24.26        17.49        40.83        16.50        29.92 
TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CB 
        9.44         4.57        12.00        33.07        30.08         0.10 
TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS 
        7.89        26.79        10.95        27.06         7.04        23.21 
TCGA-W9-A837 
       45.07 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              1.22               0.03 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
            211.17             182.33 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             14.50              16.04 
[1] "1.2 - 211.2 (14.5)" "0.0 - 182.3 (16.0)"
[1] "hr=" "1.8"
D28V2, continuous
D28V3, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    10   8
  16Q GAIN WILD-TYPE 180 232
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     10    8
  16Q GAIN WILD-TYPE  180  232
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE               10                180
  MALE                  8                232
[1] 2 2
[1] FALSE
D28V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  16Q GAIN MUTATED            12                1                 5
  16Q GAIN WILD-TYPE         147              106               159
D28V5, multiclass
                   clus
vv                  16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  ASTROCYTOMA                     12                147
  OLIGOASTROCYTOMA                 1                106
  OLIGODENDROGLIOMA                5                159
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V6, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     5  13
  16Q GAIN WILD-TYPE  84 328
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      5   13
  16Q GAIN WILD-TYPE   84  328
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  NO                 5                 84
  YES               13                328
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16Q GAIN MUTATED                                  0     0
  16Q GAIN WILD-TYPE                                1     6
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16Q GAIN MUTATED                           1    16
  16Q GAIN WILD-TYPE                        13   384
D28V7, multiclass
                                  clus
vv                                 16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  6
  BLACK OR AFRICAN AMERICAN                       1                 13
  WHITE                                          16                384
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V8, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     0  17
  16Q GAIN WILD-TYPE  16 370
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      0   17
  16Q GAIN WILD-TYPE   16  370
                        clus
vv                       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 16
  NOT HISPANIC OR LATINO               17                370
[1] 2 2
[1] FALSE

Clustering(29) Variable = 17P GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                  0   1
  17P GAIN MUTATED    12   5
  17P GAIN WILD-TYPE 340  70
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                17                410 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 5                 70 
$`17P GAIN MUTATED`
TCGA-CS-6665 TCGA-DH-A669 TCGA-DH-A66F TCGA-DU-7013 TCGA-DU-A6S7 TCGA-E1-5304 
       12.43        30.21        17.19         8.84         7.23        41.13 
TCGA-FG-5962 TCGA-FG-7634 TCGA-FG-A6J3 TCGA-HT-7477 TCGA-IK-7675 TCGA-QH-A6CV 
       47.77        15.35        10.59        24.26        19.00        14.53 
TCGA-S9-A6TS TCGA-S9-A6U1 TCGA-S9-A6WL TCGA-TM-A84M TCGA-VM-A8CA 
       62.17        17.62        10.88        16.50        13.51 

$`17P GAIN WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 
       23.84        17.95         8.48         7.56         8.02         7.40 
TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 
        6.61       122.73        81.96        75.25        47.93        72.92 
TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 
       46.65        50.17        44.52        36.56        78.28        30.08 
TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF 
       10.29        12.72        27.62        27.02        18.84        18.38 
TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q 
       72.95        12.59        11.01        18.84        16.80         5.98 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X 
       16.08        15.42        27.81        14.73        13.64        10.92 
TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 
        7.40         6.44        10.29        30.74         3.81        19.96 
TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A66B TCGA-DH-A66D 
       31.82        30.31        14.40         8.02        42.05        27.81 
TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV 
       17.19        54.25        10.22         6.58         3.45         6.21 
TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 
       18.02        14.56        17.46         6.74        13.38         8.45 
TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 
        6.81       182.33        18.94        17.49        15.16       211.17 
TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 
       52.11        22.42        49.02        75.16        46.06        65.75 
TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 
        1.22        87.45         7.04        11.64       133.74        19.89 
TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 
       16.83        94.52       114.08         7.96         7.73        11.47 
TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 
       62.96       156.23       138.28        14.99       105.21         6.54 
TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 
      117.40        90.77        30.67        26.30        10.36         7.96 
TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 
       94.32        18.94        44.02        62.01        25.91        60.30 
TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 
       23.31        41.98         2.76         5.10        23.74         3.98 
TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 
       20.68        21.40        19.13        16.96        15.48        14.17 
TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW 
       14.24        12.59        15.12         4.96         3.65         5.65 
TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S8 TCGA-DU-A76K 
       12.20         8.65         2.70        77.98         5.98        11.41 
TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 TCGA-DU-A7TG TCGA-E1-5302 
       26.76         7.13        21.30       124.50        44.42        50.14 
TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 
       67.46        79.99        57.93       134.27        78.21        95.57 
TCGA-E1-5322 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5963 TCGA-FG-5964 
      130.78        14.33         0.23         0.20        17.98        34.36 
TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 
       32.19        18.77        14.93        24.99        23.97        13.58 
TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 
       17.88        22.55        20.61        20.09        12.95        13.68 
TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 
       14.24        16.01        20.09        14.96        22.52        15.52 
TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J 
       38.27        10.72         5.26        18.71        23.70        14.76 
TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A70Y TCGA-FG-A70Z 
       17.82        16.41        15.02        16.44        28.54        10.78 
TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 
       22.95        43.69         5.23         7.43         5.72         0.13 
TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 
        0.10         6.67         7.82         8.81         0.13         0.03 
TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7478 TCGA-HT-7479 
       16.54         3.75        17.42         6.54         6.38         7.10 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
       75.19        59.18        60.03       154.19         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 
       29.85        23.18       107.93         4.57        17.29         3.16 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
       22.06        45.99        56.09        57.60         0.23        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 
        0.16        16.24         0.76        44.68         6.05        42.74 
TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 
        0.10        31.69        14.96         0.10         0.10         2.96 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 
       17.52         6.90        14.53        39.48        19.23        39.09 
TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 
        0.23        50.63         0.49        23.61        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 
        0.13         3.68         5.33         2.93         1.71        11.28 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 
       31.43         1.64        16.24         9.40        63.55         0.10 
TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 
       21.50        33.01        12.23         6.25         0.10         0.46 
TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 
        2.50         3.95         4.70         0.23        29.59         3.88 
TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 
       16.04        15.72         0.23        10.49         0.13        14.01 
TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 
        0.07        14.70         0.10         5.33         2.70        13.02 
TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 
        1.81        16.14         5.33         0.10        29.92        13.45 
TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 
        8.32        19.23        40.18        35.90         4.31        21.70 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
       21.60        19.59        17.82        20.35         7.89        20.81 
TCGA-HW-A5KM TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW 
       20.71        42.77         5.23         4.73         0.23         6.71 
TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 
        1.64         2.37         2.30         4.11         5.88         7.63 
TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X 
        0.76         1.28         5.75         2.53         4.83         7.79 
TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ 
        4.11         4.18        14.83        12.23         2.20         3.16 
TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA 
        0.59         6.31         3.91         4.73         1.91         0.23 
TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO 
        5.03         3.48         0.07        88.83        94.03        32.65 
TCGA-R8-A73M TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY 
       59.38        69.07        18.77        37.84        34.49        31.33 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       21.63        16.37        23.64        32.61         9.86        94.62 
TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG 
       83.70         5.85       106.39        62.37        72.59        80.12 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP 
       32.45        84.99        19.86        15.91         7.59        15.16 
TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ 
       14.07        14.27         7.92        19.63        12.59         4.21 
TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX 
        9.37         8.19         2.04         8.12         3.58         4.04 
TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 
       28.37        13.02       164.38        10.39        99.06        17.42 
TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 
       83.80        31.59        18.71         5.00        49.45        48.33 
TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F 
       49.32        34.78        48.39        12.00        15.09        50.76 
TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84O 
       34.36        24.26        19.36        17.49        40.83        29.92 
TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-VM-A8C8 TCGA-VM-A8C9 
       18.90         9.44         4.57        12.00        33.07        30.08 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M 
        0.10         7.89        26.79        10.95        27.06         7.04 
TCGA-VW-A7QS TCGA-W9-A837 
       23.21        45.07 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              7.23               0.03 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             62.17             211.17 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
            16.500             15.815 
[1] "7.2 - 62.2 (16.5)"  "0.0 - 211.2 (15.8)"
[1] "hr=" "2.3"
D29V2, continuous
D29V3, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     5  12
  17P GAIN WILD-TYPE 185 228
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      5   12
  17P GAIN WILD-TYPE  185  228
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE                5                185
  MALE                 12                228
[1] 2 2
[1] FALSE
D29V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  17P GAIN MUTATED             9                1                 7
  17P GAIN WILD-TYPE         150              106               157
D29V5, multiclass
                   clus
vv                  17P GAIN MUTATED 17P GAIN WILD-TYPE
  ASTROCYTOMA                      9                150
  OLIGOASTROCYTOMA                 1                106
  OLIGODENDROGLIOMA                7                157
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V6, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     4  13
  17P GAIN WILD-TYPE  85 328
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      4   13
  17P GAIN WILD-TYPE   85  328
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  NO                 4                 85
  YES               13                328
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17P GAIN MUTATED                                  0     1
  17P GAIN WILD-TYPE                                1     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17P GAIN MUTATED                           0    15
  17P GAIN WILD-TYPE                        14   385
D29V7, multiclass
                                  clus
vv                                 17P GAIN MUTATED 17P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  5
  BLACK OR AFRICAN AMERICAN                       0                 14
  WHITE                                          15                385
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V8, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     1  15
  17P GAIN WILD-TYPE  15 372
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      1   15
  17P GAIN WILD-TYPE   15  372
                        clus
vv                       17P GAIN MUTATED 17P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 15
  NOT HISPANIC OR LATINO               15                372
[1] 2 2
[1] FALSE

Clustering(30) Variable = 17Q GAIN MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                  0   1
  17Q GAIN MUTATED    13   6
  17Q GAIN WILD-TYPE 339  69
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                19                408 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 6                 69 
$`17Q GAIN MUTATED`
TCGA-CS-6665 TCGA-DB-A64Q TCGA-DH-A669 TCGA-DH-A66F TCGA-DU-7013 TCGA-DU-A6S7 
       12.43         5.98        30.21        17.19         8.84         7.23 
TCGA-E1-5304 TCGA-FG-5962 TCGA-FG-7634 TCGA-HT-7477 TCGA-IK-7675 TCGA-QH-A6CV 
       41.13        47.77        15.35        24.26        19.00        14.53 
TCGA-S9-A6TS TCGA-S9-A6U1 TCGA-S9-A6UA TCGA-S9-A6WL TCGA-TM-A84M TCGA-VM-A8CA 
       62.17        17.62         5.85        10.88        16.50        13.51 
TCGA-VM-A8CH 
       10.95 

$`17Q GAIN WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 
       23.84        17.95         8.48         7.56         8.02         7.40 
TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 
        6.61       122.73        81.96        75.25        47.93        72.92 
TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 
       46.65        50.17        44.52        36.56        78.28        30.08 
TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF 
       10.29        12.72        27.62        27.02        18.84        18.38 
TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64R 
       72.95        12.59        11.01        18.84        16.80        16.08 
TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K 
       15.42        27.81        14.73        13.64        10.92         7.40 
TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 
        6.44        10.29        30.74         3.81        19.96        31.82 
TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66G 
       30.31        14.40         8.02        42.05        27.81        17.19 
TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 
       54.25        10.22         6.58         3.45         6.21        18.02 
TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 
       14.56        17.46         6.74        13.38         8.45         6.81 
TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 
      182.33        18.94        17.49        15.16       211.17        52.11 
TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 
       22.42        49.02        75.16        46.06        65.75         1.22 
TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 
       87.45         7.04        11.64       133.74        19.89        16.83 
TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 
       94.52       114.08         7.96         7.73        11.47        62.96 
TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7014 
      156.23       138.28        14.99       105.21         6.54       117.40 
TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 
       90.77        30.67        26.30        10.36         7.96        94.32 
TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 
       18.94        44.02        62.01        25.91        60.30        23.31 
TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 
       41.98         2.76         5.10        23.74         3.98        20.68 
TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP 
       21.40        19.13        16.96        15.48        14.17        14.24 
TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY 
       12.59        15.12         4.96         3.65         5.65        12.20 
TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L 
        8.65         2.70        77.98         5.98        11.41        26.76 
TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 TCGA-DU-A7TG TCGA-E1-5302 TCGA-E1-5303 
        7.13        21.30       124.50        44.42        50.14        67.46 
TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 
       79.99        57.93       134.27        78.21        95.57       130.78 
TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 
       14.33         0.23         0.20        17.98        34.36        32.19 
TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7636 
       18.77        14.93        24.99        23.97        13.58        17.88 
TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 
       22.55        20.61        20.09        12.95        13.68        14.24 
TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT 
       16.01        20.09        14.96        22.52        15.52        38.27 
TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K 
       10.72         5.26        18.71        23.70        14.76        17.82 
TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z 
       16.41        15.02        16.44        10.59        28.54        10.78 
TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 
       22.95        43.69         5.23         7.43         5.72         0.13 
TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 
        0.10         6.67         7.82         8.81         0.13         0.03 
TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7478 TCGA-HT-7479 
       16.54         3.75        17.42         6.54         6.38         7.10 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
       75.19        59.18        60.03       154.19         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 
       29.85        23.18       107.93         4.57        17.29         3.16 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
       22.06        45.99        56.09        57.60         0.23        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 
        0.16        16.24         0.76        44.68         6.05        42.74 
TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 
        0.10        31.69        14.96         0.10         0.10         2.96 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 
       17.52         6.90        14.53        39.48        19.23        39.09 
TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 
        0.23        50.63         0.49        23.61        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 
        0.13         3.68         5.33         2.93         1.71        11.28 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 
       31.43         1.64        16.24         9.40        63.55         0.10 
TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 
       21.50        33.01        12.23         6.25         0.10         0.46 
TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 
        2.50         3.95         4.70         0.23        29.59         3.88 
TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 
       16.04        15.72         0.23        10.49         0.13        14.01 
TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 
        0.07        14.70         0.10         5.33         2.70        13.02 
TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 
        1.81        16.14         5.33         0.10        29.92        13.45 
TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 
        8.32        19.23        40.18        35.90         4.31        21.70 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
       21.60        19.59        17.82        20.35         7.89        20.81 
TCGA-HW-A5KM TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW 
       20.71        42.77         5.23         4.73         0.23         6.71 
TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 
        1.64         2.37         2.30         4.11         5.88         7.63 
TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X 
        0.76         1.28         5.75         2.53         4.83         7.79 
TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ 
        4.11         4.18        14.83        12.23         2.20         3.16 
TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA 
        0.59         6.31         3.91         4.73         1.91         0.23 
TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO 
        5.03         3.48         0.07        88.83        94.03        32.65 
TCGA-R8-A73M TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY 
       59.38        69.07        18.77        37.84        34.49        31.33 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       21.63        16.37        23.64        32.61         9.86        94.62 
TCGA-S9-A6U9 TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH 
       83.70       106.39        62.37        72.59        80.12        32.45 
TCGA-S9-A6WI TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ 
       84.99        19.86        15.91         7.59        15.16        14.07 
TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 
       14.27         7.92        19.63        12.59         4.21         9.37 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY 
        8.19         2.04         8.12         3.58         4.04        28.37 
TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 
       13.02       164.38        10.39        99.06        17.42        83.80 
TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 
       31.59        18.71         5.00        49.45        48.33        49.32 
TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G 
       34.78        48.39        12.00        15.09        50.76        34.36 
TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84O TCGA-TM-A84Q 
       24.26        19.36        17.49        40.83        29.92        18.90 
TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CB 
        9.44         4.57        12.00        33.07        30.08         0.10 
TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-W9-A837 
        7.89        26.79        27.06         7.04        23.21        45.07 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              5.85               0.03 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             62.17             211.17 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             15.35              15.96 
[1] "5.8 - 62.2 (15.3)"  "0.0 - 211.2 (16.0)"
[1] "hr=" "2.7"
D30V2, continuous
D30V3, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED     6  13
  17Q GAIN WILD-TYPE 184 227
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      6   13
  17Q GAIN WILD-TYPE  184  227
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE                6                184
  MALE                 13                227
[1] 2 2
[1] FALSE
D30V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  17Q GAIN MUTATED            10                2                 7
  17Q GAIN WILD-TYPE         149              105               157
D30V5, multiclass
                   clus
vv                  17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  ASTROCYTOMA                     10                149
  OLIGOASTROCYTOMA                 2                105
  OLIGODENDROGLIOMA                7                157
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V6, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED     4  15
  17Q GAIN WILD-TYPE  85 326
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      4   15
  17Q GAIN WILD-TYPE   85  326
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  NO                 4                 85
  YES               15                326
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17Q GAIN MUTATED                                  0     1
  17Q GAIN WILD-TYPE                                1     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17Q GAIN MUTATED                           0    16
  17Q GAIN WILD-TYPE                        14   384
D30V7, multiclass
                                  clus
vv                                 17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  5
  BLACK OR AFRICAN AMERICAN                       0                 14
  WHITE                                          16                384
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V8, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED     1  15
  17Q GAIN WILD-TYPE  15 372
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      1   15
  17Q GAIN WILD-TYPE   15  372
                        clus
vv                       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 15
  NOT HISPANIC OR LATINO               15                372
[1] 2 2
[1] FALSE

Clustering(31) Variable = 18P GAIN MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                  0   1
  18P GAIN MUTATED    10   3
  18P GAIN WILD-TYPE 342  72
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                13                414 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 3                 72 
$`18P GAIN MUTATED`
TCGA-CS-4938 TCGA-DB-5277 TCGA-DH-A7UT TCGA-DU-7010 TCGA-DU-8165 TCGA-DU-A5TS 
        4.70        46.65         6.58        14.99        19.13        15.12 
TCGA-DU-A5TY TCGA-E1-5304 TCGA-HT-8111 TCGA-HW-7489 TCGA-QH-A6CS TCGA-QH-A6X9 
       12.20        41.13         0.23         8.32         4.18         1.91 
TCGA-S9-A89Z 
        5.00 

$`18P GAIN WILD-TYPE`
TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5393 
        7.69        43.89        18.15        10.62        64.64        40.18 
TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
        0.10        21.01         9.96         6.38        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 
       17.95        12.43         8.48         7.56         8.02         7.40 
TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 
        6.61       122.73        81.96        75.25        47.93        72.92 
TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA 
       50.17        44.52        36.56        78.28        30.08        10.29 
TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG 
       12.72        27.62        27.02        18.84        18.38        72.95 
TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R 
       12.59        11.01        18.84        16.80         5.98        16.08 
TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K 
       15.42        27.81        14.73        13.64        10.92         7.40 
TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 
        6.44        10.29        30.74         3.81        19.96        31.82 
TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D 
       30.31        14.40         8.02        30.21        42.05        27.81 
TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UU TCGA-DH-A7UV 
       17.19        17.19        54.25        10.22         3.45         6.21 
TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 
       18.02        14.56        17.46         6.74        13.38         8.45 
TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 
        6.81       182.33        18.94        17.49        15.16       211.17 
TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 
       52.11        22.42        49.02        75.16        46.06        65.75 
TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 
        1.22        87.45         7.04        11.64       133.74        19.89 
TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 
       16.83        94.52       114.08         7.96         7.73        11.47 
TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 
       62.96       156.23       138.28       105.21         6.54         8.84 
TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 
      117.40        90.77        30.67        26.30        10.36         7.96 
TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 
       94.32        18.94        44.02        62.01        25.91        60.30 
TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 
       23.31        41.98         2.76         5.10        23.74         3.98 
TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP 
       20.68        21.40        16.96        15.48        14.17        14.24 
TCGA-DU-A5TR TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A6S2 TCGA-DU-A6S3 
       12.59         4.96         3.65         5.65         8.65         2.70 
TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O 
       77.98         7.23         5.98        11.41        26.76         7.13 
TCGA-DU-A76R TCGA-DU-A7T8 TCGA-DU-A7TG TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5305 
       21.30       124.50        44.42        50.14        67.46        79.99 
TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 
       57.93       134.27        78.21        95.57       130.78        14.33 
TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 
        0.23         0.20        47.77        17.98        34.36        32.19 
TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 
       18.77        14.93        24.99        23.97        13.58        15.35 
TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 
       17.88        22.55        20.61        20.09        12.95        13.68 
TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 
       14.24        16.01        20.09        14.96        22.52        15.52 
TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J 
       38.27        10.72         5.26        18.71        23.70        14.76 
TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y 
       17.82        16.41        15.02        16.44        10.59        28.54 
TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q 
       10.78        22.95        43.69         5.23         7.43         5.72 
TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 
        0.13         0.10         6.67         7.82         8.81         0.13 
TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 
        0.03        16.54         3.75        17.42         6.54        24.26 
TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 
        6.38         7.10        75.19        59.18        60.03       154.19 
TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 
        4.01         5.03        29.85        23.18       107.93         4.57 
TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 
       17.29         3.16        22.06        45.99        56.09        57.60 
TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 
        0.23        14.27         0.16        16.24         0.76        44.68 
TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 
        6.05        42.74         0.10        31.69        14.96         0.10 
TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 
        0.10         2.96        17.52         6.90        14.53        39.48 
TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 
       19.23        39.09         0.23        50.63         0.49        23.61 
TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 
       37.15         0.33         0.13         3.68         5.33         2.93 
TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 
        1.71        11.28        31.43         1.64        16.24         9.40 
TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 
       63.55         0.10        21.50        33.01        12.23         6.25 
TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8113 
        0.10         0.46         2.50         3.95         4.70        29.59 
TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
        3.88        16.04        15.72         0.23        10.49         0.13 
TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 
       14.01         0.07        14.70         0.10         5.33         2.70 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A74O TCGA-HW-7486 
       13.02         1.81        16.14         5.33         0.10        29.92 
TCGA-HW-7487 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 
       13.45        19.23        40.18        35.90         4.31        21.70 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
       21.60        19.59        17.82        20.35         7.89        20.81 
TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV 
       20.71        19.00        42.77         5.23         4.73         0.23 
TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 
        6.71         1.64         2.37         2.30         4.11         5.88 
TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V 
        7.63         0.76         1.28         5.75         2.53         4.83 
TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CX TCGA-QH-A6CY 
        7.79         4.11        14.83        14.53        12.23         2.20 
TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6XA 
        3.16         0.59         6.31         3.91         4.73         0.23 
TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO 
        5.03         3.48         0.07        88.83        94.03        32.65 
TCGA-R8-A73M TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX 
       59.38        62.17        69.07        18.77        37.84        34.49 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       31.33        21.63        16.37        17.62        23.64        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
        9.86        94.62        83.70         5.85       106.39        62.37 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM 
       72.59        80.12        32.45        84.99        10.88        19.86 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
       15.91         7.59        15.16        14.07        14.27         7.92 
TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 
       19.63        12.59         4.21         9.37         8.19         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 
        8.12         3.58         4.04        28.37        13.02       164.38 
TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V 
       10.39        99.06        17.42        83.80        31.59        18.71 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B 
       49.45        48.33        49.32        34.78        48.39        12.00 
TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J 
       15.09        50.76        34.36        24.26        19.36        17.49 
TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S 
       40.83        16.50        29.92        18.90         9.44         4.57 
TCGA-TM-A84T TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD 
       12.00        33.07        30.08        13.51         0.10         7.89 
TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-W9-A837 
       26.79        10.95        27.06         7.04        23.21        45.07 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              0.23               0.03 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             46.65             211.17 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              8.32              16.11 
[1] "0.2 - 46.6 (8.3)"   "0.0 - 211.2 (16.1)"
[1] "hr=" "2.9"
D31V2, continuous
D31V3, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     5   8
  18P GAIN WILD-TYPE 185 232
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      5    8
  18P GAIN WILD-TYPE  185  232
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE                5                185
  MALE                  8                232
[1] 2 2
[1] FALSE
D31V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  18P GAIN MUTATED             8                2                 3
  18P GAIN WILD-TYPE         151              105               161
D31V5, multiclass
                   clus
vv                  18P GAIN MUTATED 18P GAIN WILD-TYPE
  ASTROCYTOMA                      8                151
  OLIGOASTROCYTOMA                 2                105
  OLIGODENDROGLIOMA                3                161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V6, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     2  11
  18P GAIN WILD-TYPE  87 330
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      2   11
  18P GAIN WILD-TYPE   87  330
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  NO                 2                 87
  YES               11                330
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18P GAIN MUTATED                                  0     0
  18P GAIN WILD-TYPE                                1     6
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18P GAIN MUTATED                           1    12
  18P GAIN WILD-TYPE                        13   388
D31V7, multiclass
                                  clus
vv                                 18P GAIN MUTATED 18P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  6
  BLACK OR AFRICAN AMERICAN                       1                 13
  WHITE                                          12                388
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V8, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     0  13
  18P GAIN WILD-TYPE  16 374
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      0   13
  18P GAIN WILD-TYPE   16  374
                        clus
vv                       18P GAIN MUTATED 18P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 16
  NOT HISPANIC OR LATINO               13                374
[1] 2 2
[1] FALSE

Clustering(32) Variable = 18Q GAIN MUTATION ANALYSIS
D32V1, survival
                    sevent
clus2                  0   1
  18Q GAIN MUTATED     7   2
  18Q GAIN WILD-TYPE 345  73
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 9                418 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 2                 73 
$`18Q GAIN MUTATED`
TCGA-DU-7010 TCGA-DU-8165 TCGA-DU-A5TS TCGA-DU-A5TY TCGA-E1-5304 TCGA-HT-8111 
       14.99        19.13        15.12        12.20        41.13         0.23 
TCGA-HW-7489 TCGA-QH-A6CS TCGA-S9-A89Z 
        8.32         4.18         5.00 

$`18Q GAIN WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        46.65        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       30.08        10.29        12.72        27.62        27.02        18.84 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       18.38        72.95        12.59        11.01        18.84        16.80 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        16.08        15.42        27.81        14.73        13.64 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       10.92         7.40         6.44        10.29        30.74         3.81 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       42.05        27.81        17.19        17.19        54.25        10.22 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
        6.58         3.45         6.21        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
        6.74        13.38         8.45         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 
       17.49        15.16       211.17        52.11        22.42        49.02 
TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 
       75.16        46.06        65.75         1.22        87.45         7.04 
TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 
       11.64       133.74        19.89        16.83        94.52       114.08 
TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 
        7.96         7.73        11.47        62.96       156.23       138.28 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 
      105.21         6.54         8.84       117.40        90.77        30.67 
TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 
       26.30        10.36         7.96        94.32        18.94        44.02 
TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 
       62.01        25.91        60.30        23.31        41.98         2.76 
TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8166 
        5.10        23.74         3.98        20.68        21.40        16.96 
TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TT TCGA-DU-A5TU 
       15.48        14.17        14.24        12.59         4.96         3.65 
TCGA-DU-A5TW TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 
        5.65         8.65         2.70        77.98         7.23         5.98 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 TCGA-DU-A7TG 
       11.41        26.76         7.13        21.30       124.50        44.42 
TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 
       50.14        67.46        79.99        57.93       134.27        78.21 
TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 
       95.57       130.78        14.33         0.23         0.20        47.77 
TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 
       17.98        34.36        32.19        18.77        14.93        24.99 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 
       23.97        13.58        15.35        17.88        22.55        20.61 
TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 
       20.09        12.95        13.68        14.24        16.01        20.09 
TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW 
       14.96        22.52        15.52        38.27        10.72         5.26 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ 
       18.71        23.70        14.76        17.82        16.41        15.02 
TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 
       16.44        10.59        28.54        10.78        22.95        43.69 
TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 
        5.23         7.43         5.72         0.13         0.10         6.67 
TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 
        7.82         8.81         0.13         0.03        16.54         3.75 
TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 
       17.42         6.54        24.26         6.38         7.10        75.19 
TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 
       59.18        60.03       154.19         4.01         5.03        29.85 
TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 
       23.18       107.93         4.57        17.29         3.16        22.06 
TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 
       45.99        56.09        57.60         0.23        14.27         0.16 
TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 
       16.24         0.76        44.68         6.05        42.74         0.10 
TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 
       31.69        14.96         0.10         0.10         2.96        17.52 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 
        6.90        14.53        39.48        19.23        39.09         0.23 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
       50.63         0.49        23.61        37.15         0.33         0.13 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 
        3.68         5.33         2.93         1.71        11.28        31.43 
TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 
        1.64        16.24         9.40        63.55         0.10        21.50 
TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 
       33.01        12.23         6.25         0.10         0.46         2.50 
TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 
        3.95         4.70        29.59         3.88        16.04        15.72 
TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA 
        0.23        10.49         0.13        14.01         0.07        14.70 
TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 
        0.10         5.33         2.70        13.02         1.81        16.14 
TCGA-HT-A618 TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7490 TCGA-HW-7491 
        5.33         0.10        29.92        13.45        19.23        40.18 
TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 
       35.90         4.31        21.70        21.60        19.59        17.82 
TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 
       20.35         7.89        20.81        20.71        19.00        42.77 
TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY 
        5.23         4.73         0.23         6.71         1.64         2.37 
TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 
        2.30         4.11         5.88         7.63         0.76         1.28 
TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CU 
        5.75         2.53         4.83         7.79         4.11        14.83 
TCGA-QH-A6CV TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
       14.53        12.23         2.20         3.16         0.59         6.31 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X 
        3.91         4.73         1.91         0.23         5.03         3.48 
TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TS 
        0.07        88.83        94.03        32.65        59.38        62.17 
TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ 
       69.07        18.77        37.84        34.49        31.33        21.63 
TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       16.37        17.62        23.64        32.61         9.86        94.62 
TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG 
       83.70         5.85       106.39        62.37        72.59        80.12 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO 
       32.45        84.99        10.88        19.86        15.91         7.59 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY 
       15.16        14.07        14.27         7.92        19.63        12.59 
TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW 
        4.21         9.37         8.19         2.04         8.12         3.58 
TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 
        4.04        28.37        13.02       164.38        10.39        99.06 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-TM-A7C3 TCGA-TM-A7C4 
       17.42        83.80        31.59        18.71        49.45        48.33 
TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F 
       49.32        34.78        48.39        12.00        15.09        50.76 
TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M 
       34.36        24.26        19.36        17.49        40.83        16.50 
TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-VM-A8C8 
       29.92        18.90         9.44         4.57        12.00        33.07 
TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH 
       30.08        13.51         0.10         7.89        26.79        10.95 
TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-W9-A837 
       27.06         7.04        23.21        45.07 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              0.23               0.03 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             41.13             211.17 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             12.20              16.06 
[1] "0.2 - 41.1 (12.2)"  "0.0 - 211.2 (16.1)"
[1] "hr=" "2.9"
D32V2, continuous
D32V3, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     3   6
  18Q GAIN WILD-TYPE 187 234
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      3    6
  18Q GAIN WILD-TYPE  187  234
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE                3                187
  MALE                  6                234
[1] 2 2
[1] FALSE
D32V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  18Q GAIN MUTATED             5                2                 2
  18Q GAIN WILD-TYPE         154              105               162
D32V5, multiclass
                   clus
vv                  18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  ASTROCYTOMA                      5                154
  OLIGOASTROCYTOMA                 2                105
  OLIGODENDROGLIOMA                2                162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V6, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     1   8
  18Q GAIN WILD-TYPE  88 333
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      1    8
  18Q GAIN WILD-TYPE   88  333
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  NO                 1                 88
  YES                8                333
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18Q GAIN MUTATED                                  0     0
  18Q GAIN WILD-TYPE                                1     6
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18Q GAIN MUTATED                           1     8
  18Q GAIN WILD-TYPE                        13   392
D32V7, multiclass
                                  clus
vv                                 18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  6
  BLACK OR AFRICAN AMERICAN                       1                 13
  WHITE                                           8                392
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V8, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     0   9
  18Q GAIN WILD-TYPE  16 378
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      0    9
  18Q GAIN WILD-TYPE   16  378
                        clus
vv                       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 16
  NOT HISPANIC OR LATINO                9                378
[1] 2 2
[1] FALSE

Clustering(33) Variable = 19P GAIN MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                  0   1
  19P GAIN MUTATED    67  16
  19P GAIN WILD-TYPE 285  59
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                83                344 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                16                 59 
$`19P GAIN MUTATED`
TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6668 TCGA-DB-5274 
       21.01         9.96        17.69        23.84         8.02        75.25 
TCGA-DB-5278 TCGA-DB-A4XD TCGA-DB-A4XG TCGA-DB-A64L TCGA-DB-A64P TCGA-DB-A64R 
       50.17        27.02        72.95        11.01        16.80        16.08 
TCGA-DB-A75L TCGA-DH-A669 TCGA-DH-A66F TCGA-DU-5854 TCGA-DU-5874 TCGA-DU-6393 
        6.44        30.21        17.19         8.45        15.16        52.11 
TCGA-DU-6394 TCGA-DU-6397 TCGA-DU-6400 TCGA-DU-6406 TCGA-DU-7009 TCGA-DU-7015 
       22.42        46.06         1.22        16.83       138.28        90.77 
TCGA-DU-7019 TCGA-DU-7298 TCGA-DU-7306 TCGA-DU-8164 TCGA-DU-A5TT TCGA-DU-A6S2 
       26.30        18.94        41.98        21.40         4.96         8.65 
TCGA-DU-A76K TCGA-E1-5304 TCGA-FG-5962 TCGA-FG-6692 TCGA-FG-7643 TCGA-FG-8186 
       11.41        41.13        47.77        13.58        20.09        16.01 
TCGA-FG-8188 TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A60K TCGA-FG-A87Q TCGA-HT-7468 
       14.96        10.72         5.26        17.82         5.72         6.67 
TCGA-HT-7469 TCGA-HT-7480 TCGA-HT-7687 TCGA-HT-7695 TCGA-HT-7860 TCGA-HT-7873 
        7.82        75.19         0.10        14.53         0.49        23.61 
TCGA-HT-7875 TCGA-HT-7882 TCGA-HT-8012 TCGA-HT-8104 TCGA-HT-A5RA TCGA-HT-A5RC 
        0.33         1.71         9.40        12.23        14.70         5.33 
TCGA-HT-A615 TCGA-HW-7495 TCGA-KT-A7W1 TCGA-P5-A5F0 TCGA-QH-A65X TCGA-QH-A6CV 
       13.02         4.31         4.73         4.11         7.79        14.53 
TCGA-QH-A6CZ TCGA-QH-A6XC TCGA-QH-A86X TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A73M 
        3.16         5.03         3.48        88.83        94.03        59.38 
TCGA-S9-A6TV TCGA-S9-A6TY TCGA-S9-A6U2 TCGA-S9-A6WE TCGA-S9-A6WM TCGA-S9-A7J1 
       18.77        31.33        23.64        72.59        19.86         8.19 
TCGA-S9-A7J2 TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-TM-A7C3 TCGA-TM-A84B TCGA-TM-A84G 
        2.04        13.02       164.38        49.45        12.00        34.36 
TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CE TCGA-VW-A7QS TCGA-W9-A837 
       13.51         0.10        26.79        23.21        45.07 

$`19P GAIN WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5397 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 
       40.18         0.10         6.38        17.95        12.43         8.48 
TCGA-CS-6667 TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5275 
        7.56         7.40         6.61       122.73        81.96        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 
       72.92        46.65        44.52        36.56        78.28        30.08 
TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XH 
       10.29        12.72        27.62        18.84        18.38        12.59 
TCGA-DB-A64O TCGA-DB-A64Q TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
       18.84         5.98        15.42        27.81        14.73        13.64 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 
       10.92         7.40        10.29        30.74         3.81        19.96 
TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A66B TCGA-DH-A66D 
       31.82        30.31        14.40         8.02        42.05        27.81 
TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV 
       17.19        54.25        10.22         6.58         3.45         6.21 
TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5855 
       18.02        14.56        17.46         6.74        13.38         6.81 
TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-6392 TCGA-DU-6395 TCGA-DU-6396 
      182.33        18.94        17.49       211.17        49.02        75.16 
TCGA-DU-6399 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 
       65.75        87.45         7.04        11.64       133.74        19.89 
TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 
       94.52       114.08         7.96         7.73        11.47        62.96 
TCGA-DU-7008 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 
      156.23        14.99       105.21         6.54         8.84       117.40 
TCGA-DU-7018 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7299 TCGA-DU-7300 
       30.67        10.36         7.96        94.32        44.02        62.01 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 
       25.91        60.30        23.31         2.76         5.10        23.74 
TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 
        3.98        20.68        19.13        16.96        15.48        14.17 
TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY 
       14.24        12.59        15.12         3.65         5.65        12.20 
TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76L TCGA-DU-A76O 
        2.70        77.98         7.23         5.98        26.76         7.13 
TCGA-DU-A76R TCGA-DU-A7T8 TCGA-DU-A7TG TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5305 
       21.30       124.50        44.42        50.14        67.46        79.99 
TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 
       57.93       134.27        78.21        95.57       130.78        14.33 
TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 
        0.23         0.20        17.98        34.36        32.19        18.77 
TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 
       14.93        24.99        23.97        15.35        17.88        22.55 
TCGA-FG-7641 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8187 TCGA-FG-8189 
       20.61        12.95        13.68        14.24        20.09        22.52 
TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60L 
       15.52        38.27        18.71        23.70        14.76        16.41 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 
       15.02        16.44        10.59        28.54        10.78        22.95 
TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7470 
       43.69         5.23         7.43         0.13         0.10         8.81 
TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 
        0.13         0.03        16.54         3.75        17.42         6.54 
TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 
       24.26         6.38         7.10        59.18        60.03       154.19 
TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 
        4.01         5.03        29.85        23.18       107.93         4.57 
TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 
       17.29         3.16        22.06        45.99        56.09        57.60 
TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 
        0.23        14.27         0.16        16.24         0.76        44.68 
TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 
        6.05        42.74        31.69        14.96         0.10         0.10 
TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 
        2.96        17.52         6.90        39.48        19.23        39.09 
TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7874 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 
        0.23        50.63        37.15         0.13         3.68         5.33 
TCGA-HT-7881 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8013 
        2.93        11.28        31.43         1.64        16.24        63.55 
TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 
        0.10        21.50        33.01         6.25         0.10         0.46 
TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 
        2.50         3.95         4.70         0.23        29.59         3.88 
TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 
       16.04        15.72         0.23        10.49         0.13        14.01 
TCGA-HT-A5R9 TCGA-HT-A5RB TCGA-HT-A614 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 
        0.07         0.10         2.70         1.81        16.14         5.33 
TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 
        0.10        29.92        13.45         8.32        19.23        40.18 
TCGA-HW-7493 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
       35.90        21.70        21.60        19.59        17.82        20.35 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X 
        7.89        20.81        20.71        19.00        42.77         5.23 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F1 
        0.23         6.71         1.64         2.37         2.30         5.88 
TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V 
        7.63         0.76         1.28         5.75         2.53         4.83 
TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6X3 
        4.11         4.18        14.83        12.23         2.20         0.59 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A870 
        6.31         3.91         4.73         1.91         0.23         0.07 
TCGA-R8-A6MO TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TZ 
       32.65        62.17        69.07        37.84        34.49        21.63 
TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
       16.37        17.62        32.61         9.86        94.62        83.70 
TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI 
        5.85       106.39        62.37        80.12        32.45        84.99 
TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ 
       10.88        15.91         7.59        15.16        14.07        14.27 
TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J3 
        7.92        19.63        12.59         4.21         9.37         8.12 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 
        3.58         4.04        28.37        10.39        99.06        17.42 
TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C4 TCGA-TM-A7C5 
       83.80        31.59        18.71         5.00        48.33        49.32 
TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84H TCGA-TM-A84I 
       34.78        48.39        15.09        50.76        24.26        19.36 
TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R 
       17.49        40.83        16.50        29.92        18.90         9.44 
TCGA-TM-A84S TCGA-TM-A84T TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CD TCGA-VM-A8CH 
        4.57        12.00        33.07        30.08         7.89        10.95 
TCGA-VV-A829 TCGA-VV-A86M 
       27.06         7.04 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              0.10               0.03 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            164.38             211.17 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            16.010             15.815 
[1] "0.1 - 164.4 (16.0)" "0.0 - 211.2 (15.8)"
[1] "hr=" "1.1"
D33V2, continuous
D33V3, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    34  50
  19P GAIN WILD-TYPE 156 190
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     34   50
  19P GAIN WILD-TYPE  156  190
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE               34                156
  MALE                 50                190
[1] 2 2
[1] FALSE
D33V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  19P GAIN MUTATED            16               16                52
  19P GAIN WILD-TYPE         143               91               112
D33V5, multiclass
                   clus
vv                  19P GAIN MUTATED 19P GAIN WILD-TYPE
  ASTROCYTOMA                     16                143
  OLIGOASTROCYTOMA                16                 91
  OLIGODENDROGLIOMA               52                112
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V6, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    16  68
  19P GAIN WILD-TYPE  73 273
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     16   68
  19P GAIN WILD-TYPE   73  273
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  NO                16                 73
  YES               68                273
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19P GAIN MUTATED                                  0     2
  19P GAIN WILD-TYPE                                1     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19P GAIN MUTATED                           3    76
  19P GAIN WILD-TYPE                        11   324
D33V7, multiclass
                                  clus
vv                                 19P GAIN MUTATED 19P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           2                  4
  BLACK OR AFRICAN AMERICAN                       3                 11
  WHITE                                          76                324
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V8, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     4  75
  19P GAIN WILD-TYPE  12 312
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      4   75
  19P GAIN WILD-TYPE   12  312
                        clus
vv                       19P GAIN MUTATED 19P GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                 12
  NOT HISPANIC OR LATINO               75                312
[1] 2 2
[1] FALSE

Clustering(34) Variable = 19Q GAIN MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                  0   1
  19Q GAIN MUTATED    12   8
  19Q GAIN WILD-TYPE 340  67
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                20                407 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 8                 67 
$`19Q GAIN MUTATED`
TCGA-CS-5395 TCGA-CS-6186 TCGA-DU-6402 TCGA-DU-6406 TCGA-DU-7019 TCGA-DU-A76K 
       21.01        17.69         7.04        16.83        26.30        11.41 
TCGA-FG-6692 TCGA-FG-7643 TCGA-FG-A4MU TCGA-FG-A4MW TCGA-HT-7860 TCGA-HT-7873 
       13.58        20.09        10.72         5.26         0.49        23.61 
TCGA-HT-7882 TCGA-HT-8104 TCGA-HT-A5RA TCGA-KT-A7W1 TCGA-QH-A6CV TCGA-QH-A6XC 
        1.71        12.23        14.70         4.73        14.53         5.03 
TCGA-S9-A6WM TCGA-TM-A7C3 
       19.86        49.45 

$`19Q GAIN WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6188 TCGA-CS-6290 
       40.18         0.10         9.96         6.38        23.84        17.95 
TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 
       12.43         8.48         7.56         8.02         7.40         6.61 
TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 
      122.73        81.96        75.25        47.93        72.92        46.65 
TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA 
       50.17        44.52        36.56        78.28        30.08        10.29 
TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG 
       12.72        27.62        27.02        18.84        18.38        72.95 
TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R 
       12.59        11.01        18.84        16.80         5.98        16.08 
TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K 
       15.42        27.81        14.73        13.64        10.92         7.40 
TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 
        6.44        10.29        30.74         3.81        19.96        31.82 
TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D 
       30.31        14.40         8.02        30.21        42.05        27.81 
TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU 
       17.19        17.19        54.25        10.22         6.58         3.45 
TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 
        6.21        18.02        14.56        17.46         6.74        13.38 
TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 
        8.45         6.81       182.33        18.94        17.49        15.16 
TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 
      211.17        52.11        22.42        49.02        75.16        46.06 
TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 
       65.75         1.22        87.45        11.64       133.74        19.89 
TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 
       94.52       114.08         7.96         7.73        11.47        62.96 
TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 
      156.23       138.28        14.99       105.21         6.54         8.84 
TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 
      117.40        90.77        30.67        10.36         7.96        94.32 
TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 
       18.94        44.02        62.01        25.91        60.30        23.31 
TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 
       41.98         2.76         5.10        23.74         3.98        20.68 
TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP 
       21.40        19.13        16.96        15.48        14.17        14.24 
TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY 
       12.59        15.12         4.96         3.65         5.65        12.20 
TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76L 
        8.65         2.70        77.98         7.23         5.98        26.76 
TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 TCGA-DU-A7TG TCGA-E1-5302 TCGA-E1-5303 
        7.13        21.30       124.50        44.42        50.14        67.46 
TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 
       41.13        79.99        57.93       134.27        78.21        95.57 
TCGA-E1-5322 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 
      130.78        14.33         0.23         0.20        47.77        17.98 
TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 
       34.36        32.19        18.77        14.93        24.99        23.97 
TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-8181 TCGA-FG-8182 
       15.35        17.88        22.55        20.61        12.95        13.68 
TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 
       14.24        16.01        20.09        14.96        22.52        15.52 
TCGA-FG-A4MT TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
       38.27        18.71        23.70        14.76        17.82        16.41 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 
       15.02        16.44        10.59        28.54        10.78        22.95 
TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 
       43.69         5.23         7.43         5.72         0.13         0.10 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 
        6.67         7.82         8.81         0.13         0.03        16.54 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 
        3.75        17.42         6.54        24.26         6.38         7.10 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
       75.19        59.18        60.03       154.19         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 
       29.85        23.18       107.93         4.57        17.29         3.16 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
       22.06        45.99        56.09        57.60         0.23        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 
        0.16        16.24         0.76        44.68         6.05        42.74 
TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 
        0.10        31.69        14.96         0.10         0.10         2.96 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 
       17.52         6.90        14.53        39.48        19.23        39.09 
TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 
        0.23        50.63        37.15         0.33         0.13         3.68 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 
        5.33         2.93        11.28        31.43         1.64        16.24 
TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8105 
        9.40        63.55         0.10        21.50        33.01         6.25 
TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 
        0.10         0.46         2.50         3.95         4.70         0.23 
TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV 
       29.59         3.88        16.04        15.72         0.23        10.49 
TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 
        0.13        14.01         0.07         0.10         5.33         2.70 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A74O TCGA-HW-7486 
       13.02         1.81        16.14         5.33         0.10        29.92 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 
       13.45         8.32        19.23        40.18        35.90         4.31 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
       21.70        21.60        19.59        17.82        20.35         7.89 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-P5-A5EV 
       20.81        20.71        19.00        42.77         5.23         0.23 
TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 
        6.71         1.64         2.37         2.30         4.11         5.88 
TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V 
        7.63         0.76         1.28         5.75         2.53         4.83 
TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CX TCGA-QH-A6CY 
        7.79         4.11         4.18        14.83        12.23         2.20 
TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 
        3.16         0.59         6.31         3.91         4.73         1.91 
TCGA-QH-A6XA TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO 
        0.23         3.48         0.07        88.83        94.03        32.65 
TCGA-R8-A73M TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX 
       59.38        62.17        69.07        18.77        37.84        34.49 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       31.33        21.63        16.37        17.62        23.64        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
        9.86        94.62        83.70         5.85       106.39        62.37 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN 
       72.59        80.12        32.45        84.99        10.88        15.91 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX 
        7.59        15.16        14.07        14.27         7.92        19.63 
TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       12.59         4.21         9.37         8.19         2.04         8.12 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 
        3.58         4.04        28.37        13.02       164.38        10.39 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z 
       99.06        17.42        83.80        31.59        18.71         5.00 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
       48.33        49.32        34.78        48.39        12.00        15.09 
TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L 
       50.76        34.36        24.26        19.36        17.49        40.83 
TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T 
       16.50        29.92        18.90         9.44         4.57        12.00 
TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE 
       33.07        30.08        13.51         0.10         7.89        26.79 
TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-W9-A837 
       10.95        27.06         7.04        23.21        45.07 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              0.49               0.03 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             49.45             211.17 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            14.055             16.040 
[1] "0.5 - 49.5 (14.1)"  "0.0 - 211.2 (16.0)"
[1] "hr=" "5.1"
D34V2, continuous
D34V3, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     8  12
  19Q GAIN WILD-TYPE 182 228
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      8   12
  19Q GAIN WILD-TYPE  182  228
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE                8                182
  MALE                 12                228
[1] 2 2
[1] FALSE
D34V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  19Q GAIN MUTATED             8                8                 4
  19Q GAIN WILD-TYPE         151               99               160
D34V5, multiclass
                   clus
vv                  19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  ASTROCYTOMA                      8                151
  OLIGOASTROCYTOMA                 8                 99
  OLIGODENDROGLIOMA                4                160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V6, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     5  15
  19Q GAIN WILD-TYPE  84 326
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      5   15
  19Q GAIN WILD-TYPE   84  326
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  NO                 5                 84
  YES               15                326
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19Q GAIN MUTATED                                  0     1
  19Q GAIN WILD-TYPE                                1     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19Q GAIN MUTATED                           1    18
  19Q GAIN WILD-TYPE                        13   382
D34V7, multiclass
                                  clus
vv                                 19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  5
  BLACK OR AFRICAN AMERICAN                       1                 13
  WHITE                                          18                382
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V8, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     1  18
  19Q GAIN WILD-TYPE  15 369
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      1   18
  19Q GAIN WILD-TYPE   15  369
                        clus
vv                       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 15
  NOT HISPANIC OR LATINO               18                369
[1] 2 2
[1] FALSE

Clustering(35) Variable = 20P GAIN MUTATION ANALYSIS
D35V1, survival
                    sevent
clus2                  0   1
  20P GAIN MUTATED    23  14
  20P GAIN WILD-TYPE 329  61
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                37                390 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                14                 61 
$`20P GAIN MUTATED`
TCGA-CS-5395 TCGA-CS-5397 TCGA-CS-6188 TCGA-CS-6665 TCGA-DB-A75O TCGA-DH-A669 
       21.01         6.38        23.84        12.43        30.74        30.21 
TCGA-DH-A66B TCGA-DU-5852 TCGA-DU-5854 TCGA-DU-5871 TCGA-DU-6400 TCGA-DU-6406 
       42.05         6.74         8.45        18.94         1.22        16.83 
TCGA-DU-7298 TCGA-DU-8162 TCGA-DU-8165 TCGA-DU-A5TT TCGA-DU-A5TY TCGA-DU-A6S7 
       18.94         3.98        19.13         4.96        12.20         7.23 
TCGA-DU-A76K TCGA-DU-A76L TCGA-E1-5304 TCGA-FG-5962 TCGA-FG-7634 TCGA-FG-A4MU 
       11.41        26.76        41.13        47.77        15.35        10.72 
TCGA-HT-7474 TCGA-HT-7477 TCGA-HT-7860 TCGA-HT-7882 TCGA-HT-8104 TCGA-HT-A5RC 
        3.75        24.26         0.49         1.71        12.23         5.33 
TCGA-HW-A5KK TCGA-QH-A6CV TCGA-QH-A6XC TCGA-S9-A6WH TCGA-S9-A6WM TCGA-TM-A7C3 
        7.89        14.53         5.03        32.45        19.86        49.45 
TCGA-VM-A8CA 
       13.51 

$`20P GAIN WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5396 TCGA-CS-6186 TCGA-CS-6290 TCGA-CS-6666 
       40.18         0.10         9.96        17.69        17.95         8.48 
TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 
        7.56         8.02         7.40         6.61       122.73        81.96 
TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 
       75.25        47.93        72.92        46.65        50.17        44.52 
TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC 
       36.56        78.28        30.08        10.29        12.72        27.62 
TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L 
       27.02        18.84        18.38        72.95        12.59        11.01 
TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U 
       18.84        16.80         5.98        16.08        15.42        27.81 
TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M 
       14.73        13.64        10.92         7.40         6.44        10.29 
TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 
        3.81        19.96        31.82        30.31        14.40         8.02 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT 
       27.81        17.19        17.19        54.25        10.22         6.58 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5853 
        3.45         6.21        18.02        14.56        17.46        13.38 
TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 
        6.81       182.33        17.49        15.16       211.17        52.11 
TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6401 
       22.42        49.02        75.16        46.06        65.75        87.45 
TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6407 TCGA-DU-6408 
        7.04        11.64       133.74        19.89        94.52       114.08 
TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 
        7.96         7.73        11.47        62.96       156.23       138.28 
TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 
       14.99       105.21         6.54         8.84       117.40        90.77 
TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7299 
       30.67        26.30        10.36         7.96        94.32        44.02 
TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 
       62.01        25.91        60.30        23.31        41.98         2.76 
TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-8167 
        5.10        23.74        20.68        21.40        16.96        15.48 
TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TU TCGA-DU-A5TW 
       14.17        14.24        12.59        15.12         3.65         5.65 
TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S8 TCGA-DU-A76O TCGA-DU-A76R 
        8.65         2.70        77.98         5.98         7.13        21.30 
TCGA-DU-A7T8 TCGA-DU-A7TG TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5307 
      124.50        44.42        50.14        67.46        79.99        57.93 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 TCGA-F6-A8O3 
      134.27        78.21        95.57       130.78        14.33         0.23 
TCGA-F6-A8O4 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 
        0.20        17.98        34.36        32.19        18.77        14.93 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 
       24.99        23.97        13.58        17.88        22.55        20.61 
TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 
       20.09        12.95        13.68        14.24        16.01        20.09 
TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MW TCGA-FG-A4MX 
       14.96        22.52        15.52        38.27         5.26        18.71 
TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 
       23.70        14.76        17.82        16.41        15.02        16.44 
TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 
       10.59        28.54        10.78        22.95        43.69         5.23 
TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 
        7.43         5.72         0.13         0.10         6.67         7.82 
TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7475 TCGA-HT-7476 
        8.81         0.13         0.03        16.54        17.42         6.54 
TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 
        6.38         7.10        75.19        59.18        60.03       154.19 
TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 
        4.01         5.03        29.85        23.18       107.93         4.57 
TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 
       17.29         3.16        22.06        45.99        56.09        57.60 
TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 
        0.23        14.27         0.16        16.24         0.76        44.68 
TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 
        6.05        42.74         0.10        31.69        14.96         0.10 
TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 
        0.10         2.96        17.52         6.90        14.53        39.48 
TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7873 TCGA-HT-7874 
       19.23        39.09         0.23        50.63        23.61        37.15 
TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7884 
        0.33         0.13         3.68         5.33         2.93        11.28 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 
       31.43         1.64        16.24         9.40        63.55         0.10 
TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 
       21.50        33.01         6.25         0.10         0.46         2.50 
TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 
        3.95         4.70         0.23        29.59         3.88        16.04 
TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 
       15.72         0.23        10.49         0.13        14.01         0.07 
TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 
       14.70         0.10         2.70        13.02         1.81        16.14 
TCGA-HT-A618 TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 
        5.33         0.10        29.92        13.45         8.32        19.23 
TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 
       40.18        35.90         4.31        21.70        21.60        19.59 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 
       17.82        20.35        20.81        20.71        19.00        42.77 
TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY 
        5.23         4.73         0.23         6.71         1.64         2.37 
TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 
        2.30         4.11         5.88         7.63         0.76         1.28 
TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS 
        5.75         2.53         4.83         7.79         4.11         4.18 
TCGA-QH-A6CU TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
       14.83        12.23         2.20         3.16         0.59         6.31 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A86X TCGA-QH-A870 
        3.91         4.73         1.91         0.23         3.48         0.07 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TS TCGA-S9-A6TU 
       88.83        94.03        32.65        59.38        62.17        69.07 
TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 
       18.77        37.84        34.49        31.33        21.63        16.37 
TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
       17.62        23.64        32.61         9.86        94.62        83.70 
TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WI 
        5.85       106.39        62.37        72.59        80.12        84.99 
TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ 
       10.88        15.91         7.59        15.16        14.07        14.27 
TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 
        7.92        19.63        12.59         4.21         9.37         8.19 
TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ 
        2.04         8.12         3.58         4.04        28.37        13.02 
TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 
      164.38        10.39        99.06        17.42        83.80        31.59 
TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF 
       18.71         5.00        48.33        49.32        34.78        48.39 
TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I 
       12.00        15.09        50.76        34.36        24.26        19.36 
TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R 
       17.49        40.83        16.50        29.92        18.90         9.44 
TCGA-TM-A84S TCGA-TM-A84T TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CB TCGA-VM-A8CD 
        4.57        12.00        33.07        30.08         0.10         7.89 
TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-W9-A837 
       26.79        10.95        27.06         7.04        23.21        45.07 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              0.49               0.03 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             49.45             211.17 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             13.51              16.06 
[1] "0.5 - 49.5 (13.5)"  "0.0 - 211.2 (16.1)"
[1] "hr=" "4.6"
D35V2, continuous
D35V3, binary
                    cls
clus                   0   1
  20P GAIN MUTATED    18  19
  20P GAIN WILD-TYPE 172 221
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     18   19
  20P GAIN WILD-TYPE  172  221
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE               18                172
  MALE                 19                221
[1] 2 2
[1] FALSE
D35V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  20P GAIN MUTATED            18                8                11
  20P GAIN WILD-TYPE         141               99               153
D35V5, multiclass
                   clus
vv                  20P GAIN MUTATED 20P GAIN WILD-TYPE
  ASTROCYTOMA                     18                141
  OLIGOASTROCYTOMA                 8                 99
  OLIGODENDROGLIOMA               11                153
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V6, binary
                    cls
clus                   0   1
  20P GAIN MUTATED     7  30
  20P GAIN WILD-TYPE  82 311
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      7   30
  20P GAIN WILD-TYPE   82  311
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  NO                 7                 82
  YES               30                311
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20P GAIN MUTATED                                  0     1
  20P GAIN WILD-TYPE                                1     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20P GAIN MUTATED                           2    33
  20P GAIN WILD-TYPE                        12   367
D35V7, multiclass
                                  clus
vv                                 20P GAIN MUTATED 20P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  5
  BLACK OR AFRICAN AMERICAN                       2                 12
  WHITE                                          33                367
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V8, binary
                    cls
clus                   0   1
  20P GAIN MUTATED     1  33
  20P GAIN WILD-TYPE  15 354
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      1   33
  20P GAIN WILD-TYPE   15  354
                        clus
vv                       20P GAIN MUTATED 20P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 15
  NOT HISPANIC OR LATINO               33                354
[1] 2 2
[1] FALSE

Clustering(36) Variable = 20Q GAIN MUTATION ANALYSIS
D36V1, survival
                    sevent
clus2                  0   1
  20Q GAIN MUTATED    23  14
  20Q GAIN WILD-TYPE 329  61
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                37                390 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                14                 61 
$`20Q GAIN MUTATED`
TCGA-CS-4938 TCGA-CS-5395 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6665 
        4.70        21.01         6.38        17.69        23.84        12.43 
TCGA-DH-A669 TCGA-DU-5852 TCGA-DU-5854 TCGA-DU-5871 TCGA-DU-6400 TCGA-DU-6406 
       30.21         6.74         8.45        18.94         1.22        16.83 
TCGA-DU-8162 TCGA-DU-8165 TCGA-DU-A5TT TCGA-DU-A5TY TCGA-DU-A6S7 TCGA-DU-A76K 
        3.98        19.13         4.96        12.20         7.23        11.41 
TCGA-DU-A76L TCGA-E1-5304 TCGA-FG-5962 TCGA-FG-7634 TCGA-FG-A4MU TCGA-HT-7477 
       26.76        41.13        47.77        15.35        10.72        24.26 
TCGA-HT-7693 TCGA-HT-7860 TCGA-HT-7882 TCGA-HT-8104 TCGA-HT-8563 TCGA-HT-A5RC 
       17.52         0.49         1.71        12.23        16.04         5.33 
TCGA-HW-A5KK TCGA-QH-A6CV TCGA-QH-A6XC TCGA-S9-A6WH TCGA-S9-A6WM TCGA-TM-A7C3 
        7.89        14.53         5.03        32.45        19.86        49.45 
TCGA-VM-A8CA 
       13.51 

$`20Q GAIN WILD-TYPE`
TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5393 
        7.69        43.89        18.15        10.62        64.64        40.18 
TCGA-CS-5394 TCGA-CS-5396 TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
        0.10         9.96        17.95         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        46.65        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       30.08        10.29        12.72        27.62        27.02        18.84 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       18.38        72.95        12.59        11.01        18.84        16.80 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        16.08        15.42        27.81        14.73        13.64 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       10.92         7.40         6.44        10.29        30.74         3.81 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A66B 
       19.96        31.82        30.31        14.40         8.02        42.05 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT 
       27.81        17.19        17.19        54.25        10.22         6.58 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5853 
        3.45         6.21        18.02        14.56        17.46        13.38 
TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 
        6.81       182.33        17.49        15.16       211.17        52.11 
TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6401 
       22.42        49.02        75.16        46.06        65.75        87.45 
TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6407 TCGA-DU-6408 
        7.04        11.64       133.74        19.89        94.52       114.08 
TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 
        7.96         7.73        11.47        62.96       156.23       138.28 
TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 
       14.99       105.21         6.54         8.84       117.40        90.77 
TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 
       30.67        26.30        10.36         7.96        94.32        18.94 
TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 
       44.02        62.01        25.91        60.30        23.31        41.98 
TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8166 
        2.76         5.10        23.74        20.68        21.40        16.96 
TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TU 
       15.48        14.17        14.24        12.59        15.12         3.65 
TCGA-DU-A5TW TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S8 TCGA-DU-A76O 
        5.65         8.65         2.70        77.98         5.98         7.13 
TCGA-DU-A76R TCGA-DU-A7T8 TCGA-DU-A7TG TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5305 
       21.30       124.50        44.42        50.14        67.46        79.99 
TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 
       57.93       134.27        78.21        95.57       130.78        14.33 
TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 
        0.23         0.20        17.98        34.36        32.19        18.77 
TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7636 TCGA-FG-7638 
       14.93        24.99        23.97        13.58        17.88        22.55 
TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 
       20.61        20.09        12.95        13.68        14.24        16.01 
TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MW 
       20.09        14.96        22.52        15.52        38.27         5.26 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ 
       18.71        23.70        14.76        17.82        16.41        15.02 
TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 
       16.44        10.59        28.54        10.78        22.95        43.69 
TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 
        5.23         7.43         5.72         0.13         0.10         6.67 
TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 
        7.82         8.81         0.13         0.03        16.54         3.75 
TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 
       17.42         6.54         6.38         7.10        75.19        59.18 
TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 
       60.03       154.19         4.01         5.03        29.85        23.18 
TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 
      107.93         4.57        17.29         3.16        22.06        45.99 
TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 
       56.09        57.60         0.23        14.27         0.16        16.24 
TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 
        0.76        44.68         6.05        42.74         0.10        31.69 
TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7694 TCGA-HT-7695 
       14.96         0.10         0.10         2.96         6.90        14.53 
TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7873 
       39.48        19.23        39.09         0.23        50.63        23.61 
TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 
       37.15         0.33         0.13         3.68         5.33         2.93 
TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 
       11.28        31.43         1.64        16.24         9.40        63.55 
TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 
        0.10        21.50        33.01         6.25         0.10         0.46 
TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 
        2.50         3.95         4.70         0.23        29.59         3.88 
TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 
       15.72         0.23        10.49         0.13        14.01         0.07 
TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 
       14.70         0.10         2.70        13.02         1.81        16.14 
TCGA-HT-A618 TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 
        5.33         0.10        29.92        13.45         8.32        19.23 
TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 
       40.18        35.90         4.31        21.70        21.60        19.59 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 
       17.82        20.35        20.81        20.71        19.00        42.77 
TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY 
        5.23         4.73         0.23         6.71         1.64         2.37 
TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 
        2.30         4.11         5.88         7.63         0.76         1.28 
TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS 
        5.75         2.53         4.83         7.79         4.11         4.18 
TCGA-QH-A6CU TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
       14.83        12.23         2.20         3.16         0.59         6.31 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A86X TCGA-QH-A870 
        3.91         4.73         1.91         0.23         3.48         0.07 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TS TCGA-S9-A6TU 
       88.83        94.03        32.65        59.38        62.17        69.07 
TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 
       18.77        37.84        34.49        31.33        21.63        16.37 
TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
       17.62        23.64        32.61         9.86        94.62        83.70 
TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WI 
        5.85       106.39        62.37        72.59        80.12        84.99 
TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ 
       10.88        15.91         7.59        15.16        14.07        14.27 
TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 
        7.92        19.63        12.59         4.21         9.37         8.19 
TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ 
        2.04         8.12         3.58         4.04        28.37        13.02 
TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 
      164.38        10.39        99.06        17.42        83.80        31.59 
TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF 
       18.71         5.00        48.33        49.32        34.78        48.39 
TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I 
       12.00        15.09        50.76        34.36        24.26        19.36 
TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R 
       17.49        40.83        16.50        29.92        18.90         9.44 
TCGA-TM-A84S TCGA-TM-A84T TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CB TCGA-VM-A8CD 
        4.57        12.00        33.07        30.08         0.10         7.89 
TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-W9-A837 
       26.79        10.95        27.06         7.04        23.21        45.07 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              0.49               0.03 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             49.45             211.17 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             13.51              16.11 
[1] "0.5 - 49.5 (13.5)"  "0.0 - 211.2 (16.1)"
[1] "hr=" "5"  
D36V2, continuous
D36V3, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED    20  17
  20Q GAIN WILD-TYPE 170 223
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     20   17
  20Q GAIN WILD-TYPE  170  223
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE               20                170
  MALE                 17                223
[1] 2 2
[1] FALSE
D36V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  20Q GAIN MUTATED            17                8                12
  20Q GAIN WILD-TYPE         142               99               152
D36V5, multiclass
                   clus
vv                  20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  ASTROCYTOMA                     17                142
  OLIGOASTROCYTOMA                 8                 99
  OLIGODENDROGLIOMA               12                152
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V6, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED     7  30
  20Q GAIN WILD-TYPE  82 311
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      7   30
  20Q GAIN WILD-TYPE   82  311
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  NO                 7                 82
  YES               30                311
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20Q GAIN MUTATED                                  0     1
  20Q GAIN WILD-TYPE                                1     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20Q GAIN MUTATED                           1    34
  20Q GAIN WILD-TYPE                        13   366
D36V7, multiclass
                                  clus
vv                                 20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  5
  BLACK OR AFRICAN AMERICAN                       1                 13
  WHITE                                          34                366
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V8, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED     1  33
  20Q GAIN WILD-TYPE  15 354
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      1   33
  20Q GAIN WILD-TYPE   15  354
                        clus
vv                       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 15
  NOT HISPANIC OR LATINO               33                354
[1] 2 2
[1] FALSE

Clustering(37) Variable = 21Q GAIN MUTATION ANALYSIS
D37V1, survival
                    sevent
clus2                  0   1
  21Q GAIN MUTATED    14   7
  21Q GAIN WILD-TYPE 338  68
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                21                406 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 7                 68 
$`21Q GAIN MUTATED`
TCGA-DB-5277 TCGA-DB-A64W TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6400 TCGA-DU-6407 
       46.65        13.64       211.17        52.11         1.22        94.52 
TCGA-DU-8158 TCGA-DU-A5TT TCGA-DU-A5TY TCGA-DU-A6S7 TCGA-DU-A76K TCGA-E1-5304 
        5.10         4.96        12.20         7.23        11.41        41.13 
TCGA-FG-5962 TCGA-FG-7634 TCGA-HT-7605 TCGA-HT-A5RA TCGA-QH-A6CV TCGA-QH-A6X9 
       47.77        15.35         4.57        14.70        14.53         1.91 
TCGA-S9-A6WH TCGA-S9-A6WL TCGA-TM-A84H 
       32.45        10.88        24.26 

$`21Q GAIN WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 
       72.92        50.17        44.52        36.56        78.28        30.08 
TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF 
       10.29        12.72        27.62        27.02        18.84        18.38 
TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q 
       72.95        12.59        11.01        18.84        16.80         5.98 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64X TCGA-DB-A75K 
       16.08        15.42        27.81        14.73        10.92         7.40 
TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 
        6.44        10.29        30.74         3.81        19.96        31.82 
TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D 
       30.31        14.40         8.02        30.21        42.05        27.81 
TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU 
       17.19        17.19        54.25        10.22         6.58         3.45 
TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 
        6.21        18.02        14.56        17.46         6.74        13.38 
TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 
        8.45         6.81       182.33        18.94        17.49        15.16 
TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6401 
       22.42        49.02        75.16        46.06        65.75        87.45 
TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6408 
        7.04        11.64       133.74        19.89        16.83       114.08 
TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 
        7.96         7.73        11.47        62.96       156.23       138.28 
TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 
       14.99       105.21         6.54         8.84       117.40        90.77 
TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 
       30.67        26.30        10.36         7.96        94.32        18.94 
TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 
       44.02        62.01        25.91        60.30        23.31        41.98 
TCGA-DU-7309 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 
        2.76        23.74         3.98        20.68        21.40        19.13 
TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS 
       16.96        15.48        14.17        14.24        12.59        15.12 
TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S8 
        3.65         5.65         8.65         2.70        77.98         5.98 
TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 TCGA-DU-A7TG TCGA-E1-5302 
       26.76         7.13        21.30       124.50        44.42        50.14 
TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 
       67.46        79.99        57.93       134.27        78.21        95.57 
TCGA-E1-5322 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5963 TCGA-FG-5964 
      130.78        14.33         0.23         0.20        17.98        34.36 
TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 
       32.19        18.77        14.93        24.99        23.97        13.58 
TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 
       17.88        22.55        20.61        20.09        12.95        13.68 
TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 
       14.24        16.01        20.09        14.96        22.52        15.52 
TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J 
       38.27        10.72         5.26        18.71        23.70        14.76 
TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y 
       17.82        16.41        15.02        16.44        10.59        28.54 
TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q 
       10.78        22.95        43.69         5.23         7.43         5.72 
TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 
        0.13         0.10         6.67         7.82         8.81         0.13 
TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 
        0.03        16.54         3.75        17.42         6.54        24.26 
TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 
        6.38         7.10        75.19        59.18        60.03       154.19 
TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7606 
        4.01         5.03        29.85        23.18       107.93        17.29 
TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 
        3.16        22.06        45.99        56.09        57.60         0.23 
TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 
       14.27         0.16        16.24         0.76        44.68         6.05 
TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 
       42.74         0.10        31.69        14.96         0.10         0.10 
TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 
        2.96        17.52         6.90        14.53        39.48        19.23 
TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 
       39.09         0.23        50.63         0.49        23.61        37.15 
TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 
        0.33         0.13         3.68         5.33         2.93         1.71 
TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 
       11.28        31.43         1.64        16.24         9.40        63.55 
TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 
        0.10        21.50        33.01        12.23         6.25         0.10 
TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 
        0.46         2.50         3.95         4.70         0.23        29.59 
TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
        3.88        16.04        15.72         0.23        10.49         0.13 
TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 
       14.01         0.07         0.10         5.33         2.70        13.02 
TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 
        1.81        16.14         5.33         0.10        29.92        13.45 
TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 
        8.32        19.23        40.18        35.90         4.31        21.70 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
       21.60        19.59        17.82        20.35         7.89        20.81 
TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV 
       20.71        19.00        42.77         5.23         4.73         0.23 
TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 
        6.71         1.64         2.37         2.30         4.11         5.88 
TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V 
        7.63         0.76         1.28         5.75         2.53         4.83 
TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CX TCGA-QH-A6CY 
        7.79         4.11         4.18        14.83        12.23         2.20 
TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6XA 
        3.16         0.59         6.31         3.91         4.73         0.23 
TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO 
        5.03         3.48         0.07        88.83        94.03        32.65 
TCGA-R8-A73M TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX 
       59.38        62.17        69.07        18.77        37.84        34.49 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       31.33        21.63        16.37        17.62        23.64        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
        9.86        94.62        83.70         5.85       106.39        62.37 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WI TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO 
       72.59        80.12        84.99        19.86        15.91         7.59 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY 
       15.16        14.07        14.27         7.92        19.63        12.59 
TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW 
        4.21         9.37         8.19         2.04         8.12         3.58 
TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 
        4.04        28.37        13.02       164.38        10.39        99.06 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 
       17.42        83.80        31.59        18.71         5.00        49.45 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
       48.33        49.32        34.78        48.39        12.00        15.09 
TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M 
       50.76        34.36        19.36        17.49        40.83        16.50 
TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-VM-A8C8 
       29.92        18.90         9.44         4.57        12.00        33.07 
TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH 
       30.08        13.51         0.10         7.89        26.79        10.95 
TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-W9-A837 
       27.06         7.04        23.21        45.07 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              1.22               0.03 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
            211.17             182.33 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             14.53              16.06 
[1] "1.2 - 211.2 (14.5)" "0.0 - 182.3 (16.1)"
[1] "hr=" "1.7"
D37V2, continuous
D37V3, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    11  10
  21Q GAIN WILD-TYPE 179 230
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     11   10
  21Q GAIN WILD-TYPE  179  230
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE               11                179
  MALE                 10                230
[1] 2 2
[1] FALSE
D37V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  21Q GAIN MUTATED             8                4                 9
  21Q GAIN WILD-TYPE         151              103               155
D37V5, multiclass
                   clus
vv                  21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  ASTROCYTOMA                      8                151
  OLIGOASTROCYTOMA                 4                103
  OLIGODENDROGLIOMA                9                155
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V6, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     5  16
  21Q GAIN WILD-TYPE  84 325
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      5   16
  21Q GAIN WILD-TYPE   84  325
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  NO                 5                 84
  YES               16                325
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  21Q GAIN MUTATED                                  0     1
  21Q GAIN WILD-TYPE                                1     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  21Q GAIN MUTATED                           0    20
  21Q GAIN WILD-TYPE                        14   380
D37V7, multiclass
                                  clus
vv                                 21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  5
  BLACK OR AFRICAN AMERICAN                       0                 14
  WHITE                                          20                380
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V8, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     0  21
  21Q GAIN WILD-TYPE  16 366
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      0   21
  21Q GAIN WILD-TYPE   16  366
                        clus
vv                       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 16
  NOT HISPANIC OR LATINO               21                366
[1] 2 2
[1] FALSE

Clustering(38) Variable = 22Q GAIN MUTATION ANALYSIS
D38V1, survival
                    sevent
clus2                  0   1
  22Q GAIN MUTATED    13   2
  22Q GAIN WILD-TYPE 339  73
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                15                412 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 2                 73 
$`22Q GAIN MUTATED`
TCGA-CS-6665 TCGA-CS-6668 TCGA-DU-6393 TCGA-DU-6400 TCGA-FG-5962 TCGA-HT-7468 
       12.43         8.02        52.11         1.22        47.77         6.67 
TCGA-HT-8012 TCGA-QH-A6CZ TCGA-R8-A6ML TCGA-R8-A73M TCGA-S9-A6WM TCGA-TM-A84J 
        9.40         3.16        94.03        59.38        19.86        17.49 
TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VV-A829 
       13.51         0.10        27.06 

$`22Q GAIN WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6669 TCGA-CS-6670 
       23.84        17.95         8.48         7.56         7.40         6.61 
TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 
      122.73        81.96        75.25        47.93        72.92        46.65 
TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA 
       50.17        44.52        36.56        78.28        30.08        10.29 
TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG 
       12.72        27.62        27.02        18.84        18.38        72.95 
TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R 
       12.59        11.01        18.84        16.80         5.98        16.08 
TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K 
       15.42        27.81        14.73        13.64        10.92         7.40 
TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 
        6.44        10.29        30.74         3.81        19.96        31.82 
TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D 
       30.31        14.40         8.02        30.21        42.05        27.81 
TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU 
       17.19        17.19        54.25        10.22         6.58         3.45 
TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 
        6.21        18.02        14.56        17.46         6.74        13.38 
TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 
        8.45         6.81       182.33        18.94        17.49        15.16 
TCGA-DU-6392 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 
      211.17        22.42        49.02        75.16        46.06        65.75 
TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 
       87.45         7.04        11.64       133.74        19.89        16.83 
TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 
       94.52       114.08         7.96         7.73        11.47        62.96 
TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 
      156.23       138.28        14.99       105.21         6.54         8.84 
TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 
      117.40        90.77        30.67        26.30        10.36         7.96 
TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 
       94.32        18.94        44.02        62.01        25.91        60.30 
TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 
       23.31        41.98         2.76         5.10        23.74         3.98 
TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 
       20.68        21.40        19.13        16.96        15.48        14.17 
TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW 
       14.24        12.59        15.12         4.96         3.65         5.65 
TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 
       12.20         8.65         2.70        77.98         7.23         5.98 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 TCGA-DU-A7TG 
       11.41        26.76         7.13        21.30       124.50        44.42 
TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 
       50.14        67.46        41.13        79.99        57.93       134.27 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 
       78.21        95.57       130.78        14.33         0.23         0.20 
TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 
       17.98        34.36        32.19        18.77        14.93        24.99 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 
       23.97        13.58        15.35        17.88        22.55        20.61 
TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 
       20.09        12.95        13.68        14.24        16.01        20.09 
TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW 
       14.96        22.52        15.52        38.27        10.72         5.26 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ 
       18.71        23.70        14.76        17.82        16.41        15.02 
TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 
       16.44        10.59        28.54        10.78        22.95        43.69 
TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7469 
        5.23         7.43         5.72         0.13         0.10         7.82 
TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 
        8.81         0.13         0.03        16.54         3.75        17.42 
TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 
        6.54        24.26         6.38         7.10        75.19        59.18 
TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 
       60.03       154.19         4.01         5.03        29.85        23.18 
TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 
      107.93         4.57        17.29         3.16        22.06        45.99 
TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 
       56.09        57.60         0.23        14.27         0.16        16.24 
TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 
        0.76        44.68         6.05        42.74         0.10        31.69 
TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 
       14.96         0.10         0.10         2.96        17.52         6.90 
TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 
       14.53        39.48        19.23        39.09         0.23        50.63 
TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 
        0.49        23.61        37.15         0.33         0.13         3.68 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 
        5.33         2.93         1.71        11.28        31.43         1.64 
TCGA-HT-8011 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 
       16.24        63.55         0.10        21.50        33.01        12.23 
TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 
        6.25         0.10         0.46         2.50         3.95         4.70 
TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS 
        0.23        29.59         3.88        16.04        15.72         0.23 
TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB 
       10.49         0.13        14.01         0.07        14.70         0.10 
TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 
        5.33         2.70        13.02         1.81        16.14         5.33 
TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 
        0.10        29.92        13.45         8.32        19.23        40.18 
TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 
       35.90         4.31        21.70        21.60        19.59        17.82 
TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 
       20.35         7.89        20.81        20.71        19.00        42.77 
TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY 
        5.23         4.73         0.23         6.71         1.64         2.37 
TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 
        2.30         4.11         5.88         7.63         0.76         1.28 
TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS 
        5.75         2.53         4.83         7.79         4.11         4.18 
TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6X3 TCGA-QH-A6X4 
       14.83        14.53        12.23         2.20         0.59         6.31 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X 
        3.91         4.73         1.91         0.23         5.03         3.48 
TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6MO TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV 
        0.07        88.83        32.65        62.17        69.07        18.77 
TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 
       37.84        34.49        31.33        21.63        16.37        17.62 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA 
       23.64        32.61         9.86        94.62        83.70         5.85 
TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI 
      106.39        62.37        72.59        80.12        32.45        84.99 
TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ 
       10.88        15.91         7.59        15.16        14.07        14.27 
TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 
        7.92        19.63        12.59         4.21         9.37         8.19 
TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ 
        2.04         8.12         3.58         4.04        28.37        13.02 
TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 
      164.38        10.39        99.06        17.42        83.80        31.59 
TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA 
       18.71         5.00        49.45        48.33        49.32        34.78 
TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H 
       48.39        12.00        15.09        50.76        34.36        24.26 
TCGA-TM-A84I TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R 
       19.36        40.83        16.50        29.92        18.90         9.44 
TCGA-TM-A84S TCGA-TM-A84T TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CD TCGA-VM-A8CE 
        4.57        12.00        33.07        30.08         7.89        26.79 
TCGA-VM-A8CH TCGA-VV-A86M TCGA-VW-A7QS TCGA-W9-A837 
       10.95         7.04        23.21        45.07 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              0.10               0.03 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             94.03             211.17 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             13.51              15.96 
[1] "0.1 - 94.0 (13.5)"  "0.0 - 211.2 (16.0)"
[1] "hr=" "1.2"
D38V2, continuous
D38V3, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED     6   9
  22Q GAIN WILD-TYPE 184 231
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      6    9
  22Q GAIN WILD-TYPE  184  231
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE                6                184
  MALE                  9                231
[1] 2 2
[1] FALSE
D38V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  22Q GAIN MUTATED             2                2                11
  22Q GAIN WILD-TYPE         157              105               153
D38V5, multiclass
                   clus
vv                  22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  ASTROCYTOMA                      2                157
  OLIGOASTROCYTOMA                 2                105
  OLIGODENDROGLIOMA               11                153
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V6, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED     3  12
  22Q GAIN WILD-TYPE  86 329
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      3   12
  22Q GAIN WILD-TYPE   86  329
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  NO                 3                 86
  YES               12                329
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  22Q GAIN MUTATED                                  0     0
  22Q GAIN WILD-TYPE                                1     6
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  22Q GAIN MUTATED                           0    13
  22Q GAIN WILD-TYPE                        14   387
D38V7, multiclass
                                  clus
vv                                 22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  6
  BLACK OR AFRICAN AMERICAN                       0                 14
  WHITE                                          13                387
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V8, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED     1  11
  22Q GAIN WILD-TYPE  15 376
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      1   11
  22Q GAIN WILD-TYPE   15  376
                        clus
vv                       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 15
  NOT HISPANIC OR LATINO               11                376
[1] 2 2
[1] FALSE

Clustering(39) Variable = XQ GAIN MUTATION ANALYSIS
D39V1, survival
                   sevent
clus2                 0   1
  XQ GAIN MUTATED    24   6
  XQ GAIN WILD-TYPE 328  69
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               30               397 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                6                69 
$`XQ GAIN MUTATED`
TCGA-CS-4938 TCGA-CS-6665 TCGA-DB-5281 TCGA-DU-5871 TCGA-DU-6401 TCGA-DU-6407 
        4.70        12.43        78.28        18.94        87.45        94.52 
TCGA-DU-7007 TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TW TCGA-E1-5322 TCGA-FG-A4MY 
       62.96        15.12         4.96         5.65       130.78        23.70 
TCGA-FG-A713 TCGA-HT-7476 TCGA-HT-7609 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7857 
        5.23         6.54        45.99        31.69        14.96         0.23 
TCGA-HT-7902 TCGA-HT-8013 TCGA-HT-8563 TCGA-HT-A74O TCGA-HW-7493 TCGA-QH-A65S 
       31.43        63.55        16.04         0.10        35.90         2.53 
TCGA-QH-A6CV TCGA-S9-A6TS TCGA-S9-A7IZ TCGA-S9-A7QX TCGA-TM-A84H TCGA-VV-A86M 
       14.53        62.17         4.21         4.04        24.26         7.04 

$`XQ GAIN WILD-TYPE`
TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5393 
        7.69        43.89        18.15        10.62        64.64        40.18 
TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
        0.10        21.01         9.96         6.38        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 
       17.95         8.48         7.56         8.02         7.40         6.61 
TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 
      122.73        81.96        75.25        47.93        72.92        46.65 
TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB 
       50.17        44.52        36.56        30.08        10.29        12.72 
TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH 
       27.62        27.02        18.84        18.38        72.95        12.59 
TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S 
       11.01        18.84        16.80         5.98        16.08        15.42 
TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L 
       27.81        14.73        13.64        10.92         7.40         6.44 
TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 
       10.29        30.74         3.81        19.96        31.82        30.31 
TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F 
       14.40         8.02        30.21        42.05        27.81        17.19 
TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV 
       17.19        54.25        10.22         6.58         3.45         6.21 
TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 
       18.02        14.56        17.46         6.74        13.38         8.45 
TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 
        6.81       182.33        17.49        15.16       211.17        52.11 
TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 
       22.42        49.02        75.16        46.06        65.75         1.22 
TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6408 
        7.04        11.64       133.74        19.89        16.83       114.08 
TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 
        7.96         7.73        11.47       156.23       138.28        14.99 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 
      105.21         6.54         8.84       117.40        90.77        30.67 
TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 
       26.30        10.36         7.96        94.32        18.94        44.02 
TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 
       62.01        25.91        60.30        23.31        41.98         2.76 
TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 
        5.10        23.74         3.98        20.68        21.40        19.13 
TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TU 
       16.96        15.48        14.17        14.24        12.59         3.65 
TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 
       12.20         8.65         2.70        77.98         7.23         5.98 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 TCGA-DU-A7TG 
       11.41        26.76         7.13        21.30       124.50        44.42 
TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 
       50.14        67.46        41.13        79.99        57.93       134.27 
TCGA-E1-5318 TCGA-E1-5319 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 
       78.21        95.57        14.33         0.23         0.20        47.77 
TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 
       17.98        34.36        32.19        18.77        14.93        24.99 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 
       23.97        13.58        15.35        17.88        22.55        20.61 
TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 
       20.09        12.95        13.68        14.24        16.01        20.09 
TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW 
       14.96        22.52        15.52        38.27        10.72         5.26 
TCGA-FG-A4MX TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 
       18.71        14.76        17.82        16.41        15.02        16.44 
TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A87N 
       10.59        28.54        10.78        22.95        43.69         7.43 
TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 
        5.72         0.13         0.10         6.67         7.82         8.81 
TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7477 
        0.13         0.03        16.54         3.75        17.42        24.26 
TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 
        6.38         7.10        75.19        59.18        60.03       154.19 
TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 
        4.01         5.03        29.85        23.18       107.93         4.57 
TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 
       17.29         3.16        22.06        56.09        57.60         0.23 
TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 
       14.27         0.16        16.24         0.76        44.68         6.05 
TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 
       42.74         0.10         0.10         0.10         2.96        17.52 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7858 
        6.90        14.53        39.48        19.23        39.09        50.63 
TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 
        0.49        23.61        37.15         0.33         0.13         3.68 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-8010 TCGA-HT-8011 
        5.33         2.93         1.71        11.28         1.64        16.24 
TCGA-HT-8012 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 
        9.40         0.10        21.50        33.01        12.23         6.25 
TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 
        0.10         0.46         2.50         3.95         4.70         0.23 
TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
       29.59         3.88        15.72         0.23        10.49         0.13 
TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 
       14.01         0.07        14.70         0.10         5.33         2.70 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HW-7486 TCGA-HW-7487 
       13.02         1.81        16.14         5.33        29.92        13.45 
TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 
        8.32        19.23        40.18         4.31        21.70        21.60 
TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM 
       19.59        17.82        20.35         7.89        20.81        20.71 
TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW 
       19.00        42.77         5.23         4.73         0.23         6.71 
TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 
        1.64         2.37         2.30         4.11         5.88         7.63 
TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-QH-A65R TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z 
        0.76         1.28         5.75         4.83         7.79         4.11 
TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
        4.18        14.83        12.23         2.20         3.16         0.59 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC 
        6.31         3.91         4.73         1.91         0.23         5.03 
TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
        3.48         0.07        88.83        94.03        32.65        59.38 
TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ 
       69.07        18.77        37.84        34.49        31.33        21.63 
TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       16.37        17.62        23.64        32.61         9.86        94.62 
TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG 
       83.70         5.85       106.39        62.37        72.59        80.12 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO 
       32.45        84.99        10.88        19.86        15.91         7.59 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY 
       15.16        14.07        14.27         7.92        19.63        12.59 
TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QY 
        9.37         8.19         2.04         8.12         3.58        28.37 
TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 
       13.02       164.38        10.39        99.06        17.42        83.80 
TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 
       31.59        18.71         5.00        49.45        48.33        49.32 
TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G 
       34.78        48.39        12.00        15.09        50.76        34.36 
TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q 
       19.36        17.49        40.83        16.50        29.92        18.90 
TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA 
        9.44         4.57        12.00        33.07        30.08        13.51 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VW-A7QS 
        0.10         7.89        26.79        10.95        27.06        23.21 
TCGA-W9-A837 
       45.07 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             0.10              0.03 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
           130.78            211.17 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            15.58             15.91 
[1] "0.1 - 130.8 (15.6)" "0.0 - 211.2 (15.9)"
[1] "hr=" "1"  
D39V2, continuous
D39V3, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    21   9
  XQ GAIN WILD-TYPE 169 231
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     21    9
  XQ GAIN WILD-TYPE  169  231
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE              21               169
  MALE                 9               231
[1] 2 2
[1] FALSE
D39V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  XQ GAIN MUTATED            13               11                 6
  XQ GAIN WILD-TYPE         146               96               158
D39V5, multiclass
                   clus
vv                  XQ GAIN MUTATED XQ GAIN WILD-TYPE
  ASTROCYTOMA                    13               146
  OLIGOASTROCYTOMA               11                96
  OLIGODENDROGLIOMA               6               158
[1] 3 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
  XQ GAIN MUTATED     8  22
  XQ GAIN WILD-TYPE  81 319
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      8   22
  XQ GAIN WILD-TYPE   81  319
     clus
vv    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  NO                8                81
  YES              22               319
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XQ GAIN MUTATED                                  0     1
  XQ GAIN WILD-TYPE                                1     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XQ GAIN MUTATED                           2    26
  XQ GAIN WILD-TYPE                        12   374
D39V7, multiclass
                                  clus
vv                                 XQ GAIN MUTATED XQ GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 5
  BLACK OR AFRICAN AMERICAN                      2                12
  WHITE                                         26               374
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V8, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     3  27
  XQ GAIN WILD-TYPE  13 360
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      3   27
  XQ GAIN WILD-TYPE   13  360
                        clus
vv                       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                13
  NOT HISPANIC OR LATINO              27               360
[1] 2 2
[1] FALSE

Clustering(40) Variable = 1P LOSS MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                 0   1
  1P LOSS MUTATED   141  17
  1P LOSS WILD-TYPE 211  58
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
              158               269 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               17                58 
$`1P LOSS MUTATED`
TCGA-CS-5390 TCGA-CS-5394 TCGA-CS-5396 TCGA-CS-6668 TCGA-CS-6670 TCGA-DB-5274 
       64.64         0.10         9.96         8.02         6.61        75.25 
TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-A4XA TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L 
       50.17        44.52        10.29        72.95        12.59        11.01 
TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
       16.80         5.98        16.08        27.81        14.73        13.64 
TCGA-DB-A75K TCGA-DH-5141 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66F TCGA-DH-A7UR 
        7.40        31.82         8.02        30.21        17.19        54.25 
TCGA-DH-A7US TCGA-DU-5849 TCGA-DU-5870 TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 
       10.22        14.56       182.33        15.16        52.11        22.42 
TCGA-DU-6397 TCGA-DU-6400 TCGA-DU-6410 TCGA-DU-7009 TCGA-DU-7014 TCGA-DU-7018 
       46.06         1.22         7.96       138.28       117.40        30.67 
TCGA-DU-7294 TCGA-DU-7300 TCGA-DU-7302 TCGA-DU-8158 TCGA-DU-8164 TCGA-DU-8168 
       94.32        62.01        60.30         5.10        21.40        14.17 
TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S8 TCGA-DU-A76R TCGA-DU-A7TG 
        8.65         2.70        77.98         5.98        21.30        44.42 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 TCGA-F6-A8O3 
      134.27        78.21        95.57       130.78        14.33         0.23 
TCGA-FG-5962 TCGA-FG-5964 TCGA-FG-7634 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-8185 
       47.77        34.36        15.35        22.55        20.61        14.24 
TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8189 TCGA-FG-A60K TCGA-FG-A6IZ TCGA-FG-A6J1 
       16.01        20.09        22.52        17.82        15.02        16.44 
TCGA-FG-A710 TCGA-FG-A713 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7471 TCGA-HT-7477 
       22.95         5.23         0.10         6.67         0.13        24.26 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7605 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7616 
       75.19        59.18         4.57         3.16        22.06         0.23 
TCGA-HT-7620 TCGA-HT-7677 TCGA-HT-7681 TCGA-HT-7687 TCGA-HT-7692 TCGA-HT-7694 
       14.27        16.24        44.68         0.10         2.96         6.90 
TCGA-HT-7695 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
       14.53        39.09         0.23        37.15         0.33         0.13 
TCGA-HT-7881 TCGA-HT-8010 TCGA-HT-8012 TCGA-HT-8105 TCGA-HT-8109 TCGA-HT-8113 
        2.93         1.64         9.40         6.25         3.95        29.59 
TCGA-HT-A4DV TCGA-HT-A5R9 TCGA-HT-A615 TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7491 
       10.49         0.07        13.02        29.92        13.45        40.18 
TCGA-HW-7495 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-IK-8125 TCGA-KT-A74X TCGA-P5-A5EX 
        4.31        17.82        20.35        42.77         5.23         1.64 
TCGA-P5-A5F0 TCGA-P5-A5F4 TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CU 
        4.11         0.76         4.83         7.79         4.11        14.83 
TCGA-QH-A6CV TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 
       14.53         2.20         3.16         6.31         3.91         4.73 
TCGA-QH-A86X TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TW 
        3.48        88.83        94.03        32.65        59.38        37.84 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6UB TCGA-S9-A6WD 
       34.49        31.33        23.64        32.61       106.39        62.37 
TCGA-S9-A6WE TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WP 
       72.59        32.45        84.99        10.88        15.91        15.16 
TCGA-S9-A7IQ TCGA-S9-A7IY TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QY 
       14.27        12.59         8.19         2.04         8.12        28.37 
TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-TM-A7C5 TCGA-TM-A84G TCGA-TM-A84M TCGA-TM-A84O 
       13.02       164.38        49.32        34.36        16.50        29.92 
TCGA-TM-A84R TCGA-TM-A84S TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CE TCGA-VV-A829 
        9.44         4.57        13.51         0.10        26.79        27.06 
TCGA-VW-A7QS TCGA-W9-A837 
       23.21        45.07 

$`1P LOSS WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5393 
        4.70         7.69        43.89        18.15        10.62        40.18 
TCGA-CS-5395 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 
       21.01         6.38        17.69        23.84        17.95        12.43 
TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6669 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5275 
        8.48         7.56         7.40       122.73        81.96        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XB 
       72.92        46.65        36.56        78.28        30.08        12.72 
TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A64O TCGA-DB-A64S 
       27.62        27.02        18.84        18.38        18.84        15.42 
TCGA-DB-A64X TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 
       10.92         6.44        10.29        30.74         3.81        19.96 
TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66G TCGA-DH-A7UT 
       30.31        14.40        42.05        27.81        17.19         6.58 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 
        3.45         6.21        18.02        17.46         6.74        13.38 
TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-6392 TCGA-DU-6395 
        8.45         6.81        18.94        17.49       211.17        49.02 
TCGA-DU-6396 TCGA-DU-6399 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 
       75.16        65.75        87.45         7.04        11.64       133.74 
TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6542 TCGA-DU-7006 
       19.89        16.83        94.52       114.08         7.73        11.47 
TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 
       62.96       156.23        14.99       105.21         6.54         8.84 
TCGA-DU-7015 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7298 TCGA-DU-7299 
       90.77        26.30        10.36         7.96        18.94        44.02 
TCGA-DU-7301 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8161 TCGA-DU-8162 
       25.91        23.31        41.98         2.76        23.74         3.98 
TCGA-DU-8163 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-A5TP TCGA-DU-A5TR 
       20.68        19.13        16.96        15.48        14.24        12.59 
TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S7 
       15.12         4.96         3.65         5.65        12.20         7.23 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A7T8 TCGA-E1-5302 TCGA-E1-5303 
       11.41        26.76         7.13       124.50        50.14        67.46 
TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-F6-A8O4 TCGA-FG-5963 TCGA-FG-5965 
       41.13        79.99        57.93         0.20        17.98        32.19 
TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7636 
       18.77        14.93        24.99        23.97        13.58        17.88 
TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8188 TCGA-FG-8191 TCGA-FG-A4MT 
       20.09        12.95        13.68        14.96        15.52        38.27 
TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60L 
       10.72         5.26        18.71        23.70        14.76        16.41 
TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A711 TCGA-FG-A87N TCGA-FG-A87Q 
       10.59        28.54        10.78        43.69         7.43         5.72 
TCGA-FN-7833 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 
        0.13         7.82         8.81         0.03        16.54         3.75 
TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7482 TCGA-HT-7483 
       17.42         6.54         6.38         7.10        60.03       154.19 
TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7606 
        4.01         5.03        29.85        23.18       107.93        17.29 
TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7676 TCGA-HT-7680 TCGA-HT-7684 
       45.99        56.09        57.60         0.16         0.76         6.05 
TCGA-HT-7686 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7693 
       42.74        31.69        14.96         0.10         0.10        17.52 
TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7879 
       39.48        19.23        50.63         0.49        23.61         3.68 
TCGA-HT-7880 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8011 TCGA-HT-8013 
        5.33         1.71        11.28        31.43        16.24        63.55 
TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8106 TCGA-HT-8107 
        0.10        21.50        33.01        12.23         0.10         0.46 
TCGA-HT-8108 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 
        2.50         4.70         0.23         3.88        16.04        15.72 
TCGA-HT-A4DS TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC 
        0.23         0.13        14.01        14.70         0.10         5.33 
TCGA-HT-A614 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A74O TCGA-HW-7489 
        2.70         1.81        16.14         5.33         0.10         8.32 
TCGA-HW-7490 TCGA-HW-7493 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-A5KK 
       19.23        35.90        21.70        21.60        19.59         7.89 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW 
       20.81        20.71        19.00         4.73         0.23         6.71 
TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F6 TCGA-QH-A65R 
        2.37         2.30         5.88         7.63         1.28         5.75 
TCGA-QH-A65S TCGA-QH-A6CS TCGA-QH-A6CX TCGA-QH-A6X3 TCGA-QH-A6X9 TCGA-QH-A6XA 
        2.53         4.18        12.23         0.59         1.91         0.23 
TCGA-QH-A6XC TCGA-QH-A870 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TZ 
        5.03         0.07        62.17        69.07        18.77        21.63 
TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA 
       16.37        17.62         9.86        94.62        83.70         5.85 
TCGA-S9-A6WG TCGA-S9-A6WM TCGA-S9-A6WO TCGA-S9-A6WQ TCGA-S9-A7IS TCGA-S9-A7IX 
       80.12        19.86         7.59        14.07         7.92        19.63 
TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7R2 TCGA-S9-A7R3 
        4.21         9.37         3.58         4.04        10.39        99.06 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 
       17.42        83.80        31.59        18.71         5.00        49.45 
TCGA-TM-A7C4 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F 
       48.33        34.78        48.39        12.00        15.09        50.76 
TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84Q TCGA-TM-A84T 
       24.26        19.36        17.49        40.83        18.90        12.00 
TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CD TCGA-VM-A8CH TCGA-VV-A86M 
       33.07        30.08         7.89        10.95         7.04 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             0.07              0.03 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           182.33            211.17 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            15.63             16.04 
[1] "0.1 - 182.3 (15.6)" "0.0 - 211.2 (16.0)"
[1] "hr=" "2.4"
D40V2, continuous
D40V3, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    70  89
  1P LOSS WILD-TYPE 120 151
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     70   89
  1P LOSS WILD-TYPE  120  151
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE              70               120
  MALE                89               151
[1] 2 2
[1] FALSE
D40V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  1P LOSS MUTATED             9               32               118
  1P LOSS WILD-TYPE         150               75                46
D40V5, multiclass
                   clus
vv                  1P LOSS MUTATED 1P LOSS WILD-TYPE
  ASTROCYTOMA                     9               150
  OLIGOASTROCYTOMA               32                75
  OLIGODENDROGLIOMA             118                46
[1] 3 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
  1P LOSS MUTATED    23 136
  1P LOSS WILD-TYPE  66 205
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     23  136
  1P LOSS WILD-TYPE   66  205
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  NO               23                66
  YES             136               205
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1P LOSS MUTATED                                  0     4
  1P LOSS WILD-TYPE                                1     2
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1P LOSS MUTATED                           4   146
  1P LOSS WILD-TYPE                        10   254
D40V7, multiclass
                                  clus
vv                                 1P LOSS MUTATED 1P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          4                 2
  BLACK OR AFRICAN AMERICAN                      4                10
  WHITE                                        146               254
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V8, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     6 142
  1P LOSS WILD-TYPE  10 245
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      6  142
  1P LOSS WILD-TYPE   10  245
                        clus
vv                       1P LOSS MUTATED 1P LOSS WILD-TYPE
  HISPANIC OR LATINO                   6                10
  NOT HISPANIC OR LATINO             142               245
[1] 2 2
[1] FALSE

Clustering(41) Variable = 1Q LOSS MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                 0   1
  1Q LOSS MUTATED    18   5
  1Q LOSS WILD-TYPE 334  70
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               23               404 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                5                70 
$`1Q LOSS MUTATED`
TCGA-CS-5396 TCGA-DB-5279 TCGA-DH-5141 TCGA-DH-5144 TCGA-DH-A669 TCGA-DU-5849 
        9.96        44.52        31.82         8.02        30.21        14.56 
TCGA-DU-6400 TCGA-DU-7294 TCGA-DU-8158 TCGA-DU-A5TS TCGA-DU-A7TG TCGA-E1-5322 
        1.22        94.32         5.10        15.12        44.42       130.78 
TCGA-FG-5962 TCGA-FG-8185 TCGA-HT-7477 TCGA-HT-7857 TCGA-HT-8113 TCGA-P5-A5F4 
       47.77        14.24        24.26         0.23        29.59         0.76 
TCGA-QH-A65S TCGA-QH-A65Z TCGA-QH-A6CV TCGA-S9-A6WI TCGA-S9-A7R1 
        2.53         4.11        14.53        84.99       164.38 

$`1Q LOSS WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
       40.18         0.10        21.01         6.38        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 
       17.95        12.43         8.48         7.56         8.02         7.40 
TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 
        6.61       122.73        81.96        75.25        47.93        72.92 
TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA 
       46.65        50.17        36.56        78.28        30.08        10.29 
TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG 
       12.72        27.62        27.02        18.84        18.38        72.95 
TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R 
       12.59        11.01        18.84        16.80         5.98        16.08 
TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K 
       15.42        27.81        14.73        13.64        10.92         7.40 
TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5142 
        6.44        10.29        30.74         3.81        19.96        30.31 
TCGA-DH-5143 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR 
       14.40        42.05        27.81        17.19        17.19        54.25 
TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5851 
       10.22         6.58         3.45         6.21        18.02        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
        6.74        13.38         8.45         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 
       17.49        15.16       211.17        52.11        22.42        49.02 
TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       75.16        46.06        65.75        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 
      133.74        19.89        16.83        94.52       114.08         7.96 
TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 
        7.73        11.47        62.96       156.23       138.28        14.99 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 
      105.21         6.54         8.84       117.40        90.77        30.67 
TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 
       26.30        10.36         7.96        18.94        44.02        62.01 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8161 
       25.91        60.30        23.31        41.98         2.76        23.74 
TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 
        3.98        20.68        21.40        19.13        16.96        15.48 
TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW 
       14.17        14.24        12.59         4.96         3.65         5.65 
TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 
       12.20         8.65         2.70        77.98         7.23         5.98 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 TCGA-E1-5302 
       11.41        26.76         7.13        21.30       124.50        50.14 
TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 
       67.46        41.13        79.99        57.93       134.27        78.21 
TCGA-E1-5319 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5963 TCGA-FG-5964 
       95.57        14.33         0.23         0.20        17.98        34.36 
TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 
       32.19        18.77        14.93        24.99        23.97        13.58 
TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 
       15.35        17.88        22.55        20.61        20.09        12.95 
TCGA-FG-8182 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 
       13.68        16.01        20.09        14.96        22.52        15.52 
TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J 
       38.27        10.72         5.26        18.71        23.70        14.76 
TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y 
       17.82        16.41        15.02        16.44        10.59        28.54 
TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q 
       10.78        22.95        43.69         5.23         7.43         5.72 
TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 
        0.13         0.10         6.67         7.82         8.81         0.13 
TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7478 
        0.03        16.54         3.75        17.42         6.54         6.38 
TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 
        7.10        75.19        59.18        60.03       154.19         4.01 
TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 
        5.03        29.85        23.18       107.93         4.57        17.29 
TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 
        3.16        22.06        45.99        56.09        57.60         0.23 
TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 
       14.27         0.16        16.24         0.76        44.68         6.05 
TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 
       42.74         0.10        31.69        14.96         0.10         0.10 
TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 
        2.96        17.52         6.90        14.53        39.48        19.23 
TCGA-HT-7856 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 
       39.09        50.63         0.49        23.61        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 
        0.13         3.68         5.33         2.93         1.71        11.28 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 
       31.43         1.64        16.24         9.40        63.55         0.10 
TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 
       21.50        33.01        12.23         6.25         0.10         0.46 
TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8114 TCGA-HT-8563 
        2.50         3.95         4.70         0.23         3.88        16.04 
TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 
       15.72         0.23        10.49         0.13        14.01         0.07 
TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 
       14.70         0.10         5.33         2.70        13.02         1.81 
TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 
       16.14         5.33         0.10        29.92        13.45         8.32 
TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 
       19.23        40.18        35.90         4.31        21.70        21.60 
TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM 
       19.59        17.82        20.35         7.89        20.81        20.71 
TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW 
       19.00        42.77         5.23         4.73         0.23         6.71 
TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 
        1.64         2.37         2.30         4.11         5.88         7.63 
TCGA-P5-A5F6 TCGA-QH-A65R TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A6CS TCGA-QH-A6CU 
        1.28         5.75         4.83         7.79         4.18        14.83 
TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 
       12.23         2.20         3.16         0.59         6.31         3.91 
TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 
        4.73         1.91         0.23         5.03         3.48         0.07 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TS TCGA-S9-A6TU 
       88.83        94.03        32.65        59.38        62.17        69.07 
TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 
       18.77        37.84        34.49        31.33        21.63        16.37 
TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
       17.62        23.64        32.61         9.86        94.62        83.70 
TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH 
        5.85       106.39        62.37        72.59        80.12        32.45 
TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ 
       10.88        19.86        15.91         7.59        15.16        14.07 
TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 
       14.27         7.92        19.63        12.59         4.21         9.37 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY 
        8.19         2.04         8.12         3.58         4.04        28.37 
TCGA-S9-A7QZ TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 
       13.02        10.39        99.06        17.42        83.80        31.59 
TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA 
       18.71         5.00        49.45        48.33        49.32        34.78 
TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H 
       48.39        12.00        15.09        50.76        34.36        24.26 
TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q 
       19.36        17.49        40.83        16.50        29.92        18.90 
TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA 
        9.44         4.57        12.00        33.07        30.08        13.51 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M 
        0.10         7.89        26.79        10.95        27.06         7.04 
TCGA-VW-A7QS TCGA-W9-A837 
       23.21        45.07 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
             0.23              0.03 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
           164.38            211.17 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            15.12             15.96 
[1] "0.2 - 164.4 (15.1)" "0.0 - 211.2 (16.0)"
[1] "hr=" "1.2"
D41V2, continuous
D41V3, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED    11  12
  1Q LOSS WILD-TYPE 179 228
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     11   12
  1Q LOSS WILD-TYPE  179  228
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE              11               179
  MALE                12               228
[1] 2 2
[1] FALSE
D41V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  1Q LOSS MUTATED             4                4                15
  1Q LOSS WILD-TYPE         155              103               149
D41V5, multiclass
                   clus
vv                  1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  ASTROCYTOMA                     4               155
  OLIGOASTROCYTOMA                4               103
  OLIGODENDROGLIOMA              15               149
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V6, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     6  17
  1Q LOSS WILD-TYPE  83 324
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      6   17
  1Q LOSS WILD-TYPE   83  324
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  NO                6                83
  YES              17               324
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1Q LOSS MUTATED                                  0     1
  1Q LOSS WILD-TYPE                                1     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1Q LOSS MUTATED                           2    19
  1Q LOSS WILD-TYPE                        12   381
D41V7, multiclass
                                  clus
vv                                 1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 5
  BLACK OR AFRICAN AMERICAN                      2                12
  WHITE                                         19               381
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V8, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     1  21
  1Q LOSS WILD-TYPE  15 366
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      1   21
  1Q LOSS WILD-TYPE   15  366
                        clus
vv                       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                15
  NOT HISPANIC OR LATINO              21               366
[1] 2 2
[1] FALSE

Clustering(42) Variable = 2P LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                 0   1
  2P LOSS MUTATED    11   4
  2P LOSS WILD-TYPE 341  71
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               15               412 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                4                71 
$`2P LOSS MUTATED`
TCGA-CS-6186 TCGA-CS-6666 TCGA-DH-5142 TCGA-DU-7010 TCGA-DU-7014 TCGA-FG-A6J3 
       17.69         8.48        30.31        14.99       117.40        10.59 
TCGA-HT-7469 TCGA-HT-7477 TCGA-HT-7690 TCGA-HT-7692 TCGA-HT-A5R7 TCGA-HW-7493 
        7.82        24.26         0.10         2.96        14.01        35.90 
TCGA-P5-A5F6 TCGA-S9-A89V TCGA-VM-A8C8 
        1.28        18.71        33.07 

$`2P LOSS WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6188 
       40.18         0.10        21.01         9.96         6.38        23.84 
TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 
       17.95        12.43         7.56         8.02         7.40         6.61 
TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 
      122.73        81.96        75.25        47.93        72.92        46.65 
TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA 
       50.17        44.52        36.56        78.28        30.08        10.29 
TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG 
       12.72        27.62        27.02        18.84        18.38        72.95 
TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R 
       12.59        11.01        18.84        16.80         5.98        16.08 
TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K 
       15.42        27.81        14.73        13.64        10.92         7.40 
TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 
        6.44        10.29        30.74         3.81        19.96        31.82 
TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F 
       14.40         8.02        30.21        42.05        27.81        17.19 
TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV 
       17.19        54.25        10.22         6.58         3.45         6.21 
TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 
       18.02        14.56        17.46         6.74        13.38         8.45 
TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 
        6.81       182.33        18.94        17.49        15.16       211.17 
TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 
       52.11        22.42        49.02        75.16        46.06        65.75 
TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 
        1.22        87.45         7.04        11.64       133.74        19.89 
TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 
       16.83        94.52       114.08         7.96         7.73        11.47 
TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 
       62.96       156.23       138.28       105.21         6.54         8.84 
TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 
       90.77        30.67        26.30        10.36         7.96        94.32 
TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 
       18.94        44.02        62.01        25.91        60.30        23.31 
TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 
       41.98         2.76         5.10        23.74         3.98        20.68 
TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP 
       21.40        19.13        16.96        15.48        14.17        14.24 
TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY 
       12.59        15.12         4.96         3.65         5.65        12.20 
TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K 
        8.65         2.70        77.98         7.23         5.98        11.41 
TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 TCGA-DU-A7TG TCGA-E1-5302 
       26.76         7.13        21.30       124.50        44.42        50.14 
TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 
       67.46        41.13        79.99        57.93       134.27        78.21 
TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 
       95.57       130.78        14.33         0.23         0.20        47.77 
TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 
       17.98        34.36        32.19        18.77        14.93        24.99 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 
       23.97        13.58        15.35        17.88        22.55        20.61 
TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 
       20.09        12.95        13.68        14.24        16.01        20.09 
TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW 
       14.96        22.52        15.52        38.27        10.72         5.26 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ 
       18.71        23.70        14.76        17.82        16.41        15.02 
TCGA-FG-A6J1 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 
       16.44        28.54        10.78        22.95        43.69         5.23 
TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7470 
        7.43         5.72         0.13         0.10         6.67         8.81 
TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 
        0.13         0.03        16.54         3.75        17.42         6.54 
TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 
        6.38         7.10        75.19        59.18        60.03       154.19 
TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 
        4.01         5.03        29.85        23.18       107.93         4.57 
TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 
       17.29         3.16        22.06        45.99        56.09        57.60 
TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 
        0.23        14.27         0.16        16.24         0.76        44.68 
TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7691 
        6.05        42.74         0.10        31.69        14.96         0.10 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 
       17.52         6.90        14.53        39.48        19.23        39.09 
TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 
        0.23        50.63         0.49        23.61        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 
        0.13         3.68         5.33         2.93         1.71        11.28 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 
       31.43         1.64        16.24         9.40        63.55         0.10 
TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 
       21.50        33.01        12.23         6.25         0.10         0.46 
TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 
        2.50         3.95         4.70         0.23        29.59         3.88 
TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R9 
       16.04        15.72         0.23        10.49         0.13         0.07 
TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 
       14.70         0.10         5.33         2.70        13.02         1.81 
TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 
       16.14         5.33         0.10        29.92        13.45         8.32 
TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 
       19.23        40.18         4.31        21.70        21.60        19.59 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 
       17.82        20.35         7.89        20.81        20.71        19.00 
TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX 
       42.77         5.23         4.73         0.23         6.71         1.64 
TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 
        2.37         2.30         4.11         5.88         7.63         0.76 
TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS 
        5.75         2.53         4.83         7.79         4.11         4.18 
TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
       14.83        14.53        12.23         2.20         3.16         0.59 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC 
        6.31         3.91         4.73         1.91         0.23         5.03 
TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
        3.48         0.07        88.83        94.03        32.65        59.38 
TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY 
       62.17        69.07        18.77        37.84        34.49        31.33 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       21.63        16.37        17.62        23.64        32.61         9.86 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE 
       94.62        83.70         5.85       106.39        62.37        72.59 
TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN 
       80.12        32.45        84.99        10.88        19.86        15.91 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX 
        7.59        15.16        14.07        14.27         7.92        19.63 
TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       12.59         4.21         9.37         8.19         2.04         8.12 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 
        3.58         4.04        28.37        13.02       164.38        10.39 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89Z TCGA-TM-A7C3 
       99.06        17.42        83.80        31.59         5.00        49.45 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
       48.33        49.32        34.78        48.39        12.00        15.09 
TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L 
       50.76        34.36        24.26        19.36        17.49        40.83 
TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T 
       16.50        29.92        18.90         9.44         4.57        12.00 
TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH 
       30.08        13.51         0.10         7.89        26.79        10.95 
TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-W9-A837 
       27.06         7.04        23.21        45.07 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             0.10              0.03 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
           117.40            211.17 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            14.99             15.96 
[1] "0.1 - 117.4 (15.0)" "0.0 - 211.2 (16.0)"
[1] "hr=" "1.8"
D42V2, continuous
D42V3, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     5  11
  2P LOSS WILD-TYPE 185 229
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      5   11
  2P LOSS WILD-TYPE  185  229
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE               5               185
  MALE                11               229
[1] 2 2
[1] FALSE
D42V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  2P LOSS MUTATED             8                4                 4
  2P LOSS WILD-TYPE         151              103               160
D42V5, multiclass
                   clus
vv                  2P LOSS MUTATED 2P LOSS WILD-TYPE
  ASTROCYTOMA                     8               151
  OLIGOASTROCYTOMA                4               103
  OLIGODENDROGLIOMA               4               160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V6, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     3  13
  2P LOSS WILD-TYPE  86 328
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      3   13
  2P LOSS WILD-TYPE   86  328
     clus
vv    2P LOSS MUTATED 2P LOSS WILD-TYPE
  NO                3                86
  YES              13               328
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2P LOSS MUTATED                                  0     0
  2P LOSS WILD-TYPE                                1     6
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2P LOSS MUTATED                           0    16
  2P LOSS WILD-TYPE                        14   384
D42V7, multiclass
                                  clus
vv                                 2P LOSS MUTATED 2P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 6
  BLACK OR AFRICAN AMERICAN                      0                14
  WHITE                                         16               384
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V8, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     0  15
  2P LOSS WILD-TYPE  16 372
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      0   15
  2P LOSS WILD-TYPE   16  372
                        clus
vv                       2P LOSS MUTATED 2P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                16
  NOT HISPANIC OR LATINO              15               372
[1] 2 2
[1] FALSE

Clustering(43) Variable = 2Q LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                 0   1
  2Q LOSS MUTATED    10   2
  2Q LOSS WILD-TYPE 342  73
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               12               415 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                2                73 
$`2Q LOSS MUTATED`
TCGA-CS-6666 TCGA-DB-5277 TCGA-DH-5142 TCGA-DH-A66B TCGA-DU-6408 TCGA-FG-A6J3 
        8.48        46.65        30.31        42.05       114.08        10.59 
TCGA-HT-7477 TCGA-HT-7690 TCGA-HT-7692 TCGA-HT-A618 TCGA-HW-7493 TCGA-P5-A5F6 
       24.26         0.10         2.96         5.33        35.90         1.28 

$`2Q LOSS WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 
       23.84        17.95        12.43         7.56         8.02         7.40 
TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 
        6.61       122.73        81.96        75.25        47.93        72.92 
TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA 
       50.17        44.52        36.56        78.28        30.08        10.29 
TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG 
       12.72        27.62        27.02        18.84        18.38        72.95 
TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R 
       12.59        11.01        18.84        16.80         5.98        16.08 
TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K 
       15.42        27.81        14.73        13.64        10.92         7.40 
TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 
        6.44        10.29        30.74         3.81        19.96        31.82 
TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G 
       14.40         8.02        30.21        27.81        17.19        17.19 
TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 
       54.25        10.22         6.58         3.45         6.21        18.02 
TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 
       14.56        17.46         6.74        13.38         8.45         6.81 
TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 
      182.33        18.94        17.49        15.16       211.17        52.11 
TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 
       22.42        49.02        75.16        46.06        65.75         1.22 
TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 
       87.45         7.04        11.64       133.74        19.89        16.83 
TCGA-DU-6407 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 
       94.52         7.96         7.73        11.47        62.96       156.23 
TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 
      138.28        14.99       105.21         6.54         8.84       117.40 
TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 
       90.77        30.67        26.30        10.36         7.96        94.32 
TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 
       18.94        44.02        62.01        25.91        60.30        23.31 
TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 
       41.98         2.76         5.10        23.74         3.98        20.68 
TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP 
       21.40        19.13        16.96        15.48        14.17        14.24 
TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY 
       12.59        15.12         4.96         3.65         5.65        12.20 
TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K 
        8.65         2.70        77.98         7.23         5.98        11.41 
TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 TCGA-DU-A7TG TCGA-E1-5302 
       26.76         7.13        21.30       124.50        44.42        50.14 
TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 
       67.46        41.13        79.99        57.93       134.27        78.21 
TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 
       95.57       130.78        14.33         0.23         0.20        47.77 
TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 
       17.98        34.36        32.19        18.77        14.93        24.99 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 
       23.97        13.58        15.35        17.88        22.55        20.61 
TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 
       20.09        12.95        13.68        14.24        16.01        20.09 
TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW 
       14.96        22.52        15.52        38.27        10.72         5.26 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ 
       18.71        23.70        14.76        17.82        16.41        15.02 
TCGA-FG-A6J1 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 
       16.44        28.54        10.78        22.95        43.69         5.23 
TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 
        7.43         5.72         0.13         0.10         6.67         7.82 
TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 
        8.81         0.13         0.03        16.54         3.75        17.42 
TCGA-HT-7476 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 
        6.54         6.38         7.10        75.19        59.18        60.03 
TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 
      154.19         4.01         5.03        29.85        23.18       107.93 
TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 
        4.57        17.29         3.16        22.06        45.99        56.09 
TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 
       57.60         0.23        14.27         0.16        16.24         0.76 
TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 
       44.68         6.05        42.74         0.10        31.69        14.96 
TCGA-HT-7691 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 
        0.10        17.52         6.90        14.53        39.48        19.23 
TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 
       39.09         0.23        50.63         0.49        23.61        37.15 
TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 
        0.33         0.13         3.68         5.33         2.93         1.71 
TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 
       11.28        31.43         1.64        16.24         9.40        63.55 
TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 
        0.10        21.50        33.01        12.23         6.25         0.10 
TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 
        0.46         2.50         3.95         4.70         0.23        29.59 
TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
        3.88        16.04        15.72         0.23        10.49         0.13 
TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 
       14.01         0.07        14.70         0.10         5.33         2.70 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 
       13.02         1.81        16.14         0.10        29.92        13.45 
TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 
        8.32        19.23        40.18         4.31        21.70        21.60 
TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM 
       19.59        17.82        20.35         7.89        20.81        20.71 
TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW 
       19.00        42.77         5.23         4.73         0.23         6.71 
TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 
        1.64         2.37         2.30         4.11         5.88         7.63 
TCGA-P5-A5F4 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z 
        0.76         5.75         2.53         4.83         7.79         4.11 
TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ 
        4.18        14.83        14.53        12.23         2.20         3.16 
TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA 
        0.59         6.31         3.91         4.73         1.91         0.23 
TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO 
        5.03         3.48         0.07        88.83        94.03        32.65 
TCGA-R8-A73M TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX 
       59.38        62.17        69.07        18.77        37.84        34.49 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       31.33        21.63        16.37        17.62        23.64        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
        9.86        94.62        83.70         5.85       106.39        62.37 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM 
       72.59        80.12        32.45        84.99        10.88        19.86 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
       15.91         7.59        15.16        14.07        14.27         7.92 
TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 
       19.63        12.59         4.21         9.37         8.19         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 
        8.12         3.58         4.04        28.37        13.02       164.38 
TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V 
       10.39        99.06        17.42        83.80        31.59        18.71 
TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF 
        5.00        49.45        48.33        49.32        34.78        48.39 
TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I 
       12.00        15.09        50.76        34.36        24.26        19.36 
TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R 
       17.49        40.83        16.50        29.92        18.90         9.44 
TCGA-TM-A84S TCGA-TM-A84T TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB 
        4.57        12.00        33.07        30.08        13.51         0.10 
TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS 
        7.89        26.79        10.95        27.06         7.04        23.21 
TCGA-W9-A837 
       45.07 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             0.10              0.03 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
           114.08            211.17 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
           17.425            15.910 
[1] "0.1 - 114.1 (17.4)" "0.0 - 211.2 (15.9)"
[1] "hr=" "1.1"
D43V2, continuous
D43V3, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     4   9
  2Q LOSS WILD-TYPE 186 231
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      4    9
  2Q LOSS WILD-TYPE  186  231
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE               4               186
  MALE                 9               231
[1] 2 2
[1] FALSE
D43V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  2Q LOSS MUTATED             8                3                 2
  2Q LOSS WILD-TYPE         151              104               162
D43V5, multiclass
                   clus
vv                  2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  ASTROCYTOMA                     8               151
  OLIGOASTROCYTOMA                3               104
  OLIGODENDROGLIOMA               2               162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V6, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     3  10
  2Q LOSS WILD-TYPE  86 331
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      3   10
  2Q LOSS WILD-TYPE   86  331
     clus
vv    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  NO                3                86
  YES              10               331
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2Q LOSS MUTATED                                  0     0
  2Q LOSS WILD-TYPE                                1     6
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2Q LOSS MUTATED                           0    13
  2Q LOSS WILD-TYPE                        14   387
D43V7, multiclass
                                  clus
vv                                 2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 6
  BLACK OR AFRICAN AMERICAN                      0                14
  WHITE                                         13               387
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V8, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     0  13
  2Q LOSS WILD-TYPE  16 374
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      0   13
  2Q LOSS WILD-TYPE   16  374
                        clus
vv                       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                16
  NOT HISPANIC OR LATINO              13               374
[1] 2 2
[1] FALSE

Clustering(44) Variable = 3P LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                 0   1
  3P LOSS MUTATED    14   6
  3P LOSS WILD-TYPE 338  69
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               20               407 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                6                69 
$`3P LOSS MUTATED`
TCGA-CS-6666 TCGA-DB-5277 TCGA-DH-A66D TCGA-DU-6396 TCGA-DU-7300 TCGA-DU-A5TU 
        8.48        46.65        27.81        75.16        62.01         3.65 
TCGA-DU-A76R TCGA-HT-7469 TCGA-HT-7477 TCGA-HT-7690 TCGA-HT-8111 TCGA-HT-8564 
       21.30         7.82        24.26         0.10         0.23        15.72 
TCGA-HT-A5RA TCGA-IK-7675 TCGA-P5-A5F6 TCGA-S9-A89V TCGA-TM-A84B TCGA-TM-A84J 
       14.70        19.00         1.28        18.71        12.00        17.49 
TCGA-VM-A8C8 TCGA-VV-A829 
       33.07        27.06 

$`3P LOSS WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 
       23.84        17.95        12.43         7.56         8.02         7.40 
TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 
        6.61       122.73        81.96        75.25        47.93        72.92 
TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA 
       50.17        44.52        36.56        78.28        30.08        10.29 
TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG 
       12.72        27.62        27.02        18.84        18.38        72.95 
TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R 
       12.59        11.01        18.84        16.80         5.98        16.08 
TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K 
       15.42        27.81        14.73        13.64        10.92         7.40 
TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 
        6.44        10.29        30.74         3.81        19.96        31.82 
TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66F 
       30.31        14.40         8.02        30.21        42.05        17.19 
TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV 
       17.19        54.25        10.22         6.58         3.45         6.21 
TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 
       18.02        14.56        17.46         6.74        13.38         8.45 
TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 
        6.81       182.33        18.94        17.49        15.16       211.17 
TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 
       52.11        22.42        49.02        46.06        65.75         1.22 
TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 
       87.45         7.04        11.64       133.74        19.89        16.83 
TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 
       94.52       114.08         7.96         7.73        11.47        62.96 
TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 
      156.23       138.28        14.99       105.21         6.54         8.84 
TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 
      117.40        90.77        30.67        26.30        10.36         7.96 
TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 
       94.32        18.94        44.02        25.91        60.30        23.31 
TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 
       41.98         2.76         5.10        23.74         3.98        20.68 
TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP 
       21.40        19.13        16.96        15.48        14.17        14.24 
TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 
       12.59        15.12         4.96         5.65        12.20         8.65 
TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L 
        2.70        77.98         7.23         5.98        11.41        26.76 
TCGA-DU-A76O TCGA-DU-A7T8 TCGA-DU-A7TG TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 
        7.13       124.50        44.42        50.14        67.46        41.13 
TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 
       79.99        57.93       134.27        78.21        95.57       130.78 
TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 
       14.33         0.23         0.20        47.77        17.98        34.36 
TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 
       32.19        18.77        14.93        24.99        23.97        13.58 
TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 
       15.35        17.88        22.55        20.61        20.09        12.95 
TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 
       13.68        14.24        16.01        20.09        14.96        22.52 
TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY 
       15.52        38.27        10.72         5.26        18.71        23.70 
TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 
       14.76        17.82        16.41        15.02        16.44        10.59 
TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N 
       28.54        10.78        22.95        43.69         5.23         7.43 
TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7470 TCGA-HT-7471 
        5.72         0.13         0.10         6.67         8.81         0.13 
TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7478 
        0.03        16.54         3.75        17.42         6.54         6.38 
TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 
        7.10        75.19        59.18        60.03       154.19         4.01 
TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 
        5.03        29.85        23.18       107.93         4.57        17.29 
TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 
        3.16        22.06        45.99        56.09        57.60         0.23 
TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 
       14.27         0.16        16.24         0.76        44.68         6.05 
TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7691 TCGA-HT-7692 
       42.74         0.10        31.69        14.96         0.10         2.96 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 
       17.52         6.90        14.53        39.48        19.23        39.09 
TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 
        0.23        50.63         0.49        23.61        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 
        0.13         3.68         5.33         2.93         1.71        11.28 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 
       31.43         1.64        16.24         9.40        63.55         0.10 
TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 
       21.50        33.01        12.23         6.25         0.10         0.46 
TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 
        2.50         3.95         4.70        29.59         3.88        16.04 
TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RB 
        0.23        10.49         0.13        14.01         0.07         0.10 
TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 
        5.33         2.70        13.02         1.81        16.14         5.33 
TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 
        0.10        29.92        13.45         8.32        19.23        40.18 
TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 
       35.90         4.31        21.70        21.60        19.59        17.82 
TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-8125 TCGA-KT-A74X 
       20.35         7.89        20.81        20.71        42.77         5.23 
TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ 
        4.73         0.23         6.71         1.64         2.37         2.30 
TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-QH-A65R TCGA-QH-A65S 
        4.11         5.88         7.63         0.76         5.75         2.53 
TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV 
        4.83         7.79         4.11         4.18        14.83        14.53 
TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 
       12.23         2.20         3.16         0.59         6.31         3.91 
TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 
        4.73         1.91         0.23         5.03         3.48         0.07 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TS TCGA-S9-A6TU 
       88.83        94.03        32.65        59.38        62.17        69.07 
TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 
       18.77        37.84        34.49        31.33        21.63        16.37 
TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
       17.62        23.64        32.61         9.86        94.62        83.70 
TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH 
        5.85       106.39        62.37        72.59        80.12        32.45 
TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP 
       84.99        10.88        19.86        15.91         7.59        15.16 
TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ 
       14.07        14.27         7.92        19.63        12.59         4.21 
TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX 
        9.37         8.19         2.04         8.12         3.58         4.04 
TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 
       28.37        13.02       164.38        10.39        99.06        17.42 
TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 
       83.80        31.59         5.00        49.45        48.33        49.32 
TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H 
       34.78        48.39        15.09        50.76        34.36        24.26 
TCGA-TM-A84I TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R 
       19.36        40.83        16.50        29.92        18.90         9.44 
TCGA-TM-A84S TCGA-TM-A84T TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD 
        4.57        12.00        30.08        13.51         0.10         7.89 
TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A86M TCGA-VW-A7QS TCGA-W9-A837 
       26.79        10.95         7.04        23.21        45.07 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             0.10              0.03 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            75.16            211.17 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            18.10             15.52 
[1] "0.1 - 75.2 (18.1)"  "0.0 - 211.2 (15.5)"
[1] "hr=" "2.2"
D44V2, continuous
D44V3, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     6  15
  3P LOSS WILD-TYPE 184 225
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      6   15
  3P LOSS WILD-TYPE  184  225
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE               6               184
  MALE                15               225
[1] 2 2
[1] FALSE
D44V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  3P LOSS MUTATED            10                4                 7
  3P LOSS WILD-TYPE         149              103               157
D44V5, multiclass
                   clus
vv                  3P LOSS MUTATED 3P LOSS WILD-TYPE
  ASTROCYTOMA                    10               149
  OLIGOASTROCYTOMA                4               103
  OLIGODENDROGLIOMA               7               157
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V6, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     4  17
  3P LOSS WILD-TYPE  85 324
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      4   17
  3P LOSS WILD-TYPE   85  324
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  NO                4                85
  YES              17               324
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3P LOSS MUTATED                                  0     0
  3P LOSS WILD-TYPE                                1     6
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3P LOSS MUTATED                           0    21
  3P LOSS WILD-TYPE                        14   379
D44V7, multiclass
                                  clus
vv                                 3P LOSS MUTATED 3P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 6
  BLACK OR AFRICAN AMERICAN                      0                14
  WHITE                                         21               379
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V8, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     2  18
  3P LOSS WILD-TYPE  14 369
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      2   18
  3P LOSS WILD-TYPE   14  369
                        clus
vv                       3P LOSS MUTATED 3P LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                14
  NOT HISPANIC OR LATINO              18               369
[1] 2 2
[1] FALSE

Clustering(45) Variable = 3Q LOSS MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                 0   1
  3Q LOSS MUTATED    13  10
  3Q LOSS WILD-TYPE 339  65
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               23               404 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               10                65 
$`3Q LOSS MUTATED`
TCGA-CS-6666 TCGA-DB-5277 TCGA-DB-5281 TCGA-DU-6396 TCGA-DU-7007 TCGA-DU-7014 
        8.48        46.65        78.28        75.16        62.96       117.40 
TCGA-DU-7298 TCGA-DU-7300 TCGA-DU-8167 TCGA-DU-A5TU TCGA-DU-A76R TCGA-E1-5302 
       18.94        62.01        15.48         3.65        21.30        50.14 
TCGA-HT-7469 TCGA-HT-7472 TCGA-HT-7477 TCGA-HT-8111 TCGA-HT-8564 TCGA-IK-7675 
        7.82         0.03        24.26         0.23        15.72        19.00 
TCGA-P5-A5F6 TCGA-S9-A6TV TCGA-TM-A84B TCGA-TM-A84J TCGA-VM-A8C8 
        1.28        18.77        12.00        17.49        33.07 

$`3Q LOSS WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 
       23.84        17.95        12.43         7.56         8.02         7.40 
TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 
        6.61       122.73        81.96        75.25        47.93        72.92 
TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB 
       50.17        44.52        36.56        30.08        10.29        12.72 
TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH 
       27.62        27.02        18.84        18.38        72.95        12.59 
TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S 
       11.01        18.84        16.80         5.98        16.08        15.42 
TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L 
       27.81        14.73        13.64        10.92         7.40         6.44 
TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 
       10.29        30.74         3.81        19.96        31.82        30.31 
TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F 
       14.40         8.02        30.21        42.05        27.81        17.19 
TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV 
       17.19        54.25        10.22         6.58         3.45         6.21 
TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 
       18.02        14.56        17.46         6.74        13.38         8.45 
TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 
        6.81       182.33        18.94        17.49        15.16       211.17 
TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 
       52.11        22.42        49.02        46.06        65.75         1.22 
TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 
       87.45         7.04        11.64       133.74        19.89        16.83 
TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7008 
       94.52       114.08         7.96         7.73        11.47       156.23 
TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 
      138.28        14.99       105.21         6.54         8.84        90.77 
TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7299 
       30.67        26.30        10.36         7.96        94.32        44.02 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 
       25.91        60.30        23.31        41.98         2.76         5.10 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 
       23.74         3.98        20.68        21.40        19.13        16.96 
TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TW 
       14.17        14.24        12.59        15.12         4.96         5.65 
TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 
       12.20         8.65         2.70        77.98         7.23         5.98 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A7T8 TCGA-DU-A7TG TCGA-E1-5303 
       11.41        26.76         7.13       124.50        44.42        67.46 
TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 
       41.13        79.99        57.93       134.27        78.21        95.57 
TCGA-E1-5322 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 
      130.78        14.33         0.23         0.20        47.77        17.98 
TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 
       34.36        32.19        18.77        14.93        24.99        23.97 
TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 
       13.58        15.35        17.88        22.55        20.61        20.09 
TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 
       12.95        13.68        14.24        16.01        20.09        14.96 
TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX 
       22.52        15.52        38.27        10.72         5.26        18.71 
TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 
       23.70        14.76        17.82        16.41        15.02        16.44 
TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 
       10.59        28.54        10.78        22.95        43.69         5.23 
TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7470 
        7.43         5.72         0.13         0.10         6.67         8.81 
TCGA-HT-7471 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7478 
        0.13        16.54         3.75        17.42         6.54         6.38 
TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 
        7.10        75.19        59.18        60.03       154.19         4.01 
TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 
        5.03        29.85        23.18       107.93         4.57        17.29 
TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 
        3.16        22.06        45.99        56.09        57.60         0.23 
TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 
       14.27         0.16        16.24         0.76        44.68         6.05 
TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 
       42.74         0.10        31.69        14.96         0.10         0.10 
TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 
        2.96        17.52         6.90        14.53        39.48        19.23 
TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 
       39.09         0.23        50.63         0.49        23.61        37.15 
TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 
        0.33         0.13         3.68         5.33         2.93         1.71 
TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 
       11.28        31.43         1.64        16.24         9.40        63.55 
TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 
        0.10        21.50        33.01        12.23         6.25         0.10 
TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8113 TCGA-HT-8114 
        0.46         2.50         3.95         4.70        29.59         3.88 
TCGA-HT-8563 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 
       16.04         0.23        10.49         0.13        14.01         0.07 
TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 
       14.70         0.10         5.33         2.70        13.02         1.81 
TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 
       16.14         5.33         0.10        29.92        13.45         8.32 
TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 
       19.23        40.18        35.90         4.31        21.70        21.60 
TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM 
       19.59        17.82        20.35         7.89        20.81        20.71 
TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX 
       42.77         5.23         4.73         0.23         6.71         1.64 
TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 
        2.37         2.30         4.11         5.88         7.63         0.76 
TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS 
        5.75         2.53         4.83         7.79         4.11         4.18 
TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
       14.83        14.53        12.23         2.20         3.16         0.59 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC 
        6.31         3.91         4.73         1.91         0.23         5.03 
TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
        3.48         0.07        88.83        94.03        32.65        59.38 
TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ 
       62.17        69.07        37.84        34.49        31.33        21.63 
TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       16.37        17.62        23.64        32.61         9.86        94.62 
TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG 
       83.70         5.85       106.39        62.37        72.59        80.12 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO 
       32.45        84.99        10.88        19.86        15.91         7.59 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY 
       15.16        14.07        14.27         7.92        19.63        12.59 
TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW 
        4.21         9.37         8.19         2.04         8.12         3.58 
TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 
        4.04        28.37        13.02       164.38        10.39        99.06 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 
       17.42        83.80        31.59        18.71         5.00        49.45 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84C TCGA-TM-A84F 
       48.33        49.32        34.78        48.39        15.09        50.76 
TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O 
       34.36        24.26        19.36        40.83        16.50        29.92 
TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-VM-A8C9 TCGA-VM-A8CA 
       18.90         9.44         4.57        12.00        30.08        13.51 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M 
        0.10         7.89        26.79        10.95        27.06         7.04 
TCGA-VW-A7QS TCGA-W9-A837 
       23.21        45.07 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             0.03              0.07 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
           117.40            211.17 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
           18.940            15.385 
[1] "0.0 - 117.4 (18.9)" "0.1 - 211.2 (15.4)"
[1] "hr=" "2.2"
D45V2, continuous
D45V3, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     6  17
  3Q LOSS WILD-TYPE 184 223
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      6   17
  3Q LOSS WILD-TYPE  184  223
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE               6               184
  MALE                17               223
[1] 2 2
[1] FALSE
D45V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  3Q LOSS MUTATED             9                5                 9
  3Q LOSS WILD-TYPE         150              102               155
D45V5, multiclass
                   clus
vv                  3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  ASTROCYTOMA                     9               150
  OLIGOASTROCYTOMA                5               102
  OLIGODENDROGLIOMA               9               155
[1] 3 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
  3Q LOSS MUTATED     6  17
  3Q LOSS WILD-TYPE  83 324
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      6   17
  3Q LOSS WILD-TYPE   83  324
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  NO                6                83
  YES              17               324
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3Q LOSS MUTATED                                  0     0
  3Q LOSS WILD-TYPE                                1     6
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3Q LOSS MUTATED                           1    22
  3Q LOSS WILD-TYPE                        13   378
D45V7, multiclass
                                  clus
vv                                 3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 6
  BLACK OR AFRICAN AMERICAN                      1                13
  WHITE                                         22               378
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V8, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     2  20
  3Q LOSS WILD-TYPE  14 367
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      2   20
  3Q LOSS WILD-TYPE   14  367
                        clus
vv                       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                14
  NOT HISPANIC OR LATINO              20               367
[1] 2 2
[1] FALSE

Clustering(46) Variable = 4P LOSS MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                 0   1
  4P LOSS MUTATED    47  11
  4P LOSS WILD-TYPE 305  64
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               58               369 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               11                64 
$`4P LOSS MUTATED`
TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5277 TCGA-DB-5279 TCGA-DB-A4XA TCGA-DB-A4XH 
       75.25        47.93        46.65        44.52        10.29        12.59 
TCGA-DB-A64W TCGA-DB-A64X TCGA-DH-A669 TCGA-DH-A66G TCGA-DH-A7UT TCGA-DU-6399 
       13.64        10.92        30.21        17.19         6.58        65.75 
TCGA-DU-6400 TCGA-DU-6410 TCGA-DU-7010 TCGA-DU-7018 TCGA-DU-7294 TCGA-DU-8165 
        1.22         7.96        14.99        30.67        94.32        19.13 
TCGA-DU-8166 TCGA-DU-8168 TCGA-DU-A6S3 TCGA-DU-A6S8 TCGA-DU-A76R TCGA-DU-A7T8 
       16.96        14.17         2.70         5.98        21.30       124.50 
TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5311 TCGA-F6-A8O3 TCGA-FG-5962 
       50.14        67.46        41.13       134.27         0.23        47.77 
TCGA-FG-5964 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-A60J TCGA-FG-A6IZ TCGA-FG-A6J1 
       34.36        17.88        22.55        14.76        15.02        16.44 
TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7471 TCGA-HT-7475 TCGA-HT-7480 TCGA-HT-7677 
        0.10         6.67         0.13        17.42        75.19        16.24 
TCGA-HT-7688 TCGA-HT-7692 TCGA-HT-8105 TCGA-HT-A5R9 TCGA-HW-7487 TCGA-HW-7491 
       31.69         2.96         6.25         0.07        13.45        40.18 
TCGA-IK-8125 TCGA-P5-A5EV TCGA-S9-A6TW TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WL 
       42.77         0.23        37.84       106.39        62.37        10.88 
TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-TM-A7C5 TCGA-TM-A84T 
       12.59         4.21        49.32        12.00 

$`4P LOSS WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5276 TCGA-DB-5278 
        7.40         6.61       122.73        81.96        72.92        50.17 
TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD 
       36.56        78.28        30.08        12.72        27.62        27.02 
TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       18.84        18.38        72.95        11.01        18.84        16.80 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A75K 
        5.98        16.08        15.42        27.81        14.73         7.40 
TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 
        6.44        10.29        30.74         3.81        19.96        31.82 
TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F 
       30.31        14.40         8.02        42.05        27.81        17.19 
TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 
       54.25        10.22         3.45         6.21        18.02        14.56 
TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 
       17.46         6.74        13.38         8.45         6.81       182.33 
TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 
       18.94        17.49        15.16       211.17        52.11        22.42 
TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       49.02        75.16        46.06        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6542 
      133.74        19.89        16.83        94.52       114.08         7.73 
TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7011 TCGA-DU-7012 
       11.47        62.96       156.23       138.28       105.21         6.54 
TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 
        8.84       117.40        90.77        26.30        10.36         7.96 
TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 
       18.94        44.02        62.01        25.91        60.30        23.31 
TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 
       41.98         2.76         5.10        23.74         3.98        20.68 
TCGA-DU-8164 TCGA-DU-8167 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT 
       21.40        15.48        14.24        12.59        15.12         4.96 
TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S6 TCGA-DU-A6S7 
        3.65         5.65        12.20         8.65        77.98         7.23 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A7TG TCGA-E1-5305 TCGA-E1-5307 
       11.41        26.76         7.13        44.42        79.99        57.93 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 TCGA-F6-A8O4 TCGA-FG-5963 
       78.21        95.57       130.78        14.33         0.20        17.98 
TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 
       32.19        18.77        14.93        24.99        23.97        13.58 
TCGA-FG-7634 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 
       15.35        20.61        20.09        12.95        13.68        14.24 
TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT 
       16.01        20.09        14.96        22.52        15.52        38.27 
TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60K TCGA-FG-A60L 
       10.72         5.26        18.71        23.70        17.82        16.41 
TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 
       10.59        28.54        10.78        22.95        43.69         5.23 
TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7472 
        7.43         5.72         0.13         7.82         8.81         0.03 
TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 
       16.54         3.75         6.54        24.26         6.38         7.10 
TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 
       59.18        60.03       154.19         4.01         5.03        29.85 
TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 
       23.18       107.93         4.57        17.29         3.16        22.06 
TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 
       45.99        56.09        57.60         0.23        14.27         0.16 
TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7689 
        0.76        44.68         6.05        42.74         0.10        14.96 
TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 
        0.10         0.10        17.52         6.90        14.53        39.48 
TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 
       19.23        39.09         0.23        50.63         0.49        23.61 
TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 
       37.15         0.33         0.13         3.68         5.33         2.93 
TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 
        1.71        11.28        31.43         1.64        16.24         9.40 
TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8106 
       63.55         0.10        21.50        33.01        12.23         0.10 
TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 
        0.46         2.50         3.95         4.70         0.23        29.59 
TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
        3.88        16.04        15.72         0.23        10.49         0.13 
TCGA-HT-A5R7 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 
       14.01        14.70         0.10         5.33         2.70        13.02 
TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7489 
        1.81        16.14         5.33         0.10        29.92         8.32 
TCGA-HW-7490 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 
       19.23        35.90         4.31        21.70        21.60        19.59 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 
       17.82        20.35         7.89        20.81        20.71        19.00 
TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ 
        5.23         4.73         6.71         1.64         2.37         2.30 
TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-QH-A65R 
        4.11         5.88         7.63         0.76         1.28         5.75 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU 
        2.53         4.83         7.79         4.11         4.18        14.83 
TCGA-QH-A6CV TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
       14.53        12.23         2.20         3.16         0.59         6.31 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X 
        3.91         4.73         1.91         0.23         5.03         3.48 
TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TS 
        0.07        88.83        94.03        32.65        59.38        62.17 
TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 
       69.07        18.77        34.49        31.33        21.63        16.37 
TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
       17.62        23.64        32.61         9.86        94.62        83.70 
TCGA-S9-A6UA TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WM 
        5.85        72.59        80.12        32.45        84.99        19.86 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
       15.91         7.59        15.16        14.07        14.27         7.92 
TCGA-S9-A7IX TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW 
       19.63         9.37         8.19         2.04         8.12         3.58 
TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 
        4.04        28.37        13.02       164.38        10.39        99.06 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 
       17.42        83.80        31.59        18.71         5.00        49.45 
TCGA-TM-A7C4 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F 
       48.33        34.78        48.39        12.00        15.09        50.76 
TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M 
       34.36        24.26        19.36        17.49        40.83        16.50 
TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-VM-A8C8 TCGA-VM-A8C9 
       29.92        18.90         9.44         4.57        33.07        30.08 
TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 
       13.51         0.10         7.89        26.79        10.95        27.06 
TCGA-VV-A86M TCGA-VW-A7QS TCGA-W9-A837 
        7.04        23.21        45.07 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             0.07              0.03 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
           134.27            211.17 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
           17.075            15.480 
[1] "0.1 - 134.3 (17.1)" "0.0 - 211.2 (15.5)"
[1] "hr=" "1.1"
D46V2, continuous
D46V3, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    19  39
  4P LOSS WILD-TYPE 171 201
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     19   39
  4P LOSS WILD-TYPE  171  201
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE              19               171
  MALE                39               201
[1] 2 2
[1] FALSE
D46V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  4P LOSS MUTATED            11               14                33
  4P LOSS WILD-TYPE         148               93               131
D46V5, multiclass
                   clus
vv                  4P LOSS MUTATED 4P LOSS WILD-TYPE
  ASTROCYTOMA                    11               148
  OLIGOASTROCYTOMA               14                93
  OLIGODENDROGLIOMA              33               131
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V6, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    16  42
  4P LOSS WILD-TYPE  73 299
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     16   42
  4P LOSS WILD-TYPE   73  299
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  NO               16                73
  YES              42               299
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4P LOSS MUTATED                                  0     1
  4P LOSS WILD-TYPE                                1     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4P LOSS MUTATED                           0    56
  4P LOSS WILD-TYPE                        14   344
D46V7, multiclass
                                  clus
vv                                 4P LOSS MUTATED 4P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 5
  BLACK OR AFRICAN AMERICAN                      0                14
  WHITE                                         56               344
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V8, binary
                   cls
clus                  0   1
  4P LOSS MUTATED     0  56
  4P LOSS WILD-TYPE  16 331
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      0   56
  4P LOSS WILD-TYPE   16  331
                        clus
vv                       4P LOSS MUTATED 4P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                16
  NOT HISPANIC OR LATINO              56               331
[1] 2 2
[1] FALSE

Clustering(47) Variable = 4Q LOSS MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                 0   1
  4Q LOSS MUTATED    60  14
  4Q LOSS WILD-TYPE 292  61
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               74               353 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               14                61 
$`4Q LOSS MUTATED`
TCGA-CS-4943 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5277 TCGA-DB-5279 TCGA-DB-A4XA 
       18.15        75.25        47.93        46.65        44.52        10.29 
TCGA-DB-A4XE TCGA-DB-A4XH TCGA-DB-A64W TCGA-DB-A75O TCGA-DH-A669 TCGA-DH-A66B 
       18.84        12.59        13.64        30.74        30.21        42.05 
TCGA-DH-A66G TCGA-DU-5853 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6410 TCGA-DU-7008 
       17.19        13.38        65.75         1.22         7.96       156.23 
TCGA-DU-7010 TCGA-DU-7018 TCGA-DU-7294 TCGA-DU-7299 TCGA-DU-7302 TCGA-DU-7309 
       14.99        30.67        94.32        44.02        60.30         2.76 
TCGA-DU-8165 TCGA-DU-8168 TCGA-DU-A5TS TCGA-DU-A6S3 TCGA-DU-A6S8 TCGA-DU-A76R 
       19.13        14.17        15.12         2.70         5.98        21.30 
TCGA-DU-A7T8 TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5311 TCGA-EZ-7264 
      124.50        50.14        67.46        41.13       134.27        14.33 
TCGA-F6-A8O3 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-7636 TCGA-FG-7638 
        0.23        47.77        17.98        34.36        17.88        22.55 
TCGA-FG-A60J TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7471 
       14.76        15.02        16.44         0.10         6.67         0.13 
TCGA-HT-7480 TCGA-HT-7677 TCGA-HT-7688 TCGA-HT-7692 TCGA-HT-7856 TCGA-HT-8105 
       75.19        16.24        31.69         2.96        39.09         6.25 
TCGA-HT-A5R9 TCGA-HW-7487 TCGA-HW-7491 TCGA-HW-7493 TCGA-IK-8125 TCGA-P5-A5EV 
        0.07        13.45        40.18        35.90        42.77         0.23 
TCGA-QH-A6X4 TCGA-QH-A6XA TCGA-S9-A6TW TCGA-S9-A6WD TCGA-S9-A6WL TCGA-S9-A6WP 
        6.31         0.23        37.84        62.37        10.88        15.16 
TCGA-S9-A7IS TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-TM-A7C4 TCGA-TM-A7C5 
        7.92        12.59         4.21         9.37        48.33        49.32 
TCGA-TM-A84R TCGA-TM-A84T 
        9.44        12.00 

$`4Q LOSS WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5393 
        4.70         7.69        43.89        10.62        64.64        40.18 
TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
        0.10        21.01         9.96         6.38        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 
       17.95        12.43         8.48         7.56         8.02         7.40 
TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5276 TCGA-DB-5278 TCGA-DB-5280 
        6.61       122.73        81.96        72.92        50.17        36.56 
TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XF 
       78.28        30.08        12.72        27.62        27.02        18.38 
TCGA-DB-A4XG TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R 
       72.95        11.01        18.84        16.80         5.98        16.08 
TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L 
       15.42        27.81        14.73        10.92         7.40         6.44 
TCGA-DB-A75M TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 
       10.29         3.81        19.96        31.82        30.31        14.40 
TCGA-DH-5144 TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT 
        8.02        27.81        17.19        54.25        10.22         6.58 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
        3.45         6.21        18.02        14.56        17.46         6.74 
TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 
        8.45         6.81       182.33        18.94        17.49        15.16 
TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 
      211.17        52.11        22.42        49.02        75.16        46.06 
TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 
       87.45         7.04        11.64       133.74        19.89        16.83 
TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7009 
       94.52       114.08         7.73        11.47        62.96       138.28 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7019 
      105.21         6.54         8.84       117.40        90.77        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7298 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7304 
       10.36         7.96        18.94        62.01        25.91        23.31 
TCGA-DU-7306 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 
       41.98         5.10        23.74         3.98        20.68        21.40 
TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TT TCGA-DU-A5TU 
       16.96        15.48        14.24        12.59         4.96         3.65 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A76K 
        5.65        12.20         8.65        77.98         7.23        11.41 
TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A7TG TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5318 
       26.76         7.13        44.42        79.99        57.93        78.21 
TCGA-E1-5319 TCGA-E1-5322 TCGA-F6-A8O4 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 
       95.57       130.78         0.20        32.19        18.77        14.93 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7641 TCGA-FG-7643 
       24.99        23.97        13.58        15.35        20.61        20.09 
TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 
       12.95        13.68        14.24        16.01        20.09        14.96 
TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX 
       22.52        15.52        38.27        10.72         5.26        18.71 
TCGA-FG-A4MY TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z 
       23.70        17.82        16.41        10.59        28.54        10.78 
TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 
       22.95        43.69         5.23         7.43         5.72         0.13 
TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 
        7.82         8.81         0.03        16.54         3.75        17.42 
TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7481 TCGA-HT-7482 
        6.54        24.26         6.38         7.10        59.18        60.03 
TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 
      154.19         4.01         5.03        29.85        23.18       107.93 
TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 
        4.57        17.29         3.16        22.06        45.99        56.09 
TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7680 TCGA-HT-7681 
       57.60         0.23        14.27         0.16         0.76        44.68 
TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 
        6.05        42.74         0.10        14.96         0.10         0.10 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7857 
       17.52         6.90        14.53        39.48        19.23         0.23 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
       50.63         0.49        23.61        37.15         0.33         0.13 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 
        3.68         5.33         2.93         1.71        11.28        31.43 
TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 
        1.64        16.24         9.40        63.55         0.10        21.50 
TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 
       33.01        12.23         0.10         0.46         2.50         3.95 
TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 
        4.70         0.23        29.59         3.88        16.04        15.72 
TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5RA TCGA-HT-A5RB 
        0.23        10.49         0.13        14.01        14.70         0.10 
TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 
        5.33         2.70        13.02         1.81        16.14         5.33 
TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7495 TCGA-HW-8319 
        0.10        29.92         8.32        19.23         4.31        21.70 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
       21.60        19.59        17.82        20.35         7.89        20.81 
TCGA-HW-A5KM TCGA-IK-7675 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EW TCGA-P5-A5EX 
       20.71        19.00         5.23         4.73         6.71         1.64 
TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 
        2.37         2.30         4.11         5.88         7.63         0.76 
TCGA-P5-A5F6 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z 
        1.28         5.75         2.53         4.83         7.79         4.11 
TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ 
        4.18        14.83        14.53        12.23         2.20         3.16 
TCGA-QH-A6X3 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XC TCGA-QH-A86X 
        0.59         3.91         4.73         1.91         5.03         3.48 
TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TS 
        0.07        88.83        94.03        32.65        59.38        62.17 
TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 
       69.07        18.77        34.49        31.33        21.63        16.37 
TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
       17.62        23.64        32.61         9.86        94.62        83.70 
TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI 
        5.85       106.39        72.59        80.12        32.45        84.99 
TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IX 
       19.86        15.91         7.59        14.07        14.27        19.63 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY 
        8.19         2.04         8.12         3.58         4.04        28.37 
TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 
       13.02       164.38        10.39        99.06        17.42        83.80 
TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7CA TCGA-TM-A7CF 
       31.59        18.71         5.00        49.45        34.78        48.39 
TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I 
       12.00        15.09        50.76        34.36        24.26        19.36 
TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84S 
       17.49        40.83        16.50        29.92        18.90         4.57 
TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE 
       33.07        30.08        13.51         0.10         7.89        26.79 
TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-W9-A837 
       10.95        27.06         7.04        23.21        45.07 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             0.07              0.03 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           156.23            211.17 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           17.535            15.480 
[1] "0.1 - 156.2 (17.5)" "0.0 - 211.2 (15.5)"
[1] "hr=" "1.1"
D47V2, continuous
D47V3, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED    27  47
  4Q LOSS WILD-TYPE 163 193
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     27   47
  4Q LOSS WILD-TYPE  163  193
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE              27               163
  MALE                47               193
[1] 2 2
[1] FALSE
D47V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  4Q LOSS MUTATED            17               17                40
  4Q LOSS WILD-TYPE         142               90               124
D47V5, multiclass
                   clus
vv                  4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  ASTROCYTOMA                    17               142
  OLIGOASTROCYTOMA               17                90
  OLIGODENDROGLIOMA              40               124
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V6, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED    19  55
  4Q LOSS WILD-TYPE  70 286
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     19   55
  4Q LOSS WILD-TYPE   70  286
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  NO               19                70
  YES              55               286
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4Q LOSS MUTATED                                  0     1
  4Q LOSS WILD-TYPE                                1     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4Q LOSS MUTATED                           1    71
  4Q LOSS WILD-TYPE                        13   329
D47V7, multiclass
                                  clus
vv                                 4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 5
  BLACK OR AFRICAN AMERICAN                      1                13
  WHITE                                         71               329
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V8, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED     0  71
  4Q LOSS WILD-TYPE  16 316
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      0   71
  4Q LOSS WILD-TYPE   16  316
                        clus
vv                       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                16
  NOT HISPANIC OR LATINO              71               316
[1] 2 2
[1] FALSE

Clustering(48) Variable = 5P LOSS MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                 0   1
  5P LOSS MUTATED    22   6
  5P LOSS WILD-TYPE 330  69
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               28               399 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                6                69 
$`5P LOSS MUTATED`
TCGA-CS-4943 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5281 TCGA-DB-A4XE 
       18.15        47.93        72.92        46.65        78.28        18.84 
TCGA-DB-A4XH TCGA-DB-A64X TCGA-DH-5140 TCGA-DH-A66D TCGA-DH-A66G TCGA-DU-6399 
       12.59        10.92        19.96        27.81        17.19        65.75 
TCGA-DU-7007 TCGA-DU-7306 TCGA-DU-8165 TCGA-E1-5302 TCGA-FG-5965 TCGA-FG-6689 
       62.96        41.98        19.13        50.14        32.19        14.93 
TCGA-FG-A6J3 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7688 TCGA-HT-7884 TCGA-HT-8106 
       10.59         3.75        17.42        31.69        11.28         0.10 
TCGA-HT-A614 TCGA-S9-A6WM TCGA-S9-A7R7 TCGA-TM-A84I 
        2.70        19.86        83.80        19.36 

$`5P LOSS WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5393 
        4.70         7.69        43.89        10.62        64.64        40.18 
TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
        0.10        21.01         9.96         6.38        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 
       17.95        12.43         8.48         7.56         8.02         7.40 
TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5278 TCGA-DB-5279 
        6.61       122.73        81.96        75.25        50.17        44.52 
TCGA-DB-5280 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD 
       36.56        30.08        10.29        12.72        27.62        27.02 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q 
       18.38        72.95        11.01        18.84        16.80         5.98 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A75K 
       16.08        15.42        27.81        14.73        13.64         7.40 
TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5141 TCGA-DH-5142 
        6.44        10.29        30.74         3.81        31.82        30.31 
TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66F TCGA-DH-A7UR 
       14.40         8.02        30.21        42.05        17.19        54.25 
TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 
       10.22         6.58         3.45         6.21        18.02        14.56 
TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 
       17.46         6.74        13.38         8.45         6.81       182.33 
TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 
       18.94        17.49        15.16       211.17        52.11        22.42 
TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 
       49.02        75.16        46.06         1.22        87.45         7.04 
TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 
       11.64       133.74        19.89        16.83        94.52       114.08 
TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 
        7.96         7.73        11.47       156.23       138.28        14.99 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 
      105.21         6.54         8.84       117.40        90.77        30.67 
TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 
       26.30        10.36         7.96        94.32        18.94        44.02 
TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7309 TCGA-DU-8158 
       62.01        25.91        60.30        23.31         2.76         5.10 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-8167 
       23.74         3.98        20.68        21.40        16.96        15.48 
TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU 
       14.17        14.24        12.59        15.12         4.96         3.65 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
        5.65        12.20         8.65         2.70        77.98         7.23 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 
        5.98        11.41        26.76         7.13        21.30       124.50 
TCGA-DU-A7TG TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 
       44.42        67.46        41.13        79.99        57.93       134.27 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 
       78.21        95.57       130.78        14.33         0.23         0.20 
TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-6688 TCGA-FG-6690 TCGA-FG-6691 
       47.77        17.98        34.36        18.77        24.99        23.97 
TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 
       13.58        15.35        17.88        22.55        20.61        20.09 
TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 
       12.95        13.68        14.24        16.01        20.09        14.96 
TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX 
       22.52        15.52        38.27        10.72         5.26        18.71 
TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 
       23.70        14.76        17.82        16.41        15.02        16.44 
TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N 
       28.54        10.78        22.95        43.69         5.23         7.43 
TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 
        5.72         0.13         0.10         6.67         7.82         8.81 
TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 
        0.13         0.03        16.54         6.54        24.26         6.38 
TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 
        7.10        75.19        59.18        60.03       154.19         4.01 
TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 
        5.03        29.85        23.18       107.93         4.57        17.29 
TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 
        3.16        22.06        45.99        56.09        57.60         0.23 
TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 
       14.27         0.16        16.24         0.76        44.68         6.05 
TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 
       42.74         0.10        14.96         0.10         0.10         2.96 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 
       17.52         6.90        14.53        39.48        19.23        39.09 
TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 
        0.23        50.63         0.49        23.61        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7902 
        0.13         3.68         5.33         2.93         1.71        31.43 
TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 
        1.64        16.24         9.40        63.55         0.10        21.50 
TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 
       33.01        12.23         6.25         0.46         2.50         3.95 
TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 
        4.70         0.23        29.59         3.88        16.04        15.72 
TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA 
        0.23        10.49         0.13        14.01         0.07        14.70 
TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 
        0.10         5.33        13.02         1.81        16.14         5.33 
TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 
        0.10        29.92        13.45         8.32        19.23        40.18 
TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 
       35.90         4.31        21.70        21.60        19.59        17.82 
TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 
       20.35         7.89        20.81        20.71        19.00        42.77 
TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY 
        5.23         4.73         0.23         6.71         1.64         2.37 
TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 
        2.30         4.11         5.88         7.63         0.76         1.28 
TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS 
        5.75         2.53         4.83         7.79         4.11         4.18 
TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
       14.83        14.53        12.23         2.20         3.16         0.59 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC 
        6.31         3.91         4.73         1.91         0.23         5.03 
TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
        3.48         0.07        88.83        94.03        32.65        59.38 
TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY 
       62.17        69.07        18.77        37.84        34.49        31.33 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       21.63        16.37        17.62        23.64        32.61         9.86 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE 
       94.62        83.70         5.85       106.39        62.37        72.59 
TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WO 
       80.12        32.45        84.99        10.88        15.91         7.59 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY 
       15.16        14.07        14.27         7.92        19.63        12.59 
TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW 
        4.21         9.37         8.19         2.04         8.12         3.58 
TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 
        4.04        28.37        13.02       164.38        10.39        99.06 
TCGA-S9-A7R4 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 
       17.42        31.59        18.71         5.00        49.45        48.33 
TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F 
       49.32        34.78        48.39        12.00        15.09        50.76 
TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O 
       34.36        24.26        17.49        40.83        16.50        29.92 
TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-VM-A8C8 TCGA-VM-A8C9 
       18.90         9.44         4.57        12.00        33.07        30.08 
TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 
       13.51         0.10         7.89        26.79        10.95        27.06 
TCGA-VV-A86M TCGA-VW-A7QS TCGA-W9-A837 
        7.04        23.21        45.07 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             0.10              0.03 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            83.80            211.17 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            19.61             15.16 
[1] "0.1 - 83.8 (19.6)"  "0.0 - 211.2 (15.2)"
[1] "hr=" "1.1"
D48V2, continuous
D48V3, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    11  17
  5P LOSS WILD-TYPE 179 223
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     11   17
  5P LOSS WILD-TYPE  179  223
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE              11               179
  MALE                17               223
[1] 2 2
[1] FALSE
D48V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  5P LOSS MUTATED            13               11                 4
  5P LOSS WILD-TYPE         146               96               160
D48V5, multiclass
                   clus
vv                  5P LOSS MUTATED 5P LOSS WILD-TYPE
  ASTROCYTOMA                    13               146
  OLIGOASTROCYTOMA               11                96
  OLIGODENDROGLIOMA               4               160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V6, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    12  16
  5P LOSS WILD-TYPE  77 325
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     12   16
  5P LOSS WILD-TYPE   77  325
     clus
vv    5P LOSS MUTATED 5P LOSS WILD-TYPE
  NO               12                77
  YES              16               325
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5P LOSS MUTATED                                  0     0
  5P LOSS WILD-TYPE                                1     6
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5P LOSS MUTATED                           0    28
  5P LOSS WILD-TYPE                        14   372
D48V7, multiclass
                                  clus
vv                                 5P LOSS MUTATED 5P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 6
  BLACK OR AFRICAN AMERICAN                      0                14
  WHITE                                         28               372
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V8, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     0  27
  5P LOSS WILD-TYPE  16 360
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      0   27
  5P LOSS WILD-TYPE   16  360
                        clus
vv                       5P LOSS MUTATED 5P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                16
  NOT HISPANIC OR LATINO              27               360
[1] 2 2
[1] FALSE

Clustering(49) Variable = 5Q LOSS MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                 0   1
  5Q LOSS MUTATED    17  11
  5Q LOSS WILD-TYPE 335  64
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               28               399 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               11                64 
$`5Q LOSS MUTATED`
TCGA-CS-6665 TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5281 TCGA-DB-A4XH TCGA-DB-A64X 
       12.43        72.92        46.65        78.28        12.59        10.92 
TCGA-DH-5140 TCGA-DH-A66D TCGA-DH-A66G TCGA-DU-6399 TCGA-DU-6401 TCGA-DU-6408 
       19.96        27.81        17.19        65.75        87.45       114.08 
TCGA-DU-7007 TCGA-DU-7010 TCGA-DU-8165 TCGA-E1-5302 TCGA-E1-5304 TCGA-FG-A6J3 
       62.96        14.99        19.13        50.14        41.13        10.59 
TCGA-HT-7477 TCGA-HT-7879 TCGA-HT-7884 TCGA-HT-8106 TCGA-HT-A614 TCGA-HT-A618 
       24.26         3.68        11.28         0.10         2.70         5.33 
TCGA-IK-7675 TCGA-S9-A6TS TCGA-S9-A6WM TCGA-TM-A84I 
       19.00        62.17        19.86        19.36 

$`5Q LOSS WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 
       23.84        17.95         8.48         7.56         8.02         7.40 
TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5278 
        6.61       122.73        81.96        75.25        47.93        50.17 
TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC 
       44.52        36.56        30.08        10.29        12.72        27.62 
TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A64L TCGA-DB-A64O 
       27.02        18.84        18.38        72.95        11.01        18.84 
TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V 
       16.80         5.98        16.08        15.42        27.81        14.73 
TCGA-DB-A64W TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       13.64         7.40         6.44        10.29        30.74         3.81 
TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B 
       31.82        30.31        14.40         8.02        30.21        42.05 
TCGA-DH-A66F TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV 
       17.19        54.25        10.22         6.58         3.45         6.21 
TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 
       18.02        14.56        17.46         6.74        13.38         8.45 
TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 
        6.81       182.33        18.94        17.49        15.16       211.17 
TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6400 
       52.11        22.42        49.02        75.16        46.06         1.22 
TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 
        7.04        11.64       133.74        19.89        16.83        94.52 
TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7011 
        7.96         7.73        11.47       156.23       138.28       105.21 
TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 
        6.54         8.84       117.40        90.77        30.67        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 
       10.36         7.96        94.32        18.94        44.02        62.01 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 
       25.91        60.30        23.31        41.98         2.76         5.10 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-8167 
       23.74         3.98        20.68        21.40        16.96        15.48 
TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU 
       14.17        14.24        12.59        15.12         4.96         3.65 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
        5.65        12.20         8.65         2.70        77.98         7.23 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 
        5.98        11.41        26.76         7.13        21.30       124.50 
TCGA-DU-A7TG TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 
       44.42        67.46        79.99        57.93       134.27        78.21 
TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 
       95.57       130.78        14.33         0.23         0.20        47.77 
TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 
       17.98        34.36        32.19        18.77        14.93        24.99 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 
       23.97        13.58        15.35        17.88        22.55        20.61 
TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 
       20.09        12.95        13.68        14.24        16.01        20.09 
TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW 
       14.96        22.52        15.52        38.27        10.72         5.26 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ 
       18.71        23.70        14.76        17.82        16.41        15.02 
TCGA-FG-A6J1 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 
       16.44        28.54        10.78        22.95        43.69         5.23 
TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 
        7.43         5.72         0.13         0.10         6.67         7.82 
TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 
        8.81         0.13         0.03        16.54         3.75        17.42 
TCGA-HT-7476 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 
        6.54         6.38         7.10        75.19        59.18        60.03 
TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 
      154.19         4.01         5.03        29.85        23.18       107.93 
TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 
        4.57        17.29         3.16        22.06        45.99        56.09 
TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 
       57.60         0.23        14.27         0.16        16.24         0.76 
TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 
       44.68         6.05        42.74         0.10        31.69        14.96 
TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 
        0.10         0.10         2.96        17.52         6.90        14.53 
TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 
       39.48        19.23        39.09         0.23        50.63         0.49 
TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7880 TCGA-HT-7881 
       23.61        37.15         0.33         0.13         5.33         2.93 
TCGA-HT-7882 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 
        1.71        31.43         1.64        16.24         9.40        63.55 
TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8107 
        0.10        21.50        33.01        12.23         6.25         0.46 
TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 
        2.50         3.95         4.70         0.23        29.59         3.88 
TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 
       16.04        15.72         0.23        10.49         0.13        14.01 
TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A615 TCGA-HT-A616 
        0.07        14.70         0.10         5.33        13.02         1.81 
TCGA-HT-A617 TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 
       16.14         0.10        29.92        13.45         8.32        19.23 
TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 
       40.18        35.90         4.31        21.70        21.60        19.59 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-8125 
       17.82        20.35         7.89        20.81        20.71        42.77 
TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY 
        5.23         4.73         0.23         6.71         1.64         2.37 
TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 
        2.30         4.11         5.88         7.63         0.76         1.28 
TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS 
        5.75         2.53         4.83         7.79         4.11         4.18 
TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
       14.83        14.53        12.23         2.20         3.16         0.59 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC 
        6.31         3.91         4.73         1.91         0.23         5.03 
TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
        3.48         0.07        88.83        94.03        32.65        59.38 
TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ 
       69.07        18.77        37.84        34.49        31.33        21.63 
TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       16.37        17.62        23.64        32.61         9.86        94.62 
TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG 
       83.70         5.85       106.39        62.37        72.59        80.12 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP 
       32.45        84.99        10.88        15.91         7.59        15.16 
TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ 
       14.07        14.27         7.92        19.63        12.59         4.21 
TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX 
        9.37         8.19         2.04         8.12         3.58         4.04 
TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 
       28.37        13.02       164.38        10.39        99.06        17.42 
TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 
       83.80        31.59        18.71         5.00        49.45        48.33 
TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F 
       49.32        34.78        48.39        12.00        15.09        50.76 
TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O 
       34.36        24.26        17.49        40.83        16.50        29.92 
TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-VM-A8C8 TCGA-VM-A8C9 
       18.90         9.44         4.57        12.00        33.07        30.08 
TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 
       13.51         0.10         7.89        26.79        10.95        27.06 
TCGA-VV-A86M TCGA-VW-A7QS TCGA-W9-A837 
        7.04        23.21        45.07 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             0.10              0.03 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
           114.08            211.17 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            19.61             15.42 
[1] "0.1 - 114.1 (19.6)" "0.0 - 211.2 (15.4)"
[1] "hr=" "1.9"
D49V2, continuous
D49V3, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    15  13
  5Q LOSS WILD-TYPE 175 227
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     15   13
  5Q LOSS WILD-TYPE  175  227
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE              15               175
  MALE                13               227
[1] 2 2
[1] FALSE
D49V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  5Q LOSS MUTATED            16                6                 6
  5Q LOSS WILD-TYPE         143              101               158
D49V5, multiclass
                   clus
vv                  5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  ASTROCYTOMA                    16               143
  OLIGOASTROCYTOMA                6               101
  OLIGODENDROGLIOMA               6               158
[1] 3 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
  5Q LOSS MUTATED    11  17
  5Q LOSS WILD-TYPE  78 324
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     11   17
  5Q LOSS WILD-TYPE   78  324
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  NO               11                78
  YES              17               324
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5Q LOSS MUTATED                                  0     0
  5Q LOSS WILD-TYPE                                1     6
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5Q LOSS MUTATED                           0    28
  5Q LOSS WILD-TYPE                        14   372
D49V7, multiclass
                                  clus
vv                                 5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 6
  BLACK OR AFRICAN AMERICAN                      0                14
  WHITE                                         28               372
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V8, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED     1  27
  5Q LOSS WILD-TYPE  15 360
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      1   27
  5Q LOSS WILD-TYPE   15  360
                        clus
vv                       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                15
  NOT HISPANIC OR LATINO              27               360
[1] 2 2
[1] FALSE

Clustering(50) Variable = 6P LOSS MUTATION ANALYSIS
D50V1, survival
                   sevent
clus2                 0   1
  6P LOSS MUTATED    16   9
  6P LOSS WILD-TYPE 336  66
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               25               402 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                9                66 
$`6P LOSS MUTATED`
TCGA-CS-5397 TCGA-CS-6666 TCGA-DB-5277 TCGA-DB-A4XF TCGA-DB-A4XH TCGA-DB-A64O 
        6.38         8.48        46.65        18.38        12.59        18.84 
TCGA-DH-A669 TCGA-DU-6400 TCGA-DU-8158 TCGA-DU-8161 TCGA-FG-5963 TCGA-FG-8191 
       30.21         1.22         5.10        23.74        17.98        15.52 
TCGA-HT-7692 TCGA-HT-7855 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A617 TCGA-P5-A5F4 
        2.96        19.23        15.72         0.23        16.14         0.76 
TCGA-P5-A5F6 TCGA-QH-A6CS TCGA-QH-A6CX TCGA-S9-A6TZ TCGA-TM-A7CF TCGA-VM-A8C8 
        1.28         4.18        12.23        21.63        48.39        33.07 
TCGA-VM-A8CD 
        7.89 

$`6P LOSS WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-6186 TCGA-CS-6188 
       40.18         0.10        21.01         9.96        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 
       17.95        12.43         7.56         8.02         7.40         6.61 
TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5278 
      122.73        81.96        75.25        47.93        72.92        50.17 
TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB 
       44.52        36.56        78.28        30.08        10.29        12.72 
TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XG TCGA-DB-A64L TCGA-DB-A64P 
       27.62        27.02        18.84        72.95        11.01        16.80 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        16.08        15.42        27.81        14.73        13.64 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       10.92         7.40         6.44        10.29        30.74         3.81 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A66B 
       19.96        31.82        30.31        14.40         8.02        42.05 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT 
       27.81        17.19        17.19        54.25        10.22         6.58 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
        3.45         6.21        18.02        14.56        17.46         6.74 
TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 
       13.38         8.45         6.81       182.33        18.94        17.49 
TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       15.16       211.17        52.11        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 
       46.06        65.75        87.45         7.04        11.64       133.74 
TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 
       19.89        16.83        94.52       114.08         7.96         7.73 
TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 
       11.47        62.96       156.23       138.28        14.99       105.21 
TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 
        6.54         8.84       117.40        90.77        30.67        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 
       10.36         7.96        94.32        18.94        44.02        62.01 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8162 
       25.91        60.30        23.31        41.98         2.76         3.98 
TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 
       20.68        21.40        19.13        16.96        15.48        14.17 
TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW 
       14.24        12.59        15.12         4.96         3.65         5.65 
TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 
       12.20         8.65         2.70        77.98         7.23         5.98 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 TCGA-DU-A7TG 
       11.41        26.76         7.13        21.30       124.50        44.42 
TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 
       50.14        67.46        41.13        79.99        57.93       134.27 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 
       78.21        95.57       130.78        14.33         0.23         0.20 
TCGA-FG-5962 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 
       47.77        34.36        32.19        18.77        14.93        24.99 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 
       23.97        13.58        15.35        17.88        22.55        20.61 
TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 
       20.09        12.95        13.68        14.24        16.01        20.09 
TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX 
       14.96        22.52        38.27        10.72         5.26        18.71 
TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 
       23.70        14.76        17.82        16.41        15.02        16.44 
TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 
       10.59        28.54        10.78        22.95        43.69         5.23 
TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 
        7.43         5.72         0.13         0.10         6.67         7.82 
TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 
        8.81         0.13         0.03        16.54         3.75        17.42 
TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 
        6.54        24.26         6.38         7.10        75.19        59.18 
TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 
       60.03       154.19         4.01         5.03        29.85        23.18 
TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 
      107.93         4.57        17.29         3.16        22.06        45.99 
TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 
       56.09        57.60         0.23        14.27         0.16        16.24 
TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 
        0.76        44.68         6.05        42.74         0.10        31.69 
TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 
       14.96         0.10         0.10        17.52         6.90        14.53 
TCGA-HT-7854 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 
       39.48        39.09         0.23        50.63         0.49        23.61 
TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 
       37.15         0.33         0.13         3.68         5.33         2.93 
TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 
        1.71        11.28        31.43         1.64        16.24         9.40 
TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 
       63.55         0.10        21.50        33.01        12.23         6.25 
TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 
        0.10         0.46         2.50         3.95         4.70         0.23 
TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 
       29.59         3.88        16.04        10.49         0.13        14.01 
TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 
        0.07        14.70         0.10         5.33         2.70        13.02 
TCGA-HT-A616 TCGA-HT-A618 TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 
        1.81         5.33         0.10        29.92        13.45         8.32 
TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 
       19.23        40.18        35.90         4.31        21.70        21.60 
TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM 
       19.59        17.82        20.35         7.89        20.81        20.71 
TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW 
       19.00        42.77         5.23         4.73         0.23         6.71 
TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 
        1.64         2.37         2.30         4.11         5.88         7.63 
TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CU 
        5.75         2.53         4.83         7.79         4.11        14.83 
TCGA-QH-A6CV TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 
       14.53         2.20         3.16         0.59         6.31         3.91 
TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 
        4.73         1.91         0.23         5.03         3.48         0.07 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TS TCGA-S9-A6TU 
       88.83        94.03        32.65        59.38        62.17        69.07 
TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6U0 TCGA-S9-A6U1 
       18.77        37.84        34.49        31.33        16.37        17.62 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA 
       23.64        32.61         9.86        94.62        83.70         5.85 
TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI 
      106.39        62.37        72.59        80.12        32.45        84.99 
TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ 
       10.88        19.86        15.91         7.59        15.16        14.07 
TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 
       14.27         7.92        19.63        12.59         4.21         9.37 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY 
        8.19         2.04         8.12         3.58         4.04        28.37 
TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 
       13.02       164.38        10.39        99.06        17.42        83.80 
TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 
       31.59        18.71         5.00        49.45        48.33        49.32 
TCGA-TM-A7CA TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H 
       34.78        12.00        15.09        50.76        34.36        24.26 
TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q 
       19.36        17.49        40.83        16.50        29.92        18.90 
TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB 
        9.44         4.57        12.00        30.08        13.51         0.10 
TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-W9-A837 
       26.79        10.95        27.06         7.04        23.21        45.07 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             0.23              0.03 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            48.39            211.17 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
           15.520            16.025 
[1] "0.2 - 48.4 (15.5)"  "0.0 - 211.2 (16.0)"
[1] "hr=" "4.4"
D50V2, continuous
D50V3, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    11  14
  6P LOSS WILD-TYPE 179 226
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     11   14
  6P LOSS WILD-TYPE  179  226
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE              11               179
  MALE                14               226
[1] 2 2
[1] FALSE
D50V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  6P LOSS MUTATED            14                4                 7
  6P LOSS WILD-TYPE         145              103               157
D50V5, multiclass
                   clus
vv                  6P LOSS MUTATED 6P LOSS WILD-TYPE
  ASTROCYTOMA                    14               145
  OLIGOASTROCYTOMA                4               103
  OLIGODENDROGLIOMA               7               157
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V6, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     5  20
  6P LOSS WILD-TYPE  84 321
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      5   20
  6P LOSS WILD-TYPE   84  321
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  NO                5                84
  YES              20               321
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6P LOSS MUTATED                                  1     0
  6P LOSS WILD-TYPE                                0     6
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6P LOSS MUTATED                           0    24
  6P LOSS WILD-TYPE                        14   376
D50V7, multiclass
                                  clus
vv                                 6P LOSS MUTATED 6P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          0                 6
  BLACK OR AFRICAN AMERICAN                      0                14
  WHITE                                         24               376
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V8, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     1  21
  6P LOSS WILD-TYPE  15 366
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      1   21
  6P LOSS WILD-TYPE   15  366
                        clus
vv                       6P LOSS MUTATED 6P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                15
  NOT HISPANIC OR LATINO              21               366
[1] 2 2
[1] FALSE

Clustering(51) Variable = 6Q LOSS MUTATION ANALYSIS
D51V1, survival
                   sevent
clus2                 0   1
  6Q LOSS MUTATED    35  14
  6Q LOSS WILD-TYPE 317  61
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               49               378 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               14                61 
$`6Q LOSS MUTATED`
TCGA-CS-4944 TCGA-CS-5397 TCGA-CS-6666 TCGA-DB-5280 TCGA-DB-A4XF TCGA-DB-A4XH 
       10.62         6.38         8.48        36.56        18.38        12.59 
TCGA-DB-A64O TCGA-DH-A669 TCGA-DH-A66B TCGA-DU-5847 TCGA-DU-5855 TCGA-DU-5872 
       18.84        30.21        42.05        18.02         6.81        17.49 
TCGA-DU-6400 TCGA-DU-6405 TCGA-DU-6542 TCGA-DU-7012 TCGA-DU-7298 TCGA-DU-8158 
        1.22        19.89         7.73         6.54        18.94         5.10 
TCGA-DU-8161 TCGA-E1-5307 TCGA-FG-5963 TCGA-FG-7636 TCGA-FG-8191 TCGA-FG-A6J3 
       23.74        57.93        17.98        17.88        15.52        10.59 
TCGA-HT-7475 TCGA-HT-7606 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7692 TCGA-HT-7855 
       17.42        17.29        31.69        14.96         2.96        19.23 
TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A5RB TCGA-HT-A617 TCGA-HW-A5KK TCGA-P5-A5EV 
       15.72         0.23         0.10        16.14         7.89         0.23 
TCGA-P5-A5EZ TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-QH-A6CS TCGA-QH-A6CX 
        2.30         7.63         0.76         1.28         4.18        12.23 
TCGA-QH-A870 TCGA-S9-A6TZ TCGA-S9-A7R8 TCGA-TM-A7CF TCGA-TM-A84Q TCGA-VM-A8C8 
        0.07        21.63        31.59        48.39        18.90        33.07 
TCGA-VM-A8CD 
        7.89 

$`6Q LOSS WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-5390 TCGA-CS-5393 
        4.70         7.69        43.89        18.15        64.64        40.18 
TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6290 
        0.10        21.01         9.96        17.69        23.84        17.95 
TCGA-CS-6665 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 
       12.43         7.56         8.02         7.40         6.61       122.73 
TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 
       81.96        75.25        47.93        72.92        46.65        50.17 
TCGA-DB-5279 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC 
       44.52        78.28        30.08        10.29        12.72        27.62 
TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XG TCGA-DB-A64L TCGA-DB-A64P TCGA-DB-A64Q 
       27.02        18.84        72.95        11.01        16.80         5.98 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X 
       16.08        15.42        27.81        14.73        13.64        10.92 
TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 
        7.40         6.44        10.29        30.74         3.81        19.96 
TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A66D TCGA-DH-A66F 
       31.82        30.31        14.40         8.02        27.81        17.19 
TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV 
       17.19        54.25        10.22         6.58         3.45         6.21 
TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5870 
       14.56        17.46         6.74        13.38         8.45       182.33 
TCGA-DU-5871 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 
       18.94        15.16       211.17        52.11        22.42        49.02 
TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       75.16        46.06        65.75        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-7006 
      133.74        16.83        94.52       114.08         7.96        11.47 
TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7013 
       62.96       156.23       138.28        14.99       105.21         8.84 
TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 
      117.40        90.77        30.67        26.30        10.36         7.96 
TCGA-DU-7294 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 
       94.32        44.02        62.01        25.91        60.30        23.31 
TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 
       41.98         2.76         3.98        20.68        21.40        19.13 
TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS 
       16.96        15.48        14.17        14.24        12.59        15.12 
TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 
        4.96         3.65         5.65        12.20         8.65         2.70 
TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O 
       77.98         7.23         5.98        11.41        26.76         7.13 
TCGA-DU-A76R TCGA-DU-A7T8 TCGA-DU-A7TG TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 
       21.30       124.50        44.42        50.14        67.46        41.13 
TCGA-E1-5305 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 
       79.99       134.27        78.21        95.57       130.78        14.33 
TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 
        0.23         0.20        47.77        34.36        32.19        18.77 
TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7638 
       14.93        24.99        23.97        13.58        15.35        22.55 
TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 
       20.61        20.09        12.95        13.68        14.24        16.01 
TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW 
       20.09        14.96        22.52        38.27        10.72         5.26 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ 
       18.71        23.70        14.76        17.82        16.41        15.02 
TCGA-FG-A6J1 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 
       16.44        28.54        10.78        22.95        43.69         5.23 
TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 
        7.43         5.72         0.13         0.10         6.67         7.82 
TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7476 
        8.81         0.13         0.03        16.54         3.75         6.54 
TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 
       24.26         6.38         7.10        75.19        59.18        60.03 
TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 
      154.19         4.01         5.03        29.85        23.18       107.93 
TCGA-HT-7605 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 
        4.57         3.16        22.06        45.99        56.09        57.60 
TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 
        0.23        14.27         0.16        16.24         0.76        44.68 
TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7693 
        6.05        42.74         0.10         0.10         0.10        17.52 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 
        6.90        14.53        39.48        39.09         0.23        50.63 
TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 
        0.49        23.61        37.15         0.33         0.13         3.68 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 
        5.33         2.93         1.71        11.28        31.43         1.64 
TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 
       16.24         9.40        63.55         0.10        21.50        33.01 
TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 
       12.23         6.25         0.10         0.46         2.50         3.95 
TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-A4DV 
        4.70         0.23        29.59         3.88        16.04        10.49 
TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RC TCGA-HT-A614 
        0.13        14.01         0.07        14.70         5.33         2.70 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A618 TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 
       13.02         1.81         5.33         0.10        29.92        13.45 
TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 
        8.32        19.23        40.18        35.90         4.31        21.70 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KL TCGA-HW-A5KM 
       21.60        19.59        17.82        20.35        20.81        20.71 
TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EW TCGA-P5-A5EX 
       19.00        42.77         5.23         4.73         6.71         1.64 
TCGA-P5-A5EY TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V 
        2.37         4.11         5.88         5.75         2.53         4.83 
TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CY TCGA-QH-A6CZ 
        7.79         4.11        14.83        14.53         2.20         3.16 
TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA 
        0.59         6.31         3.91         4.73         1.91         0.23 
TCGA-QH-A6XC TCGA-QH-A86X TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
        5.03         3.48        88.83        94.03        32.65        59.38 
TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY 
       62.17        69.07        18.77        37.84        34.49        31.33 
TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       16.37        17.62        23.64        32.61         9.86        94.62 
TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG 
       83.70         5.85       106.39        62.37        72.59        80.12 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO 
       32.45        84.99        10.88        19.86        15.91         7.59 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY 
       15.16        14.07        14.27         7.92        19.63        12.59 
TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW 
        4.21         9.37         8.19         2.04         8.12         3.58 
TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 
        4.04        28.37        13.02       164.38        10.39        99.06 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 
       17.42        83.80        18.71         5.00        49.45        48.33 
TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G 
       49.32        34.78        12.00        15.09        50.76        34.36 
TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O 
       24.26        19.36        17.49        40.83        16.50        29.92 
TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB 
        9.44         4.57        12.00        30.08        13.51         0.10 
TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-W9-A837 
       26.79        10.95        27.06         7.04        23.21        45.07 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             0.07              0.03 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            57.93            211.17 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           15.520            16.025 
[1] "0.1 - 57.9 (15.5)"  "0.0 - 211.2 (16.0)"
[1] "hr=" "3.8"
D51V2, continuous
D51V3, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    24  26
  6Q LOSS WILD-TYPE 166 214
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     24   26
  6Q LOSS WILD-TYPE  166  214
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE              24               166
  MALE                26               214
[1] 2 2
[1] FALSE
D51V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  6Q LOSS MUTATED            31               10                 9
  6Q LOSS WILD-TYPE         128               97               155
D51V5, multiclass
                   clus
vv                  6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  ASTROCYTOMA                    31               128
  OLIGOASTROCYTOMA               10                97
  OLIGODENDROGLIOMA               9               155
[1] 3 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
  6Q LOSS MUTATED    15  35
  6Q LOSS WILD-TYPE  74 306
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     15   35
  6Q LOSS WILD-TYPE   74  306
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  NO               15                74
  YES              35               306
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6Q LOSS MUTATED                                  1     0
  6Q LOSS WILD-TYPE                                0     6
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6Q LOSS MUTATED                           3    46
  6Q LOSS WILD-TYPE                        11   354
D51V7, multiclass
                                  clus
vv                                 6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          0                 6
  BLACK OR AFRICAN AMERICAN                      3                11
  WHITE                                         46               354
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V8, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED     2  43
  6Q LOSS WILD-TYPE  14 344
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      2   43
  6Q LOSS WILD-TYPE   14  344
                        clus
vv                       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                14
  NOT HISPANIC OR LATINO              43               344
[1] 2 2
[1] FALSE

Clustering(52) Variable = 7P LOSS MUTATION ANALYSIS
D52V1, survival
                   sevent
clus2                 0   1
  7P LOSS MUTATED     2   1
  7P LOSS WILD-TYPE 350  74
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                3               424 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                1                74 
$`7P LOSS MUTATED`
TCGA-HW-A5KL TCGA-P5-A5F6 TCGA-S9-A6TS 
       20.81         1.28        62.17 

$`7P LOSS WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        46.65        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       30.08        10.29        12.72        27.62        27.02        18.84 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       18.38        72.95        12.59        11.01        18.84        16.80 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        16.08        15.42        27.81        14.73        13.64 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       10.92         7.40         6.44        10.29        30.74         3.81 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       42.05        27.81        17.19        17.19        54.25        10.22 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
        6.58         3.45         6.21        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
        6.74        13.38         8.45         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 
       17.49        15.16       211.17        52.11        22.42        49.02 
TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 
       75.16        46.06        65.75         1.22        87.45         7.04 
TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 
       11.64       133.74        19.89        16.83        94.52       114.08 
TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 
        7.96         7.73        11.47        62.96       156.23       138.28 
TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 
       14.99       105.21         6.54         8.84       117.40        90.77 
TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 
       30.67        26.30        10.36         7.96        94.32        18.94 
TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 
       44.02        62.01        25.91        60.30        23.31        41.98 
TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 
        2.76         5.10        23.74         3.98        20.68        21.40 
TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR 
       19.13        16.96        15.48        14.17        14.24        12.59 
TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 
       15.12         4.96         3.65         5.65        12.20         8.65 
TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L 
        2.70        77.98         7.23         5.98        11.41        26.76 
TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 TCGA-DU-A7TG TCGA-E1-5302 TCGA-E1-5303 
        7.13        21.30       124.50        44.42        50.14        67.46 
TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 
       41.13        79.99        57.93       134.27        78.21        95.57 
TCGA-E1-5322 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 
      130.78        14.33         0.23         0.20        47.77        17.98 
TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 
       34.36        32.19        18.77        14.93        24.99        23.97 
TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 
       13.58        15.35        17.88        22.55        20.61        20.09 
TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 
       12.95        13.68        14.24        16.01        20.09        14.96 
TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX 
       22.52        15.52        38.27        10.72         5.26        18.71 
TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 
       23.70        14.76        17.82        16.41        15.02        16.44 
TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 
       10.59        28.54        10.78        22.95        43.69         5.23 
TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 
        7.43         5.72         0.13         0.10         6.67         7.82 
TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 
        8.81         0.13         0.03        16.54         3.75        17.42 
TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 
        6.54        24.26         6.38         7.10        75.19        59.18 
TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 
       60.03       154.19         4.01         5.03        29.85        23.18 
TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 
      107.93         4.57        17.29         3.16        22.06        45.99 
TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 
       56.09        57.60         0.23        14.27         0.16        16.24 
TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 
        0.76        44.68         6.05        42.74         0.10        31.69 
TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 
       14.96         0.10         0.10         2.96        17.52         6.90 
TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 
       14.53        39.48        19.23        39.09         0.23        50.63 
TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 
        0.49        23.61        37.15         0.33         0.13         3.68 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 
        5.33         2.93         1.71        11.28        31.43         1.64 
TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 
       16.24         9.40        63.55         0.10        21.50        33.01 
TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 
       12.23         6.25         0.10         0.46         2.50         3.95 
TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 
        4.70         0.23        29.59         3.88        16.04        15.72 
TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA 
        0.23        10.49         0.13        14.01         0.07        14.70 
TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 
        0.10         5.33         2.70        13.02         1.81        16.14 
TCGA-HT-A618 TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 
        5.33         0.10        29.92        13.45         8.32        19.23 
TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 
       40.18        35.90         4.31        21.70        21.60        19.59 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 
       17.82        20.35         7.89        20.71        19.00        42.77 
TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY 
        5.23         4.73         0.23         6.71         1.64         2.37 
TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-QH-A65R 
        2.30         4.11         5.88         7.63         0.76         5.75 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU 
        2.53         4.83         7.79         4.11         4.18        14.83 
TCGA-QH-A6CV TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
       14.53        12.23         2.20         3.16         0.59         6.31 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X 
        3.91         4.73         1.91         0.23         5.03         3.48 
TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TU 
        0.07        88.83        94.03        32.65        59.38        69.07 
TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 
       18.77        37.84        34.49        31.33        21.63        16.37 
TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
       17.62        23.64        32.61         9.86        94.62        83.70 
TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH 
        5.85       106.39        62.37        72.59        80.12        32.45 
TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP 
       84.99        10.88        19.86        15.91         7.59        15.16 
TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ 
       14.07        14.27         7.92        19.63        12.59         4.21 
TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX 
        9.37         8.19         2.04         8.12         3.58         4.04 
TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 
       28.37        13.02       164.38        10.39        99.06        17.42 
TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 
       83.80        31.59        18.71         5.00        49.45        48.33 
TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F 
       49.32        34.78        48.39        12.00        15.09        50.76 
TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M 
       34.36        24.26        19.36        17.49        40.83        16.50 
TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-VM-A8C8 
       29.92        18.90         9.44         4.57        12.00        33.07 
TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH 
       30.08        13.51         0.10         7.89        26.79        10.95 
TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-W9-A837 
       27.06         7.04        23.21        45.07 

  7P LOSS MUTATED 7P LOSS WILD-TYPE 
             1.28              0.03 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
            62.17            211.17 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
           20.810            15.815 
[1] "1.3 - 62.2 (20.8)"  "0.0 - 211.2 (15.8)"
[1] "hr=" "1.8"
D52V2, continuous
D52V3, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     2   1
  7P LOSS WILD-TYPE 188 239
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      2    1
  7P LOSS WILD-TYPE  188  239
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  FEMALE               2               188
  MALE                 1               239
[1] 2 2
[1] FALSE
D52V4, continuous
[1] "Remove cluster labels:" "7P LOSS MUTATED"       
clus
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                2               247 
       TCGA-CS-4938        TCGA-CS-4941        TCGA-CS-4942        TCGA-CS-4943 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CS-4944        TCGA-CS-5390        TCGA-CS-5393        TCGA-CS-5395 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CS-5396        TCGA-CS-5397        TCGA-CS-6186        TCGA-CS-6188 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CS-6290        TCGA-CS-6665        TCGA-CS-6666        TCGA-CS-6667 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CS-6668        TCGA-CS-6669        TCGA-DB-5274        TCGA-DB-A4XE 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DB-A64L        TCGA-DB-A64Q        TCGA-DB-A64R        TCGA-DB-A64S 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DB-A64U        TCGA-DB-A64V        TCGA-DB-A64W        TCGA-DB-A64X 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DB-A75L        TCGA-DB-A75O        TCGA-DH-5140        TCGA-DH-5142 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DH-5143        TCGA-DH-5144        TCGA-DH-A66B        TCGA-DH-A66D 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DH-A66F        TCGA-DH-A66G        TCGA-DH-A7UR        TCGA-DH-A7UU 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DH-A7UV        TCGA-DU-5851        TCGA-DU-5852        TCGA-DU-5853 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-5854        TCGA-DU-5855        TCGA-DU-5870        TCGA-DU-5871 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-5874        TCGA-DU-6396        TCGA-DU-6403        TCGA-DU-6404 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-6405        TCGA-DU-6407        TCGA-DU-6408        TCGA-DU-6410 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-7011        TCGA-DU-7013        TCGA-DU-7014        TCGA-DU-7015 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-7018        TCGA-DU-7019        TCGA-DU-7294        TCGA-DU-7298 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-7299        TCGA-DU-7300        TCGA-DU-7301        TCGA-DU-7302 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-7304        TCGA-DU-7306        TCGA-DU-7309        TCGA-DU-8158 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-8161        TCGA-DU-8162        TCGA-DU-8163        TCGA-DU-8165 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-8167        TCGA-DU-8168        TCGA-DU-A5TP        TCGA-DU-A5TR 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-A5TS        TCGA-DU-A5TU        TCGA-DU-A5TW        TCGA-DU-A6S2 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-A6S6        TCGA-DU-A6S7        TCGA-DU-A6S8        TCGA-DU-A76R 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-A7T8        TCGA-DU-A7TG        TCGA-E1-5302        TCGA-E1-5303 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-E1-5304        TCGA-E1-5305        TCGA-E1-5307        TCGA-E1-5311 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-E1-5318        TCGA-E1-5319        TCGA-E1-5322        TCGA-FG-5963 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FG-5965        TCGA-FG-6688        TCGA-FG-6689        TCGA-FG-6690 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FG-6691        TCGA-FG-7636        TCGA-FG-7638        TCGA-FG-8181 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FG-8185        TCGA-FG-8186        TCGA-FG-8187        TCGA-FG-8188 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FG-8189        TCGA-FG-A4MT        TCGA-FG-A4MW        TCGA-FG-A4MX 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FG-A60J        TCGA-FG-A60L        TCGA-FG-A6J1        TCGA-FG-A6J3 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FG-A711        TCGA-FG-A713        TCGA-FG-A87Q        TCGA-HT-7468 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7470        TCGA-HT-7475        TCGA-HT-7477        TCGA-HT-7485 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7607        TCGA-HT-7609        TCGA-HT-7611        TCGA-HT-7689 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7692        TCGA-HT-7693        TCGA-HT-7694        TCGA-HT-7854 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-7875        TCGA-HT-7884        TCGA-HT-8564        TCGA-HT-A4DV 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-A5R7        TCGA-HT-A5RA        TCGA-HT-A5RC        TCGA-HT-A615 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-A617        TCGA-HT-A618        TCGA-IK-7675        TCGA-KT-A74X 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-KT-A7W1        TCGA-P5-A5EU        TCGA-P5-A5EV        TCGA-P5-A5EW 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-P5-A5EX        TCGA-P5-A5F0        TCGA-P5-A5F2        TCGA-P5-A5F4 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-QH-A65R        TCGA-QH-A65S        TCGA-QH-A65V        TCGA-QH-A65X 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-QH-A65Z        TCGA-QH-A6CS        TCGA-QH-A6CU        TCGA-QH-A6CV 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-QH-A6CW        TCGA-QH-A6CX        TCGA-QH-A6CY        TCGA-QH-A6CZ 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-QH-A6X3        TCGA-QH-A6X4        TCGA-QH-A6X5        TCGA-QH-A6X8 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-QH-A6X9        TCGA-QH-A6XA        TCGA-QH-A6XC        TCGA-QH-A86X 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-QH-A870        TCGA-S9-A6TU        TCGA-S9-A6TV        TCGA-S9-A6TW 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-S9-A6TX        TCGA-S9-A6TY        TCGA-S9-A6TZ        TCGA-S9-A6U0 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-S9-A6U1        TCGA-S9-A6U2        TCGA-S9-A6U5        TCGA-S9-A6U6 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-S9-A6U8        TCGA-S9-A6UA        TCGA-S9-A6UB        TCGA-S9-A6WD 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-S9-A6WE        TCGA-S9-A6WG        TCGA-S9-A6WH        TCGA-S9-A6WI 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-S9-A6WL        TCGA-S9-A6WM        TCGA-S9-A6WN        TCGA-S9-A6WO 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-S9-A6WP        TCGA-S9-A6WQ        TCGA-S9-A7IQ        TCGA-S9-A7IS 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-S9-A7IX        TCGA-S9-A7IY        TCGA-S9-A7IZ        TCGA-S9-A7J0 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-S9-A7J1        TCGA-S9-A7J2        TCGA-S9-A7J3        TCGA-S9-A7QW 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-S9-A7QX        TCGA-S9-A7QY        TCGA-S9-A7QZ        TCGA-S9-A7R1 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-S9-A7R2        TCGA-S9-A7R3        TCGA-S9-A7R4        TCGA-S9-A7R7 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-S9-A7R8        TCGA-S9-A89V        TCGA-S9-A89Z        TCGA-TM-A7C3 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-TM-A7C4        TCGA-TM-A7C5        TCGA-TM-A7CA        TCGA-TM-A7CF 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-TM-A84B        TCGA-TM-A84C        TCGA-TM-A84F        TCGA-TM-A84G 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-TM-A84H        TCGA-TM-A84I        TCGA-TM-A84J        TCGA-TM-A84L 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-TM-A84M        TCGA-TM-A84O        TCGA-TM-A84Q        TCGA-TM-A84R 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-TM-A84S        TCGA-TM-A84T        TCGA-VM-A8C8        TCGA-VM-A8CA 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-VM-A8CD        TCGA-VM-A8CE        TCGA-VM-A8CH 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  7P LOSS MUTATED             2                0                 1
  7P LOSS WILD-TYPE         157              107               163
D52V5, multiclass
                   clus
vv                  7P LOSS MUTATED 7P LOSS WILD-TYPE
  ASTROCYTOMA                     2               157
  OLIGOASTROCYTOMA                0               107
  OLIGODENDROGLIOMA               1               163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V6, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     0   3
  7P LOSS WILD-TYPE  89 338
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      0    3
  7P LOSS WILD-TYPE   89  338
     clus
vv    7P LOSS MUTATED 7P LOSS WILD-TYPE
  NO                0                89
  YES               3               338
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7P LOSS MUTATED                                  0     0
  7P LOSS WILD-TYPE                                1     6
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7P LOSS MUTATED                           0     3
  7P LOSS WILD-TYPE                        14   397
D52V7, multiclass
                                  clus
vv                                 7P LOSS MUTATED 7P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 6
  BLACK OR AFRICAN AMERICAN                      0                14
  WHITE                                          3               397
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V8, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     0   2
  7P LOSS WILD-TYPE  16 385
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      0    2
  7P LOSS WILD-TYPE   16  385
                        clus
vv                       7P LOSS MUTATED 7P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                16
  NOT HISPANIC OR LATINO               2               385
[1] 2 2
[1] FALSE

Clustering(53) Variable = 7Q LOSS MUTATION ANALYSIS
D53V1, survival
                   sevent
clus2                 0   1
  7Q LOSS MUTATED     2   1
  7Q LOSS WILD-TYPE 350  74
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                3               424 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                1                74 
$`7Q LOSS MUTATED`
TCGA-DH-A66B TCGA-P5-A5F6 TCGA-S9-A6TS 
       42.05         1.28        62.17 

$`7Q LOSS WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        46.65        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       30.08        10.29        12.72        27.62        27.02        18.84 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       18.38        72.95        12.59        11.01        18.84        16.80 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        16.08        15.42        27.81        14.73        13.64 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       10.92         7.40         6.44        10.29        30.74         3.81 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT 
       27.81        17.19        17.19        54.25        10.22         6.58 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
        3.45         6.21        18.02        14.56        17.46         6.74 
TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 
       13.38         8.45         6.81       182.33        18.94        17.49 
TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       15.16       211.17        52.11        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       46.06        65.75         1.22        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 
      133.74        19.89        16.83        94.52       114.08         7.96 
TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 
        7.73        11.47        62.96       156.23       138.28        14.99 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 
      105.21         6.54         8.84       117.40        90.77        30.67 
TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 
       26.30        10.36         7.96        94.32        18.94        44.02 
TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 
       62.01        25.91        60.30        23.31        41.98         2.76 
TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 
        5.10        23.74         3.98        20.68        21.40        19.13 
TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS 
       16.96        15.48        14.17        14.24        12.59        15.12 
TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 
        4.96         3.65         5.65        12.20         8.65         2.70 
TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O 
       77.98         7.23         5.98        11.41        26.76         7.13 
TCGA-DU-A76R TCGA-DU-A7T8 TCGA-DU-A7TG TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 
       21.30       124.50        44.42        50.14        67.46        41.13 
TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 
       79.99        57.93       134.27        78.21        95.57       130.78 
TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 
       14.33         0.23         0.20        47.77        17.98        34.36 
TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 
       32.19        18.77        14.93        24.99        23.97        13.58 
TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 
       15.35        17.88        22.55        20.61        20.09        12.95 
TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 
       13.68        14.24        16.01        20.09        14.96        22.52 
TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY 
       15.52        38.27        10.72         5.26        18.71        23.70 
TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 
       14.76        17.82        16.41        15.02        16.44        10.59 
TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N 
       28.54        10.78        22.95        43.69         5.23         7.43 
TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 
        5.72         0.13         0.10         6.67         7.82         8.81 
TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 
        0.13         0.03        16.54         3.75        17.42         6.54 
TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 
       24.26         6.38         7.10        75.19        59.18        60.03 
TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 
      154.19         4.01         5.03        29.85        23.18       107.93 
TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 
        4.57        17.29         3.16        22.06        45.99        56.09 
TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 
       57.60         0.23        14.27         0.16        16.24         0.76 
TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 
       44.68         6.05        42.74         0.10        31.69        14.96 
TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 
        0.10         0.10         2.96        17.52         6.90        14.53 
TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 
       39.48        19.23        39.09         0.23        50.63         0.49 
TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 
       23.61        37.15         0.33         0.13         3.68         5.33 
TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 
        2.93         1.71        11.28        31.43         1.64        16.24 
TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 
        9.40        63.55         0.10        21.50        33.01        12.23 
TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 
        6.25         0.10         0.46         2.50         3.95         4.70 
TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS 
        0.23        29.59         3.88        16.04        15.72         0.23 
TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB 
       10.49         0.13        14.01         0.07        14.70         0.10 
TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 
        5.33         2.70        13.02         1.81        16.14         5.33 
TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 
        0.10        29.92        13.45         8.32        19.23        40.18 
TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 
       35.90         4.31        21.70        21.60        19.59        17.82 
TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 
       20.35         7.89        20.81        20.71        19.00        42.77 
TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY 
        5.23         4.73         0.23         6.71         1.64         2.37 
TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-QH-A65R 
        2.30         4.11         5.88         7.63         0.76         5.75 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU 
        2.53         4.83         7.79         4.11         4.18        14.83 
TCGA-QH-A6CV TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
       14.53        12.23         2.20         3.16         0.59         6.31 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X 
        3.91         4.73         1.91         0.23         5.03         3.48 
TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TU 
        0.07        88.83        94.03        32.65        59.38        69.07 
TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 
       18.77        37.84        34.49        31.33        21.63        16.37 
TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
       17.62        23.64        32.61         9.86        94.62        83.70 
TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH 
        5.85       106.39        62.37        72.59        80.12        32.45 
TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP 
       84.99        10.88        19.86        15.91         7.59        15.16 
TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ 
       14.07        14.27         7.92        19.63        12.59         4.21 
TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX 
        9.37         8.19         2.04         8.12         3.58         4.04 
TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 
       28.37        13.02       164.38        10.39        99.06        17.42 
TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 
       83.80        31.59        18.71         5.00        49.45        48.33 
TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F 
       49.32        34.78        48.39        12.00        15.09        50.76 
TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M 
       34.36        24.26        19.36        17.49        40.83        16.50 
TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-VM-A8C8 
       29.92        18.90         9.44         4.57        12.00        33.07 
TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH 
       30.08        13.51         0.10         7.89        26.79        10.95 
TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-W9-A837 
       27.06         7.04        23.21        45.07 

  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
             1.28              0.03 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            62.17            211.17 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
           42.050            15.815 
[1] "1.3 - 62.2 (42.0)"  "0.0 - 211.2 (15.8)"
[1] "hr=" "1.5"
D53V2, continuous
D53V3, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     1   2
  7Q LOSS WILD-TYPE 189 238
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      1    2
  7Q LOSS WILD-TYPE  189  238
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  FEMALE               1               189
  MALE                 2               238
[1] 2 2
[1] FALSE
D53V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  7Q LOSS MUTATED             2                0                 1
  7Q LOSS WILD-TYPE         157              107               163
D53V5, multiclass
                   clus
vv                  7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  ASTROCYTOMA                     2               157
  OLIGOASTROCYTOMA                0               107
  OLIGODENDROGLIOMA               1               163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V6, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     0   3
  7Q LOSS WILD-TYPE  89 338
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      0    3
  7Q LOSS WILD-TYPE   89  338
     clus
vv    7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  NO                0                89
  YES               3               338
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7Q LOSS MUTATED                                  0     0
  7Q LOSS WILD-TYPE                                1     6
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7Q LOSS MUTATED                           0     3
  7Q LOSS WILD-TYPE                        14   397
D53V7, multiclass
                                  clus
vv                                 7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 6
  BLACK OR AFRICAN AMERICAN                      0                14
  WHITE                                          3               397
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V8, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     0   3
  7Q LOSS WILD-TYPE  16 384
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      0    3
  7Q LOSS WILD-TYPE   16  384
                        clus
vv                       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                16
  NOT HISPANIC OR LATINO               3               384
[1] 2 2
[1] FALSE

Clustering(54) Variable = 8P LOSS MUTATION ANALYSIS
D54V1, survival
                   sevent
clus2                 0   1
  8P LOSS MUTATED     8   4
  8P LOSS WILD-TYPE 344  71
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               12               415 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                4                71 
$`8P LOSS MUTATED`
TCGA-DB-5277 TCGA-DH-5140 TCGA-DH-A66B TCGA-DU-7006 TCGA-DU-8165 TCGA-E1-5304 
       46.65        19.96        42.05        11.47        19.13        41.13 
TCGA-HT-7688 TCGA-HT-8564 TCGA-HT-A4DS TCGA-P5-A5F6 TCGA-QH-A6CV TCGA-S9-A6WM 
       31.69        15.72         0.23         1.28        14.53        19.86 

$`8P LOSS WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 
       72.92        50.17        44.52        36.56        78.28        30.08 
TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF 
       10.29        12.72        27.62        27.02        18.84        18.38 
TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q 
       72.95        12.59        11.01        18.84        16.80         5.98 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X 
       16.08        15.42        27.81        14.73        13.64        10.92 
TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5141 
        7.40         6.44        10.29        30.74         3.81        31.82 
TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66D TCGA-DH-A66F 
       30.31        14.40         8.02        30.21        27.81        17.19 
TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV 
       17.19        54.25        10.22         6.58         3.45         6.21 
TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 
       18.02        14.56        17.46         6.74        13.38         8.45 
TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 
        6.81       182.33        18.94        17.49        15.16       211.17 
TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 
       52.11        22.42        49.02        75.16        46.06        65.75 
TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 
        1.22        87.45         7.04        11.64       133.74        19.89 
TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7007 
       16.83        94.52       114.08         7.96         7.73        62.96 
TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 
      156.23       138.28        14.99       105.21         6.54         8.84 
TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 
      117.40        90.77        30.67        26.30        10.36         7.96 
TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 
       94.32        18.94        44.02        62.01        25.91        60.30 
TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 
       23.31        41.98         2.76         5.10        23.74         3.98 
TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP 
       20.68        21.40        16.96        15.48        14.17        14.24 
TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY 
       12.59        15.12         4.96         3.65         5.65        12.20 
TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K 
        8.65         2.70        77.98         7.23         5.98        11.41 
TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 TCGA-DU-A7TG TCGA-E1-5302 
       26.76         7.13        21.30       124.50        44.42        50.14 
TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 
       67.46        79.99        57.93       134.27        78.21        95.57 
TCGA-E1-5322 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 
      130.78        14.33         0.23         0.20        47.77        17.98 
TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 
       34.36        32.19        18.77        14.93        24.99        23.97 
TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 
       13.58        15.35        17.88        22.55        20.61        20.09 
TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 
       12.95        13.68        14.24        16.01        20.09        14.96 
TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX 
       22.52        15.52        38.27        10.72         5.26        18.71 
TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 
       23.70        14.76        17.82        16.41        15.02        16.44 
TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 
       10.59        28.54        10.78        22.95        43.69         5.23 
TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 
        7.43         5.72         0.13         0.10         6.67         7.82 
TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 
        8.81         0.13         0.03        16.54         3.75        17.42 
TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 
        6.54        24.26         6.38         7.10        75.19        59.18 
TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 
       60.03       154.19         4.01         5.03        29.85        23.18 
TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 
      107.93         4.57        17.29         3.16        22.06        45.99 
TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 
       56.09        57.60         0.23        14.27         0.16        16.24 
TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7689 
        0.76        44.68         6.05        42.74         0.10        14.96 
TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 
        0.10         0.10         2.96        17.52         6.90        14.53 
TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 
       39.48        19.23        39.09         0.23        50.63         0.49 
TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 
       23.61        37.15         0.33         0.13         3.68         5.33 
TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 
        2.93         1.71        11.28        31.43         1.64        16.24 
TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 
        9.40        63.55         0.10        21.50        33.01        12.23 
TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 
        6.25         0.10         0.46         2.50         3.95         4.70 
TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-A4DV TCGA-HT-A5R5 
        0.23        29.59         3.88        16.04        10.49         0.13 
TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 
       14.01         0.07        14.70         0.10         5.33         2.70 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A74O TCGA-HW-7486 
       13.02         1.81        16.14         5.33         0.10        29.92 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 
       13.45         8.32        19.23        40.18        35.90         4.31 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
       21.70        21.60        19.59        17.82        20.35         7.89 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 
       20.81        20.71        19.00        42.77         5.23         4.73 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 
        0.23         6.71         1.64         2.37         2.30         4.11 
TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V 
        5.88         7.63         0.76         5.75         2.53         4.83 
TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CX TCGA-QH-A6CY 
        7.79         4.11         4.18        14.83        12.23         2.20 
TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 
        3.16         0.59         6.31         3.91         4.73         1.91 
TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML 
        0.23         5.03         3.48         0.07        88.83        94.03 
TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW 
       32.65        59.38        62.17        69.07        18.77        37.84 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 
       34.49        31.33        21.63        16.37        17.62        23.64 
TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB 
       32.61         9.86        94.62        83.70         5.85       106.39 
TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL 
       62.37        72.59        80.12        32.45        84.99        10.88 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
       15.91         7.59        15.16        14.07        14.27         7.92 
TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 
       19.63        12.59         4.21         9.37         8.19         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 
        8.12         3.58         4.04        28.37        13.02       164.38 
TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V 
       10.39        99.06        17.42        83.80        31.59        18.71 
TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF 
        5.00        49.45        48.33        49.32        34.78        48.39 
TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I 
       12.00        15.09        50.76        34.36        24.26        19.36 
TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R 
       17.49        40.83        16.50        29.92        18.90         9.44 
TCGA-TM-A84S TCGA-TM-A84T TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB 
        4.57        12.00        33.07        30.08        13.51         0.10 
TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS 
        7.89        26.79        10.95        27.06         7.04        23.21 
TCGA-W9-A837 
       45.07 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             0.23              0.03 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            46.65            211.17 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           19.495            15.520 
[1] "0.2 - 46.6 (19.5)"  "0.0 - 211.2 (15.5)"
[1] "hr=" "2.6"
D54V2, continuous
D54V3, binary
                   cls
clus                  0   1
  8P LOSS MUTATED     5   8
  8P LOSS WILD-TYPE 185 232
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      5    8
  8P LOSS WILD-TYPE  185  232
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE               5               185
  MALE                 8               232
[1] 2 2
[1] FALSE
D54V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  8P LOSS MUTATED             8                2                 3
  8P LOSS WILD-TYPE         151              105               161
D54V5, multiclass
                   clus
vv                  8P LOSS MUTATED 8P LOSS WILD-TYPE
  ASTROCYTOMA                     8               151
  OLIGOASTROCYTOMA                2               105
  OLIGODENDROGLIOMA               3               161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V6, binary
                   cls
clus                  0   1
  8P LOSS MUTATED     4   9
  8P LOSS WILD-TYPE  85 332
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      4    9
  8P LOSS WILD-TYPE   85  332
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  NO                4                85
  YES               9               332
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8P LOSS MUTATED                                  0     1
  8P LOSS WILD-TYPE                                1     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8P LOSS MUTATED                           0    12
  8P LOSS WILD-TYPE                        14   388
D54V7, multiclass
                                  clus
vv                                 8P LOSS MUTATED 8P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 5
  BLACK OR AFRICAN AMERICAN                      0                14
  WHITE                                         12               388
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V8, binary
                   cls
clus                  0   1
  8P LOSS MUTATED     1  12
  8P LOSS WILD-TYPE  15 375
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      1   12
  8P LOSS WILD-TYPE   15  375
                        clus
vv                       8P LOSS MUTATED 8P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                15
  NOT HISPANIC OR LATINO              12               375
[1] 2 2
[1] FALSE

Clustering(55) Variable = 8Q LOSS MUTATION ANALYSIS
D55V1, survival
                   sevent
clus2                 0   1
  8Q LOSS MUTATED     6   3
  8Q LOSS WILD-TYPE 346  72
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                9               418 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                3                72 
$`8Q LOSS MUTATED`
TCGA-DH-5140 TCGA-DU-7006 TCGA-DU-8165 TCGA-E1-5304 TCGA-HT-8564 TCGA-HT-A4DS 
       19.96        11.47        19.13        41.13        15.72         0.23 
TCGA-P5-A5F6 TCGA-QH-A6CV TCGA-S9-A6WM 
        1.28        14.53        19.86 

$`8Q LOSS WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        46.65        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       30.08        10.29        12.72        27.62        27.02        18.84 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       18.38        72.95        12.59        11.01        18.84        16.80 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        16.08        15.42        27.81        14.73        13.64 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       10.92         7.40         6.44        10.29        30.74         3.81 
TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B 
       31.82        30.31        14.40         8.02        30.21        42.05 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT 
       27.81        17.19        17.19        54.25        10.22         6.58 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
        3.45         6.21        18.02        14.56        17.46         6.74 
TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 
       13.38         8.45         6.81       182.33        18.94        17.49 
TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       15.16       211.17        52.11        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       46.06        65.75         1.22        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 
      133.74        19.89        16.83        94.52       114.08         7.96 
TCGA-DU-6542 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 
        7.73        62.96       156.23       138.28        14.99       105.21 
TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 
        6.54         8.84       117.40        90.77        30.67        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 
       10.36         7.96        94.32        18.94        44.02        62.01 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 
       25.91        60.30        23.31        41.98         2.76         5.10 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-8167 
       23.74         3.98        20.68        21.40        16.96        15.48 
TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU 
       14.17        14.24        12.59        15.12         4.96         3.65 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
        5.65        12.20         8.65         2.70        77.98         7.23 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 
        5.98        11.41        26.76         7.13        21.30       124.50 
TCGA-DU-A7TG TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 
       44.42        50.14        67.46        79.99        57.93       134.27 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 
       78.21        95.57       130.78        14.33         0.23         0.20 
TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 
       47.77        17.98        34.36        32.19        18.77        14.93 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 
       24.99        23.97        13.58        15.35        17.88        22.55 
TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 
       20.61        20.09        12.95        13.68        14.24        16.01 
TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU 
       20.09        14.96        22.52        15.52        38.27        10.72 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
        5.26        18.71        23.70        14.76        17.82        16.41 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 
       15.02        16.44        10.59        28.54        10.78        22.95 
TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 
       43.69         5.23         7.43         5.72         0.13         0.10 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 
        6.67         7.82         8.81         0.13         0.03        16.54 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 
        3.75        17.42         6.54        24.26         6.38         7.10 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
       75.19        59.18        60.03       154.19         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 
       29.85        23.18       107.93         4.57        17.29         3.16 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
       22.06        45.99        56.09        57.60         0.23        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 
        0.16        16.24         0.76        44.68         6.05        42.74 
TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 
        0.10        31.69        14.96         0.10         0.10         2.96 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 
       17.52         6.90        14.53        39.48        19.23        39.09 
TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 
        0.23        50.63         0.49        23.61        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 
        0.13         3.68         5.33         2.93         1.71        11.28 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 
       31.43         1.64        16.24         9.40        63.55         0.10 
TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 
       21.50        33.01        12.23         6.25         0.10         0.46 
TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 
        2.50         3.95         4.70         0.23        29.59         3.88 
TCGA-HT-8563 TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA 
       16.04        10.49         0.13        14.01         0.07        14.70 
TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 
        0.10         5.33         2.70        13.02         1.81        16.14 
TCGA-HT-A618 TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 
        5.33         0.10        29.92        13.45         8.32        19.23 
TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 
       40.18        35.90         4.31        21.70        21.60        19.59 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 
       17.82        20.35         7.89        20.81        20.71        19.00 
TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX 
       42.77         5.23         4.73         0.23         6.71         1.64 
TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 
        2.37         2.30         4.11         5.88         7.63         0.76 
TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS 
        5.75         2.53         4.83         7.79         4.11         4.18 
TCGA-QH-A6CU TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
       14.83        12.23         2.20         3.16         0.59         6.31 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X 
        3.91         4.73         1.91         0.23         5.03         3.48 
TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TS 
        0.07        88.83        94.03        32.65        59.38        62.17 
TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ 
       69.07        18.77        37.84        34.49        31.33        21.63 
TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       16.37        17.62        23.64        32.61         9.86        94.62 
TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG 
       83.70         5.85       106.39        62.37        72.59        80.12 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP 
       32.45        84.99        10.88        15.91         7.59        15.16 
TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ 
       14.07        14.27         7.92        19.63        12.59         4.21 
TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX 
        9.37         8.19         2.04         8.12         3.58         4.04 
TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 
       28.37        13.02       164.38        10.39        99.06        17.42 
TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 
       83.80        31.59        18.71         5.00        49.45        48.33 
TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F 
       49.32        34.78        48.39        12.00        15.09        50.76 
TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M 
       34.36        24.26        19.36        17.49        40.83        16.50 
TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-VM-A8C8 
       29.92        18.90         9.44         4.57        12.00        33.07 
TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH 
       30.08        13.51         0.10         7.89        26.79        10.95 
TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-W9-A837 
       27.06         7.04        23.21        45.07 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             0.23              0.03 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            41.13            211.17 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            15.72             15.96 
[1] "0.2 - 41.1 (15.7)"  "0.0 - 211.2 (16.0)"
[1] "hr=" "3.6"
D55V2, continuous
D55V3, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     5   4
  8Q LOSS WILD-TYPE 185 236
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      5    4
  8Q LOSS WILD-TYPE  185  236
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE               5               185
  MALE                 4               236
[1] 2 2
[1] FALSE
D55V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  8Q LOSS MUTATED             5                2                 2
  8Q LOSS WILD-TYPE         154              105               162
D55V5, multiclass
                   clus
vv                  8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  ASTROCYTOMA                     5               154
  OLIGOASTROCYTOMA                2               105
  OLIGODENDROGLIOMA               2               162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V6, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     2   7
  8Q LOSS WILD-TYPE  87 334
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      2    7
  8Q LOSS WILD-TYPE   87  334
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  NO                2                87
  YES               7               334
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8Q LOSS MUTATED                                  0     1
  8Q LOSS WILD-TYPE                                1     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8Q LOSS MUTATED                           0     8
  8Q LOSS WILD-TYPE                        14   392
D55V7, multiclass
                                  clus
vv                                 8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 5
  BLACK OR AFRICAN AMERICAN                      0                14
  WHITE                                          8               392
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V8, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     1   8
  8Q LOSS WILD-TYPE  15 379
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      1    8
  8Q LOSS WILD-TYPE   15  379
                        clus
vv                       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                15
  NOT HISPANIC OR LATINO               8               379
[1] 2 2
[1] FALSE

Clustering(56) Variable = 9P LOSS MUTATION ANALYSIS
D56V1, survival
                   sevent
clus2                 0   1
  9P LOSS MUTATED    68  27
  9P LOSS WILD-TYPE 284  48
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               95               332 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               27                48 
$`9P LOSS MUTATED`
TCGA-CS-4943 TCGA-CS-5393 TCGA-CS-5395 TCGA-CS-5397 TCGA-CS-6188 TCGA-CS-6666 
       18.15        40.18        21.01         6.38        23.84         8.48 
TCGA-CS-6670 TCGA-DB-5277 TCGA-DB-5279 TCGA-DB-5281 TCGA-DB-A4XB TCGA-DB-A4XC 
        6.61        46.65        44.52        78.28        12.72        27.62 
TCGA-DB-A4XF TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64V TCGA-DB-A75L TCGA-DB-A75P 
       18.38        12.59        11.01        14.73         6.44         3.81 
TCGA-DH-A7UR TCGA-DU-5847 TCGA-DU-5851 TCGA-DU-5855 TCGA-DU-6395 TCGA-DU-6397 
       54.25        18.02        17.46         6.81        49.02        46.06 
TCGA-DU-6399 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 
       65.75         7.04        11.64         7.73        11.47        62.96 
TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7019 TCGA-DU-7292 TCGA-DU-7298 TCGA-DU-7301 
      117.40        90.77        26.30         7.96        18.94        25.91 
TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-8162 TCGA-DU-8168 TCGA-DU-A5TY TCGA-DU-A6S7 
       23.31        41.98         3.98        14.17        12.20         7.23 
TCGA-DU-A6S8 TCGA-E1-5304 TCGA-E1-5307 TCGA-EZ-7264 TCGA-F6-A8O4 TCGA-FG-5963 
        5.98        41.13        57.93        14.33         0.20        17.98 
TCGA-FG-5965 TCGA-FG-6690 TCGA-FG-6692 TCGA-FG-7636 TCGA-FG-8185 TCGA-FG-A4MW 
       32.19        24.99        13.58        17.88        14.24         5.26 
TCGA-FG-A4MX TCGA-FG-A711 TCGA-FG-A87Q TCGA-HT-7471 TCGA-HT-7477 TCGA-HT-7606 
       18.71        43.69         5.72         0.13        24.26        17.29 
TCGA-HT-7687 TCGA-HT-7689 TCGA-HT-7692 TCGA-HT-7902 TCGA-HT-8104 TCGA-HT-8108 
        0.10        14.96         2.96        31.43        12.23         2.50 
TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A614 TCGA-HW-7490 TCGA-HW-8320 TCGA-HW-8322 
       14.70         0.10         2.70        19.23        21.60        17.82 
TCGA-HW-A5KM TCGA-IK-7675 TCGA-P5-A5EV TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 
       20.71        19.00         0.23         7.63         0.76         1.28 
TCGA-QH-A6CV TCGA-QH-A6CZ TCGA-S9-A6TS TCGA-S9-A6TW TCGA-S9-A7IS TCGA-S9-A7IX 
       14.53         3.16        62.17        37.84         7.92        19.63 
TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7R1 TCGA-S9-A7R3 TCGA-S9-A7R8 TCGA-TM-A7CF 
        4.21         9.37       164.38        99.06        31.59        48.39 
TCGA-TM-A84H TCGA-TM-A84J TCGA-VM-A8CB TCGA-VM-A8CD TCGA-W9-A837 
       24.26        17.49         0.10         7.89        45.07 

$`9P LOSS WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5394 
        4.70         7.69        43.89        10.62        64.64         0.10 
TCGA-CS-5396 TCGA-CS-6186 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6667 TCGA-CS-6668 
        9.96        17.69        17.95        12.43         7.56         8.02 
TCGA-CS-6669 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 
        7.40       122.73        81.96        75.25        47.93        72.92 
TCGA-DB-5278 TCGA-DB-5280 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XD TCGA-DB-A4XE 
       50.17        36.56        30.08        10.29        27.02        18.84 
TCGA-DB-A4XG TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S 
       72.95        18.84        16.80         5.98        16.08        15.42 
TCGA-DB-A64U TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75M TCGA-DB-A75O 
       27.81        13.64        10.92         7.40        10.29        30.74 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7US TCGA-DH-A7UT 
       42.05        27.81        17.19        17.19        10.22         6.58 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5849 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 
        3.45         6.21        14.56         6.74        13.38         8.45 
TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 
      182.33        18.94        17.49        15.16       211.17        52.11 
TCGA-DU-6394 TCGA-DU-6396 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6404 TCGA-DU-6405 
       22.42        75.16         1.22        87.45       133.74        19.89 
TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-7008 TCGA-DU-7009 
       16.83        94.52       114.08         7.96       156.23       138.28 
TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7018 TCGA-DU-7290 
       14.99       105.21         6.54         8.84        30.67        10.36 
TCGA-DU-7294 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7302 TCGA-DU-7309 TCGA-DU-8158 
       94.32        44.02        62.01        60.30         2.76         5.10 
TCGA-DU-8161 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 
       23.74        20.68        21.40        19.13        16.96        15.48 
TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW 
       14.24        12.59        15.12         4.96         3.65         5.65 
TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O 
        8.65         2.70        77.98        11.41        26.76         7.13 
TCGA-DU-A76R TCGA-DU-A7T8 TCGA-DU-A7TG TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5305 
       21.30       124.50        44.42        50.14        67.46        79.99 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-F6-A8O3 TCGA-FG-5962 
      134.27        78.21        95.57       130.78         0.23        47.77 
TCGA-FG-5964 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6691 TCGA-FG-7634 TCGA-FG-7638 
       34.36        18.77        14.93        23.97        15.35        22.55 
TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8186 TCGA-FG-8187 
       20.61        20.09        12.95        13.68        16.01        20.09 
TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MY 
       14.96        22.52        15.52        38.27        10.72        23.70 
TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 
       14.76        17.82        16.41        15.02        16.44        10.59 
TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A713 TCGA-FG-A87N TCGA-FN-7833 
       28.54        10.78        22.95         5.23         7.43         0.13 
TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7472 TCGA-HT-7473 
        0.10         6.67         7.82         8.81         0.03        16.54 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 
        3.75        17.42         6.54         6.38         7.10        75.19 
TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 
       59.18        60.03       154.19         4.01         5.03        29.85 
TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 
       23.18       107.93         4.57         3.16        22.06        45.99 
TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 
       56.09        57.60         0.23        14.27         0.16        16.24 
TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7688 TCGA-HT-7690 
        0.76        44.68         6.05        42.74        31.69         0.10 
TCGA-HT-7691 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 
        0.10        17.52         6.90        14.53        39.48        19.23 
TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 
       39.09         0.23        50.63         0.49        23.61        37.15 
TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 
        0.33         0.13         3.68         5.33         2.93         1.71 
TCGA-HT-7884 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 
       11.28         1.64        16.24         9.40        63.55         0.10 
TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8109 
       21.50        33.01         6.25         0.10         0.46         3.95 
TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 
        4.70         0.23        29.59         3.88        16.04        15.72 
TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RC 
        0.23        10.49         0.13        14.01         0.07         5.33 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A74O TCGA-HW-7486 
       13.02         1.81        16.14         5.33         0.10        29.92 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 
       13.45         8.32        40.18        35.90         4.31        21.70 
TCGA-HW-8321 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-IK-8125 TCGA-KT-A74X 
       19.59        20.35         7.89        20.81        42.77         5.23 
TCGA-KT-A7W1 TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 
        4.73         6.71         1.64         2.37         2.30         4.11 
TCGA-P5-A5F1 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z 
        5.88         5.75         2.53         4.83         7.79         4.11 
TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6X3 TCGA-QH-A6X4 
        4.18        14.83        12.23         2.20         0.59         6.31 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X 
        3.91         4.73         1.91         0.23         5.03         3.48 
TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TU 
        0.07        88.83        94.03        32.65        59.38        69.07 
TCGA-S9-A6TV TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 
       18.77        34.49        31.33        21.63        16.37        17.62 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA 
       23.64        32.61         9.86        94.62        83.70         5.85 
TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI 
      106.39        62.37        72.59        80.12        32.45        84.99 
TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ 
       10.88        19.86        15.91         7.59        15.16        14.07 
TCGA-S9-A7IQ TCGA-S9-A7IY TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW 
       14.27        12.59         8.19         2.04         8.12         3.58 
TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R2 TCGA-S9-A7R4 TCGA-S9-A7R7 
        4.04        28.37        13.02        10.39        17.42        83.80 
TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA 
       18.71         5.00        49.45        48.33        49.32        34.78 
TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84I TCGA-TM-A84L 
       12.00        15.09        50.76        34.36        19.36        40.83 
TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T 
       16.50        29.92        18.90         9.44         4.57        12.00 
TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 
       33.07        30.08        13.51        26.79        10.95        27.06 
TCGA-VV-A86M TCGA-VW-A7QS 
        7.04        23.21 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             0.10              0.03 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           164.38            211.17 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            17.46             15.62 
[1] "0.1 - 164.4 (17.5)" "0.0 - 211.2 (15.6)"
[1] "hr=" "2.3"
D56V2, continuous
D56V3, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    41  55
  9P LOSS WILD-TYPE 149 185
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     41   55
  9P LOSS WILD-TYPE  149  185
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE              41               149
  MALE                55               185
[1] 2 2
[1] FALSE
D56V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  9P LOSS MUTATED            45               20                31
  9P LOSS WILD-TYPE         114               87               133
D56V5, multiclass
                   clus
vv                  9P LOSS MUTATED 9P LOSS WILD-TYPE
  ASTROCYTOMA                    45               114
  OLIGOASTROCYTOMA               20                87
  OLIGODENDROGLIOMA              31               133
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V6, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    27  69
  9P LOSS WILD-TYPE  62 272
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     27   69
  9P LOSS WILD-TYPE   62  272
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  NO               27                62
  YES              69               272
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9P LOSS MUTATED                                  0     2
  9P LOSS WILD-TYPE                                1     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9P LOSS MUTATED                           2    89
  9P LOSS WILD-TYPE                        12   311
D56V7, multiclass
                                  clus
vv                                 9P LOSS MUTATED 9P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 4
  BLACK OR AFRICAN AMERICAN                      2                12
  WHITE                                         89               311
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V8, binary
                   cls
clus                  0   1
  9P LOSS MUTATED     2  86
  9P LOSS WILD-TYPE  14 301
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      2   86
  9P LOSS WILD-TYPE   14  301
                        clus
vv                       9P LOSS MUTATED 9P LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                14
  NOT HISPANIC OR LATINO              86               301
[1] 2 2
[1] FALSE

Clustering(57) Variable = 9Q LOSS MUTATION ANALYSIS
D57V1, survival
                   sevent
clus2                 0   1
  9Q LOSS MUTATED    27  11
  9Q LOSS WILD-TYPE 325  64
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               38               389 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               11                64 
$`9Q LOSS MUTATED`
TCGA-CS-5397 TCGA-CS-6188 TCGA-CS-6666 TCGA-DB-5277 TCGA-DB-5279 TCGA-DB-A4XH 
        6.38        23.84         8.48        46.65        44.52        12.59 
TCGA-DB-A64L TCGA-DB-A75P TCGA-DU-6397 TCGA-DU-7007 TCGA-DU-7014 TCGA-DU-7304 
       11.01         3.81        46.06        62.96       117.40        23.31 
TCGA-DU-8162 TCGA-DU-8168 TCGA-DU-A5TY TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-E1-5304 
        3.98        14.17        12.20         7.23         5.98        41.13 
TCGA-E1-5307 TCGA-EZ-7264 TCGA-F6-A8O4 TCGA-FG-A87Q TCGA-HT-7471 TCGA-HT-7687 
       57.93        14.33         0.20         5.72         0.13         0.10 
TCGA-HT-7689 TCGA-HT-7692 TCGA-HT-A5RB TCGA-HT-A614 TCGA-IK-7675 TCGA-P5-A5F6 
       14.96         2.96         0.10         2.70        19.00         1.28 
TCGA-QH-A6CV TCGA-QH-A6CZ TCGA-S9-A6U9 TCGA-S9-A7IS TCGA-S9-A7R1 TCGA-TM-A84H 
       14.53         3.16        83.70         7.92       164.38        24.26 
TCGA-TM-A84J TCGA-TM-A84T 
       17.49        12.00 

$`9Q LOSS WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-6186 TCGA-CS-6290 
       40.18         0.10        21.01         9.96        17.69        17.95 
TCGA-CS-6665 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 
       12.43         7.56         8.02         7.40         6.61       122.73 
TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5278 TCGA-DB-5280 
       81.96        75.25        47.93        72.92        50.17        36.56 
TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD 
       78.28        30.08        10.29        12.72        27.62        27.02 
TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q 
       18.84        18.38        72.95        18.84        16.80         5.98 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X 
       16.08        15.42        27.81        14.73        13.64        10.92 
TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DH-5140 TCGA-DH-5141 
        7.40         6.44        10.29        30.74        19.96        31.82 
TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D 
       30.31        14.40         8.02        30.21        42.05        27.81 
TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU 
       17.19        17.19        54.25        10.22         6.58         3.45 
TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 
        6.21        18.02        14.56        17.46         6.74        13.38 
TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 
        8.45         6.81       182.33        18.94        17.49        15.16 
TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6399 
      211.17        52.11        22.42        49.02        75.16        65.75 
TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 
        1.22        87.45         7.04        11.64       133.74        19.89 
TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 
       16.83        94.52       114.08         7.96         7.73        11.47 
TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 
      156.23       138.28        14.99       105.21         6.54         8.84 
TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 
       90.77        30.67        26.30        10.36         7.96        94.32 
TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7306 
       18.94        44.02        62.01        25.91        60.30        41.98 
TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 
        2.76         5.10        23.74        20.68        21.40        19.13 
TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT 
       16.96        15.48        14.24        12.59        15.12         4.96 
TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A76K 
        3.65         5.65         8.65         2.70        77.98        11.41 
TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 TCGA-DU-A7TG TCGA-E1-5302 
       26.76         7.13        21.30       124.50        44.42        50.14 
TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 
       67.46        79.99       134.27        78.21        95.57       130.78 
TCGA-F6-A8O3 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 
        0.23        47.77        17.98        34.36        32.19        18.77 
TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 
       14.93        24.99        23.97        13.58        15.35        17.88 
TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 
       22.55        20.61        20.09        12.95        13.68        14.24 
TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT 
       16.01        20.09        14.96        22.52        15.52        38.27 
TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K 
       10.72         5.26        18.71        23.70        14.76        17.82 
TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z 
       16.41        15.02        16.44        10.59        28.54        10.78 
TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FN-7833 TCGA-HT-7467 
       22.95        43.69         5.23         7.43         0.13         0.10 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 
        6.67         7.82         8.81         0.03        16.54         3.75 
TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 
       17.42         6.54        24.26         6.38         7.10        75.19 
TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 
       59.18        60.03       154.19         4.01         5.03        29.85 
TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 
       23.18       107.93         4.57        17.29         3.16        22.06 
TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 
       45.99        56.09        57.60         0.23        14.27         0.16 
TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7688 
       16.24         0.76        44.68         6.05        42.74        31.69 
TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 
        0.10         0.10        17.52         6.90        14.53        39.48 
TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 
       19.23        39.09         0.23        50.63         0.49        23.61 
TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 
       37.15         0.33         0.13         3.68         5.33         2.93 
TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 
        1.71        11.28        31.43         1.64        16.24         9.40 
TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 
       63.55         0.10        21.50        33.01        12.23         6.25 
TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 
        0.10         0.46         2.50         3.95         4.70         0.23 
TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV 
       29.59         3.88        16.04        15.72         0.23        10.49 
TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RC TCGA-HT-A615 
        0.13        14.01         0.07        14.70         5.33        13.02 
TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 
        1.81        16.14         5.33         0.10        29.92        13.45 
TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 
        8.32        19.23        40.18        35.90         4.31        21.70 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
       21.60        19.59        17.82        20.35         7.89        20.81 
TCGA-HW-A5KM TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW 
       20.71        42.77         5.23         4.73         0.23         6.71 
TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 
        1.64         2.37         2.30         4.11         5.88         7.63 
TCGA-P5-A5F4 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z 
        0.76         5.75         2.53         4.83         7.79         4.11 
TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6X3 TCGA-QH-A6X4 
        4.18        14.83        12.23         2.20         0.59         6.31 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X 
        3.91         4.73         1.91         0.23         5.03         3.48 
TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TS 
        0.07        88.83        94.03        32.65        59.38        62.17 
TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ 
       69.07        18.77        37.84        34.49        31.33        21.63 
TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       16.37        17.62        23.64        32.61         9.86        94.62 
TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH 
        5.85       106.39        62.37        72.59        80.12        32.45 
TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP 
       84.99        10.88        19.86        15.91         7.59        15.16 
TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 
       14.07        14.27        19.63        12.59         4.21         9.37 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY 
        8.19         2.04         8.12         3.58         4.04        28.37 
TCGA-S9-A7QZ TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 
       13.02        10.39        99.06        17.42        83.80        31.59 
TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA 
       18.71         5.00        49.45        48.33        49.32        34.78 
TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84I 
       48.39        12.00        15.09        50.76        34.36        19.36 
TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S 
       40.83        16.50        29.92        18.90         9.44         4.57 
TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE 
       33.07        30.08        13.51         0.10         7.89        26.79 
TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-W9-A837 
       10.95        27.06         7.04        23.21        45.07 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             0.10              0.03 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           164.38            211.17 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           12.395            16.240 
[1] "0.1 - 164.4 (12.4)" "0.0 - 211.2 (16.2)"
[1] "hr=" "1.8"
D57V2, continuous
D57V3, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    16  22
  9Q LOSS WILD-TYPE 174 218
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     16   22
  9Q LOSS WILD-TYPE  174  218
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE              16               174
  MALE                22               218
[1] 2 2
[1] FALSE
D57V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  9Q LOSS MUTATED            15                9                14
  9Q LOSS WILD-TYPE         144               98               150
D57V5, multiclass
                   clus
vv                  9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  ASTROCYTOMA                    15               144
  OLIGOASTROCYTOMA                9                98
  OLIGODENDROGLIOMA              14               150
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V6, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED     8  30
  9Q LOSS WILD-TYPE  81 311
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      8   30
  9Q LOSS WILD-TYPE   81  311
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  NO                8                81
  YES              30               311
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9Q LOSS MUTATED                                  0     2
  9Q LOSS WILD-TYPE                                1     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9Q LOSS MUTATED                           0    34
  9Q LOSS WILD-TYPE                        14   366
D57V7, multiclass
                                  clus
vv                                 9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 4
  BLACK OR AFRICAN AMERICAN                      0                14
  WHITE                                         34               366
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V8, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED     2  34
  9Q LOSS WILD-TYPE  14 353
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      2   34
  9Q LOSS WILD-TYPE   14  353
                        clus
vv                       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                14
  NOT HISPANIC OR LATINO              34               353
[1] 2 2
[1] FALSE

Clustering(58) Variable = 10P LOSS MUTATION ANALYSIS
D58V1, survival
                    sevent
clus2                  0   1
  10P LOSS MUTATED    36  32
  10P LOSS WILD-TYPE 316  43
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                68                359 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                32                 43 
$`10P LOSS MUTATED`
TCGA-CS-4941 TCGA-CS-5395 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 TCGA-DB-5279 
        7.69        21.01         6.38        17.69        23.84        44.52 
TCGA-DB-A64L TCGA-DB-A64O TCGA-DH-5140 TCGA-DH-A669 TCGA-DU-5847 TCGA-DU-5852 
       11.01        18.84        19.96        30.21        18.02         6.74 
TCGA-DU-5854 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-7006 
        8.45         7.04        11.64        19.89        16.83        11.47 
TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7298 TCGA-DU-8158 
        6.54         8.84        10.36         7.96        18.94         5.10 
TCGA-DU-8161 TCGA-DU-8165 TCGA-DU-8167 TCGA-DU-A5TY TCGA-DU-A76K TCGA-DU-A76L 
       23.74        19.13        15.48        12.20        11.41        26.76 
TCGA-DU-A76R TCGA-E1-5311 TCGA-FG-6688 TCGA-FG-6692 TCGA-FG-7643 TCGA-FG-A4MU 
       21.30       134.27        18.77        13.58        20.09        10.72 
TCGA-FG-A4MW TCGA-FG-A70Z TCGA-FG-A87Q TCGA-HT-7471 TCGA-HT-7857 TCGA-HT-7860 
        5.26        10.78         5.72         0.13         0.23         0.49 
TCGA-HT-7882 TCGA-HT-8011 TCGA-HT-8104 TCGA-HT-8110 TCGA-HT-8564 TCGA-HT-A4DS 
        1.71        16.24        12.23         4.70        15.72         0.23 
TCGA-HT-A5RA TCGA-HT-A5RC TCGA-HT-A617 TCGA-HW-A5KK TCGA-KT-A7W1 TCGA-QH-A6CS 
       14.70         5.33        16.14         7.89         4.73         4.18 
TCGA-QH-A6CV TCGA-QH-A6XC TCGA-S9-A6TS TCGA-S9-A6U0 TCGA-S9-A6UA TCGA-S9-A6WM 
       14.53         5.03        62.17        16.37         5.85        19.86 
TCGA-S9-A7IX TCGA-S9-A7R2 TCGA-S9-A89V TCGA-TM-A7C3 TCGA-TM-A84B TCGA-TM-A84I 
       19.63        10.39        18.71        49.45        12.00        19.36 
TCGA-TM-A84J TCGA-VM-A8CD 
       17.49         7.89 

$`10P LOSS WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5393 
        4.70        43.89        18.15        10.62        64.64        40.18 
TCGA-CS-5394 TCGA-CS-5396 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 
        0.10         9.96        17.95        12.43         8.48         7.56 
TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 
        8.02         7.40         6.61       122.73        81.96        75.25 
TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5280 TCGA-DB-5281 
       47.93        72.92        46.65        50.17        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       30.08        10.29        12.72        27.62        27.02        18.84 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R 
       18.38        72.95        12.59        16.80         5.98        16.08 
TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K 
       15.42        27.81        14.73        13.64        10.92         7.40 
TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5141 TCGA-DH-5142 
        6.44        10.29        30.74         3.81        31.82        30.31 
TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G 
       14.40         8.02        42.05        27.81        17.19        17.19 
TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5849 
       54.25        10.22         6.58         3.45         6.21        14.56 
TCGA-DU-5851 TCGA-DU-5853 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 
       17.46        13.38         6.81       182.33        18.94        17.49 
TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       15.16       211.17        52.11        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6404 TCGA-DU-6407 
       46.06        65.75         1.22        87.45       133.74        94.52 
TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 
      114.08         7.96         7.73        62.96       156.23       138.28 
TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 
       14.99       105.21       117.40        90.77        30.67        26.30 
TCGA-DU-7294 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 
       94.32        44.02        62.01        25.91        60.30        23.31 
TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8166 
       41.98         2.76         3.98        20.68        21.40        16.96 
TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU 
       14.17        14.24        12.59        15.12         4.96         3.65 
TCGA-DU-A5TW TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 
        5.65         8.65         2.70        77.98         7.23         5.98 
TCGA-DU-A76O TCGA-DU-A7T8 TCGA-DU-A7TG TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 
        7.13       124.50        44.42        50.14        67.46        41.13 
TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 
       79.99        57.93        78.21        95.57       130.78        14.33 
TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 
        0.23         0.20        47.77        17.98        34.36        32.19 
TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 
       14.93        24.99        23.97        15.35        17.88        22.55 
TCGA-FG-7641 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 
       20.61        12.95        13.68        14.24        16.01        20.09 
TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MX TCGA-FG-A4MY 
       14.96        22.52        15.52        38.27        18.71        23.70 
TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 
       14.76        17.82        16.41        15.02        16.44        10.59 
TCGA-FG-A70Y TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FN-7833 
       28.54        22.95        43.69         5.23         7.43         0.13 
TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7472 TCGA-HT-7473 
        0.10         6.67         7.82         8.81         0.03        16.54 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 
        3.75        17.42         6.54        24.26         6.38         7.10 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
       75.19        59.18        60.03       154.19         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 
       29.85        23.18       107.93         4.57        17.29         3.16 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
       22.06        45.99        56.09        57.60         0.23        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 
        0.16        16.24         0.76        44.68         6.05        42.74 
TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 
        0.10        31.69        14.96         0.10         0.10         2.96 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 
       17.52         6.90        14.53        39.48        19.23        39.09 
TCGA-HT-7858 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 
       50.63        23.61        37.15         0.33         0.13         3.68 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8012 
        5.33         2.93        11.28        31.43         1.64         9.40 
TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8105 TCGA-HT-8106 
       63.55         0.10        21.50        33.01         6.25         0.10 
TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 
        0.46         2.50         3.95         0.23        29.59         3.88 
TCGA-HT-8563 TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RB 
       16.04        10.49         0.13        14.01         0.07         0.10 
TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A618 TCGA-HT-A74O TCGA-HW-7486 
        2.70        13.02         1.81         5.33         0.10        29.92 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 
       13.45         8.32        19.23        40.18        35.90         4.31 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KL 
       21.70        21.60        19.59        17.82        20.35        20.81 
TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-P5-A5EV TCGA-P5-A5EW 
       20.71        19.00        42.77         5.23         0.23         6.71 
TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 
        1.64         2.37         2.30         4.11         5.88         7.63 
TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X 
        0.76         1.28         5.75         2.53         4.83         7.79 
TCGA-QH-A65Z TCGA-QH-A6CU TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
        4.11        14.83        12.23         2.20         3.16         0.59 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A86X 
        6.31         3.91         4.73         1.91         0.23         3.48 
TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TU 
        0.07        88.83        94.03        32.65        59.38        69.07 
TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U1 
       18.77        37.84        34.49        31.33        21.63        17.62 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UB 
       23.64        32.61         9.86        94.62        83.70       106.39 
TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL 
       62.37        72.59        80.12        32.45        84.99        10.88 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
       15.91         7.59        15.16        14.07        14.27         7.92 
TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       12.59         4.21         9.37         8.19         2.04         8.12 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R3 
        3.58         4.04        28.37        13.02       164.38        99.06 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89Z TCGA-TM-A7C4 TCGA-TM-A7C5 
       17.42        83.80        31.59         5.00        48.33        49.32 
TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H 
       34.78        48.39        15.09        50.76        34.36        24.26 
TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S 
       40.83        16.50        29.92        18.90         9.44         4.57 
TCGA-TM-A84T TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CE 
       12.00        33.07        30.08        13.51         0.10        26.79 
TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-W9-A837 
       10.95        27.06         7.04        23.21        45.07 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              0.13               0.03 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            134.27             211.17 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            12.215             16.440 
[1] "0.1 - 134.3 (12.2)" "0.0 - 211.2 (16.4)"
[1] "hr=" "8.2"
D58V2, continuous
D58V3, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    33  35
  10P LOSS WILD-TYPE 157 205
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     33   35
  10P LOSS WILD-TYPE  157  205
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE               33                157
  MALE                 35                205
[1] 2 2
[1] FALSE
D58V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  10P LOSS MUTATED            41               13                14
  10P LOSS WILD-TYPE         118               94               150
D58V5, multiclass
                   clus
vv                  10P LOSS MUTATED 10P LOSS WILD-TYPE
  ASTROCYTOMA                     41                118
  OLIGOASTROCYTOMA                13                 94
  OLIGODENDROGLIOMA               14                150
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V6, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    12  56
  10P LOSS WILD-TYPE  77 285
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     12   56
  10P LOSS WILD-TYPE   77  285
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  NO                12                 77
  YES               56                285
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10P LOSS MUTATED                                  1     1
  10P LOSS WILD-TYPE                                0     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10P LOSS MUTATED                           5    60
  10P LOSS WILD-TYPE                         9   340
D58V7, multiclass
                                  clus
vv                                 10P LOSS MUTATED 10P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           1                  5
  BLACK OR AFRICAN AMERICAN                       5                  9
  WHITE                                          60                340
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V8, binary
                    cls
clus                   0   1
  10P LOSS MUTATED     2  61
  10P LOSS WILD-TYPE  14 326
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      2   61
  10P LOSS WILD-TYPE   14  326
                        clus
vv                       10P LOSS MUTATED 10P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                 14
  NOT HISPANIC OR LATINO               61                326
[1] 2 2
[1] FALSE

Clustering(59) Variable = 10Q LOSS MUTATION ANALYSIS
D59V1, survival
                    sevent
clus2                  0   1
  10Q LOSS MUTATED    43  37
  10Q LOSS WILD-TYPE 309  38
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                80                347 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                37                 38 
$`10Q LOSS MUTATED`
TCGA-CS-4941 TCGA-CS-5395 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6665 
        7.69        21.01         6.38        17.69        23.84        12.43 
TCGA-DB-5279 TCGA-DB-A64L TCGA-DB-A64O TCGA-DH-5140 TCGA-DH-A669 TCGA-DH-A7UU 
       44.52        11.01        18.84        19.96        30.21         3.45 
TCGA-DU-5847 TCGA-DU-5852 TCGA-DU-5854 TCGA-DU-6396 TCGA-DU-6399 TCGA-DU-6402 
       18.02         6.74         8.45        75.16        65.75         7.04 
TCGA-DU-6403 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-7006 TCGA-DU-7008 TCGA-DU-7010 
       11.64        19.89        16.83        11.47       156.23        14.99 
TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7298 
        6.54         8.84       117.40        10.36         7.96        18.94 
TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8165 TCGA-DU-8167 TCGA-DU-A5TY TCGA-DU-A76K 
        5.10        23.74        19.13        15.48        12.20        11.41 
TCGA-DU-A76L TCGA-DU-A76R TCGA-E1-5311 TCGA-FG-6688 TCGA-FG-6692 TCGA-FG-7643 
       26.76        21.30       134.27        18.77        13.58        20.09 
TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A6J3 TCGA-FG-A70Z TCGA-FG-A87Q TCGA-HT-7471 
       10.72         5.26        10.59        10.78         5.72         0.13 
TCGA-HT-7483 TCGA-HT-7857 TCGA-HT-7860 TCGA-HT-7882 TCGA-HT-8011 TCGA-HT-8104 
      154.19         0.23         0.49         1.71        16.24        12.23 
TCGA-HT-8110 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A5R7 TCGA-HT-A5RA TCGA-HT-A5RC 
        4.70        15.72         0.23        14.01        14.70         5.33 
TCGA-HT-A617 TCGA-HW-8321 TCGA-HW-A5KK TCGA-KT-A7W1 TCGA-P5-A5EZ TCGA-QH-A6CS 
       16.14        19.59         7.89         4.73         2.30         4.18 
TCGA-QH-A6CV TCGA-QH-A6CX TCGA-QH-A6XC TCGA-S9-A6TS TCGA-S9-A6U0 TCGA-S9-A6UA 
       14.53        12.23         5.03        62.17        16.37         5.85 
TCGA-S9-A6WM TCGA-S9-A7IX TCGA-S9-A7R2 TCGA-TM-A7C3 TCGA-TM-A84B TCGA-TM-A84I 
       19.86        19.63        10.39        49.45        12.00        19.36 
TCGA-TM-A84J TCGA-VM-A8CD 
       17.49         7.89 

$`10Q LOSS WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5393 
        4.70        43.89        18.15        10.62        64.64        40.18 
TCGA-CS-5394 TCGA-CS-5396 TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
        0.10         9.96        17.95         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 
       72.92        46.65        50.17        36.56        78.28        30.08 
TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF 
       10.29        12.72        27.62        27.02        18.84        18.38 
TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S 
       72.95        12.59        16.80         5.98        16.08        15.42 
TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L 
       27.81        14.73        13.64        10.92         7.40         6.44 
TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 
       10.29        30.74         3.81        31.82        30.31        14.40 
TCGA-DH-5144 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR 
        8.02        42.05        27.81        17.19        17.19        54.25 
TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UV TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5853 
       10.22         6.58         6.21        14.56        17.46        13.38 
TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 
        6.81       182.33        18.94        17.49        15.16       211.17 
TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6397 TCGA-DU-6400 TCGA-DU-6401 
       52.11        22.42        49.02        46.06         1.22        87.45 
TCGA-DU-6404 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7007 
      133.74        94.52       114.08         7.96         7.73        62.96 
TCGA-DU-7009 TCGA-DU-7011 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7294 
      138.28       105.21        90.77        30.67        26.30        94.32 
TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 
       44.02        62.01        25.91        60.30        23.31        41.98 
TCGA-DU-7309 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-8168 
        2.76         3.98        20.68        21.40        16.96        14.17 
TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW 
       14.24        12.59        15.12         4.96         3.65         5.65 
TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76O 
        8.65         2.70        77.98         7.23         5.98         7.13 
TCGA-DU-A7T8 TCGA-DU-A7TG TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 
      124.50        44.42        50.14        67.46        41.13        79.99 
TCGA-E1-5307 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 TCGA-F6-A8O3 
       57.93        78.21        95.57       130.78        14.33         0.23 
TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6689 
        0.20        47.77        17.98        34.36        32.19        14.93 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 
       24.99        23.97        15.35        17.88        22.55        20.61 
TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 
       12.95        13.68        14.24        16.01        20.09        14.96 
TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J 
       22.52        15.52        38.27        18.71        23.70        14.76 
TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A70Y TCGA-FG-A710 
       17.82        16.41        15.02        16.44        28.54        22.95 
TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 
       43.69         5.23         7.43         0.13         0.10         6.67 
TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 
        7.82         8.81         0.03        16.54         3.75        17.42 
TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 
        6.54        24.26         6.38         7.10        75.19        59.18 
TCGA-HT-7482 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 
       60.03         4.01         5.03        29.85        23.18       107.93 
TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 
        4.57        17.29         3.16        22.06        45.99        56.09 
TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 
       57.60         0.23        14.27         0.16        16.24         0.76 
TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 
       44.68         6.05        42.74         0.10        31.69        14.96 
TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 
        0.10         0.10         2.96        17.52         6.90        14.53 
TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7858 TCGA-HT-7873 TCGA-HT-7874 
       39.48        19.23        39.09        50.63        23.61        37.15 
TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7884 
        0.33         0.13         3.68         5.33         2.93        11.28 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 
       31.43         1.64         9.40        63.55         0.10        21.50 
TCGA-HT-8019 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 
       33.01         6.25         0.10         0.46         2.50         3.95 
TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-A4DV TCGA-HT-A5R5 
        0.23        29.59         3.88        16.04        10.49         0.13 
TCGA-HT-A5R9 TCGA-HT-A5RB TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A618 
        0.07         0.10         2.70        13.02         1.81         5.33 
TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 
        0.10        29.92        13.45         8.32        19.23        40.18 
TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8322 TCGA-HW-A5KJ 
       35.90         4.31        21.70        21.60        17.82        20.35 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-P5-A5EV 
       20.81        20.71        19.00        42.77         5.23         0.23 
TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 
        6.71         1.64         2.37         4.11         5.88         7.63 
TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X 
        0.76         1.28         5.75         2.53         4.83         7.79 
TCGA-QH-A65Z TCGA-QH-A6CU TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
        4.11        14.83         2.20         3.16         0.59         6.31 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A86X TCGA-QH-A870 
        3.91         4.73         1.91         0.23         3.48         0.07 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TU TCGA-S9-A6TV 
       88.83        94.03        32.65        59.38        69.07        18.77 
TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U1 TCGA-S9-A6U2 
       37.84        34.49        31.33        21.63        17.62        23.64 
TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UB TCGA-S9-A6WD 
       32.61         9.86        94.62        83.70       106.39        62.37 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN 
       72.59        80.12        32.45        84.99        10.88        15.91 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IY 
        7.59        15.16        14.07        14.27         7.92        12.59 
TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW 
        4.21         9.37         8.19         2.04         8.12         3.58 
TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R3 TCGA-S9-A7R4 
        4.04        28.37        13.02       164.38        99.06        17.42 
TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C4 TCGA-TM-A7C5 
       83.80        31.59        18.71         5.00        48.33        49.32 
TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H 
       34.78        48.39        15.09        50.76        34.36        24.26 
TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S 
       40.83        16.50        29.92        18.90         9.44         4.57 
TCGA-TM-A84T TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CE 
       12.00        33.07        30.08        13.51         0.10        26.79 
TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-W9-A837 
       10.95        27.06         7.04        23.21        45.07 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              0.13               0.03 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            156.23             211.17 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            13.005             16.500 
[1] "0.1 - 156.2 (13.0)" "0.0 - 211.2 (16.5)"
[1] "hr=" "5.3"
D59V2, continuous
D59V3, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    39  41
  10Q LOSS WILD-TYPE 151 199
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     39   41
  10Q LOSS WILD-TYPE  151  199
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE               39                151
  MALE                 41                199
[1] 2 2
[1] FALSE
D59V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  10Q LOSS MUTATED            48               15                17
  10Q LOSS WILD-TYPE         111               92               147
D59V5, multiclass
                   clus
vv                  10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  ASTROCYTOMA                     48                111
  OLIGOASTROCYTOMA                15                 92
  OLIGODENDROGLIOMA               17                147
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V6, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    15  65
  10Q LOSS WILD-TYPE  74 276
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     15   65
  10Q LOSS WILD-TYPE   74  276
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  NO                15                 74
  YES               65                276
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10Q LOSS MUTATED                                  1     1
  10Q LOSS WILD-TYPE                                0     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10Q LOSS MUTATED                           5    72
  10Q LOSS WILD-TYPE                         9   328
D59V7, multiclass
                                  clus
vv                                 10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           1                  5
  BLACK OR AFRICAN AMERICAN                       5                  9
  WHITE                                          72                328
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V8, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED     2  73
  10Q LOSS WILD-TYPE  14 314
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      2   73
  10Q LOSS WILD-TYPE   14  314
                        clus
vv                       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                 14
  NOT HISPANIC OR LATINO               73                314
[1] 2 2
[1] FALSE

Clustering(60) Variable = 11P LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                  0   1
  11P LOSS MUTATED    39  14
  11P LOSS WILD-TYPE 313  61
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                53                374 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                14                 61 
$`11P LOSS MUTATED`
TCGA-CS-6665 TCGA-DB-5277 TCGA-DH-5140 TCGA-DH-5142 TCGA-DH-A66G TCGA-DH-A7UT 
       12.43        46.65        19.96        30.31        17.19         6.58 
TCGA-DH-A7UU TCGA-DU-6396 TCGA-DU-6408 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 
        3.45        75.16       114.08        11.47        62.96       156.23 
TCGA-DU-7010 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-8158 TCGA-DU-8165 TCGA-DU-A5TR 
       14.99       117.40        90.77         5.10        19.13        12.59 
TCGA-DU-A5TS TCGA-E1-5302 TCGA-E1-5304 TCGA-FG-6689 TCGA-FG-A4MW TCGA-FG-A60L 
       15.12        50.14        41.13        14.93         5.26        16.41 
TCGA-HT-7470 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7601 TCGA-HT-7686 TCGA-HT-7693 
        8.81        24.26         6.38         5.03        42.74        17.52 
TCGA-HT-7873 TCGA-HT-7902 TCGA-HT-8013 TCGA-HT-8018 TCGA-HT-8111 TCGA-HT-8564 
       23.61        31.43        63.55        21.50         0.23        15.72 
TCGA-HT-A5R7 TCGA-HT-A614 TCGA-HT-A616 TCGA-HT-A618 TCGA-HW-8319 TCGA-IK-7675 
       14.01         2.70         1.81         5.33        21.70        19.00 
TCGA-P5-A5F6 TCGA-QH-A65S TCGA-S9-A6TV TCGA-S9-A6WM TCGA-S9-A7R7 TCGA-S9-A89V 
        1.28         2.53        18.77        19.86        83.80        18.71 
TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A84I TCGA-TM-A84J 
        5.00        49.45        48.33        19.36        17.49 

$`11P LOSS WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 
       23.84        17.95         8.48         7.56         8.02         7.40 
TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 
        6.61       122.73        81.96        75.25        47.93        72.92 
TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA 
       50.17        44.52        36.56        78.28        30.08        10.29 
TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG 
       12.72        27.62        27.02        18.84        18.38        72.95 
TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R 
       12.59        11.01        18.84        16.80         5.98        16.08 
TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K 
       15.42        27.81        14.73        13.64        10.92         7.40 
TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5141 TCGA-DH-5143 
        6.44        10.29        30.74         3.81        31.82        14.40 
TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A7UR 
        8.02        30.21        42.05        27.81        17.19        54.25 
TCGA-DH-A7US TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
       10.22         6.21        18.02        14.56        17.46         6.74 
TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 
       13.38         8.45         6.81       182.33        18.94        17.49 
TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6397 
       15.16       211.17        52.11        22.42        49.02        46.06 
TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 
       65.75         1.22        87.45         7.04        11.64       133.74 
TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7009 
       19.89        16.83        94.52         7.96         7.73       138.28 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 
      105.21         6.54         8.84        30.67        26.30        10.36 
TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 
        7.96        94.32        18.94        44.02        62.01        25.91 
TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8161 TCGA-DU-8162 
       60.30        23.31        41.98         2.76        23.74         3.98 
TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP 
       20.68        21.40        16.96        15.48        14.17        14.24 
TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 
        4.96         3.65         5.65        12.20         8.65         2.70 
TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O 
       77.98         7.23         5.98        11.41        26.76         7.13 
TCGA-DU-A76R TCGA-DU-A7T8 TCGA-DU-A7TG TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5307 
       21.30       124.50        44.42        67.46        79.99        57.93 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 TCGA-F6-A8O3 
      134.27        78.21        95.57       130.78        14.33         0.23 
TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 
        0.20        47.77        17.98        34.36        32.19        18.77 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 
       24.99        23.97        13.58        15.35        17.88        22.55 
TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 
       20.61        20.09        12.95        13.68        14.24        16.01 
TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU 
       20.09        14.96        22.52        15.52        38.27        10.72 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A6IZ TCGA-FG-A6J1 
       18.71        23.70        14.76        17.82        15.02        16.44 
TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 
       10.59        28.54        10.78        22.95        43.69         5.23 
TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 
        7.43         5.72         0.13         0.10         6.67         7.82 
TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 
        0.13         0.03        16.54         3.75        17.42         6.54 
TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 
        7.10        75.19        59.18        60.03       154.19         4.01 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 
       29.85        23.18       107.93         4.57        17.29         3.16 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
       22.06        45.99        56.09        57.60         0.23        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7687 
        0.16        16.24         0.76        44.68         6.05         0.10 
TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7694 
       31.69        14.96         0.10         0.10         2.96         6.90 
TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 
       14.53        39.48        19.23        39.09         0.23        50.63 
TCGA-HT-7860 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 
        0.49        37.15         0.33         0.13         3.68         5.33 
TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 
        2.93         1.71        11.28         1.64        16.24         9.40 
TCGA-HT-8015 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 
        0.10        33.01        12.23         6.25         0.10         0.46 
TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 
        2.50         3.95         4.70        29.59         3.88        16.04 
TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB 
        0.23        10.49         0.13         0.07        14.70         0.10 
TCGA-HT-A5RC TCGA-HT-A615 TCGA-HT-A617 TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 
        5.33        13.02        16.14         0.10        29.92        13.45 
TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8320 
        8.32        19.23        40.18        35.90         4.31        21.60 
TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM 
       19.59        17.82        20.35         7.89        20.81        20.71 
TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX 
       42.77         5.23         4.73         0.23         6.71         1.64 
TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 
        2.37         2.30         4.11         5.88         7.63         0.76 
TCGA-QH-A65R TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU 
        5.75         4.83         7.79         4.11         4.18        14.83 
TCGA-QH-A6CV TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
       14.53        12.23         2.20         3.16         0.59         6.31 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X 
        3.91         4.73         1.91         0.23         5.03         3.48 
TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TS 
        0.07        88.83        94.03        32.65        59.38        62.17 
TCGA-S9-A6TU TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 
       69.07        37.84        34.49        31.33        21.63        16.37 
TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
       17.62        23.64        32.61         9.86        94.62        83.70 
TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH 
        5.85       106.39        62.37        72.59        80.12        32.45 
TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ 
       84.99        10.88        15.91         7.59        15.16        14.07 
TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 
       14.27         7.92        19.63        12.59         4.21         9.37 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY 
        8.19         2.04         8.12         3.58         4.04        28.37 
TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R8 
       13.02       164.38        10.39        99.06        17.42        31.59 
TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F 
       49.32        34.78        48.39        12.00        15.09        50.76 
TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q 
       34.36        24.26        40.83        16.50        29.92        18.90 
TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA 
        9.44         4.57        12.00        33.07        30.08        13.51 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M 
        0.10         7.89        26.79        10.95        27.06         7.04 
TCGA-VW-A7QS TCGA-W9-A837 
       23.21        45.07 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              0.23               0.03 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
            156.23             211.17 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
            18.710             15.255 
[1] "0.2 - 156.2 (18.7)" "0.0 - 211.2 (15.3)"
[1] "hr=" "1.4"
D60V2, continuous
D60V3, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    26  27
  11P LOSS WILD-TYPE 164 213
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     26   27
  11P LOSS WILD-TYPE  164  213
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE               26                164
  MALE                 27                213
[1] 2 2
[1] FALSE
D60V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  11P LOSS MUTATED            29               12                12
  11P LOSS WILD-TYPE         130               95               152
D60V5, multiclass
                   clus
vv                  11P LOSS MUTATED 11P LOSS WILD-TYPE
  ASTROCYTOMA                     29                130
  OLIGOASTROCYTOMA                12                 95
  OLIGODENDROGLIOMA               12                152
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V6, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    13  40
  11P LOSS WILD-TYPE  76 301
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     13   40
  11P LOSS WILD-TYPE   76  301
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  NO                13                 76
  YES               40                301
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11P LOSS MUTATED                                  0     0
  11P LOSS WILD-TYPE                                1     6
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11P LOSS MUTATED                           1    52
  11P LOSS WILD-TYPE                        13   348
D60V7, multiclass
                                  clus
vv                                 11P LOSS MUTATED 11P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  6
  BLACK OR AFRICAN AMERICAN                       1                 13
  WHITE                                          52                348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V8, binary
                    cls
clus                   0   1
  11P LOSS MUTATED     2  51
  11P LOSS WILD-TYPE  14 336
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      2   51
  11P LOSS WILD-TYPE   14  336
                        clus
vv                       11P LOSS MUTATED 11P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                 14
  NOT HISPANIC OR LATINO               51                336
[1] 2 2
[1] FALSE

Clustering(61) Variable = 11Q LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                  0   1
  11Q LOSS MUTATED    13   6
  11Q LOSS WILD-TYPE 339  69
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                19                408 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 6                 69 
$`11Q LOSS MUTATED`
TCGA-DH-5140 TCGA-DU-7006 TCGA-DU-7010 TCGA-DU-8158 TCGA-DU-8165 TCGA-E1-5304 
       19.96        11.47        14.99         5.10        19.13        41.13 
TCGA-FG-A4MW TCGA-HT-7477 TCGA-HT-8018 TCGA-HT-8111 TCGA-HT-8564 TCGA-HT-A5R7 
        5.26        24.26        21.50         0.23        15.72        14.01 
TCGA-HT-A614 TCGA-P5-A5F6 TCGA-S9-A6TV TCGA-S9-A6WM TCGA-S9-A89V TCGA-TM-A7C3 
        2.70         1.28        18.77        19.86        18.71        49.45 
TCGA-TM-A84I 
       19.36 

$`11Q LOSS WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        46.65        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       30.08        10.29        12.72        27.62        27.02        18.84 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       18.38        72.95        12.59        11.01        18.84        16.80 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        16.08        15.42        27.81        14.73        13.64 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       10.92         7.40         6.44        10.29        30.74         3.81 
TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B 
       31.82        30.31        14.40         8.02        30.21        42.05 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT 
       27.81        17.19        17.19        54.25        10.22         6.58 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
        3.45         6.21        18.02        14.56        17.46         6.74 
TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 
       13.38         8.45         6.81       182.33        18.94        17.49 
TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       15.16       211.17        52.11        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       46.06        65.75         1.22        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 
      133.74        19.89        16.83        94.52       114.08         7.96 
TCGA-DU-6542 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7011 TCGA-DU-7012 
        7.73        62.96       156.23       138.28       105.21         6.54 
TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 
        8.84       117.40        90.77        30.67        26.30        10.36 
TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 
        7.96        94.32        18.94        44.02        62.01        25.91 
TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8161 TCGA-DU-8162 
       60.30        23.31        41.98         2.76        23.74         3.98 
TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP 
       20.68        21.40        16.96        15.48        14.17        14.24 
TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY 
       12.59        15.12         4.96         3.65         5.65        12.20 
TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K 
        8.65         2.70        77.98         7.23         5.98        11.41 
TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 TCGA-DU-A7TG TCGA-E1-5302 
       26.76         7.13        21.30       124.50        44.42        50.14 
TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 
       67.46        79.99        57.93       134.27        78.21        95.57 
TCGA-E1-5322 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 
      130.78        14.33         0.23         0.20        47.77        17.98 
TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 
       34.36        32.19        18.77        14.93        24.99        23.97 
TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 
       13.58        15.35        17.88        22.55        20.61        20.09 
TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 
       12.95        13.68        14.24        16.01        20.09        14.96 
TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MX TCGA-FG-A4MY 
       22.52        15.52        38.27        10.72        18.71        23.70 
TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 
       14.76        17.82        16.41        15.02        16.44        10.59 
TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N 
       28.54        10.78        22.95        43.69         5.23         7.43 
TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 
        5.72         0.13         0.10         6.67         7.82         8.81 
TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 
        0.13         0.03        16.54         3.75        17.42         6.54 
TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 
        6.38         7.10        75.19        59.18        60.03       154.19 
TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 
        4.01         5.03        29.85        23.18       107.93         4.57 
TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 
       17.29         3.16        22.06        45.99        56.09        57.60 
TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 
        0.23        14.27         0.16        16.24         0.76        44.68 
TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 
        6.05        42.74         0.10        31.69        14.96         0.10 
TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 
        0.10         2.96        17.52         6.90        14.53        39.48 
TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 
       19.23        39.09         0.23        50.63         0.49        23.61 
TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 
       37.15         0.33         0.13         3.68         5.33         2.93 
TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 
        1.71        11.28        31.43         1.64        16.24         9.40 
TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 
       63.55         0.10        33.01        12.23         6.25         0.10 
TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8113 TCGA-HT-8114 
        0.46         2.50         3.95         4.70        29.59         3.88 
TCGA-HT-8563 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R9 TCGA-HT-A5RA 
       16.04         0.23        10.49         0.13         0.07        14.70 
TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 
        0.10         5.33        13.02         1.81        16.14         5.33 
TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 
        0.10        29.92        13.45         8.32        19.23        40.18 
TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 
       35.90         4.31        21.70        21.60        19.59        17.82 
TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 
       20.35         7.89        20.81        20.71        19.00        42.77 
TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY 
        5.23         4.73         0.23         6.71         1.64         2.37 
TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-QH-A65R 
        2.30         4.11         5.88         7.63         0.76         5.75 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU 
        2.53         4.83         7.79         4.11         4.18        14.83 
TCGA-QH-A6CV TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
       14.53        12.23         2.20         3.16         0.59         6.31 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X 
        3.91         4.73         1.91         0.23         5.03         3.48 
TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TS 
        0.07        88.83        94.03        32.65        59.38        62.17 
TCGA-S9-A6TU TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 
       69.07        37.84        34.49        31.33        21.63        16.37 
TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
       17.62        23.64        32.61         9.86        94.62        83.70 
TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH 
        5.85       106.39        62.37        72.59        80.12        32.45 
TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ 
       84.99        10.88        15.91         7.59        15.16        14.07 
TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 
       14.27         7.92        19.63        12.59         4.21         9.37 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY 
        8.19         2.04         8.12         3.58         4.04        28.37 
TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 
       13.02       164.38        10.39        99.06        17.42        83.80 
TCGA-S9-A7R8 TCGA-S9-A89Z TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF 
       31.59         5.00        48.33        49.32        34.78        48.39 
TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84J 
       12.00        15.09        50.76        34.36        24.26        17.49 
TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S 
       40.83        16.50        29.92        18.90         9.44         4.57 
TCGA-TM-A84T TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD 
       12.00        33.07        30.08        13.51         0.10         7.89 
TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-W9-A837 
       26.79        10.95        27.06         7.04        23.21        45.07 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              0.23               0.03 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             49.45             211.17 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            18.710             15.715 
[1] "0.2 - 49.5 (18.7)"  "0.0 - 211.2 (15.7)"
[1] "hr=" "3.3"
D61V2, continuous
D61V3, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED     9  10
  11Q LOSS WILD-TYPE 181 230
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      9   10
  11Q LOSS WILD-TYPE  181  230
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE                9                181
  MALE                 10                230
[1] 2 2
[1] FALSE
D61V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  11Q LOSS MUTATED            11                6                 2
  11Q LOSS WILD-TYPE         148              101               162
D61V5, multiclass
                   clus
vv                  11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  ASTROCYTOMA                     11                148
  OLIGOASTROCYTOMA                 6                101
  OLIGODENDROGLIOMA                2                162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V6, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED     2  17
  11Q LOSS WILD-TYPE  87 324
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      2   17
  11Q LOSS WILD-TYPE   87  324
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  NO                 2                 87
  YES               17                324
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11Q LOSS MUTATED                                  0     0
  11Q LOSS WILD-TYPE                                1     6
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11Q LOSS MUTATED                           0    19
  11Q LOSS WILD-TYPE                        14   381
D61V7, multiclass
                                  clus
vv                                 11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  6
  BLACK OR AFRICAN AMERICAN                       0                 14
  WHITE                                          19                381
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V8, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED     1  18
  11Q LOSS WILD-TYPE  15 369
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      1   18
  11Q LOSS WILD-TYPE   15  369
                        clus
vv                       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 15
  NOT HISPANIC OR LATINO               18                369
[1] 2 2
[1] FALSE

Clustering(62) Variable = 12P LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                  0   1
  12P LOSS MUTATED    18   2
  12P LOSS WILD-TYPE 334  73
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                20                407 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 2                 73 
$`12P LOSS MUTATED`
TCGA-CS-6665 TCGA-DB-5279 TCGA-DB-A4XH TCGA-DU-5871 TCGA-DU-6542 TCGA-DU-A6S6 
       12.43        44.52        12.59        18.94         7.73        77.98 
TCGA-DU-A76R TCGA-E1-5302 TCGA-FG-A6J3 TCGA-HT-7470 TCGA-HT-7478 TCGA-HT-7686 
       21.30        50.14        10.59         8.81         6.38        42.74 
TCGA-HT-8106 TCGA-HT-8108 TCGA-HT-A5R7 TCGA-P5-A5EW TCGA-P5-A5F4 TCGA-S9-A6U1 
        0.10         2.50        14.01         6.71         0.76        17.62 
TCGA-S9-A7R4 TCGA-S9-A89V 
       17.42        18.71 

$`12P LOSS WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 
       23.84        17.95         8.48         7.56         8.02         7.40 
TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 
        6.61       122.73        81.96        75.25        47.93        72.92 
TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA 
       46.65        50.17        36.56        78.28        30.08        10.29 
TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG 
       12.72        27.62        27.02        18.84        18.38        72.95 
TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S 
       11.01        18.84        16.80         5.98        16.08        15.42 
TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L 
       27.81        14.73        13.64        10.92         7.40         6.44 
TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 
       10.29        30.74         3.81        19.96        31.82        30.31 
TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F 
       14.40         8.02        30.21        42.05        27.81        17.19 
TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV 
       17.19        54.25        10.22         6.58         3.45         6.21 
TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 
       18.02        14.56        17.46         6.74        13.38         8.45 
TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 
        6.81       182.33        17.49        15.16       211.17        52.11 
TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 
       22.42        49.02        75.16        46.06        65.75         1.22 
TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 
       87.45         7.04        11.64       133.74        19.89        16.83 
TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 
       94.52       114.08         7.96        11.47        62.96       156.23 
TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 
      138.28        14.99       105.21         6.54         8.84       117.40 
TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 
       90.77        30.67        26.30        10.36         7.96        94.32 
TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 
       18.94        44.02        62.01        25.91        60.30        23.31 
TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 
       41.98         2.76         5.10        23.74         3.98        20.68 
TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP 
       21.40        19.13        16.96        15.48        14.17        14.24 
TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY 
       12.59        15.12         4.96         3.65         5.65        12.20 
TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L 
        8.65         2.70         7.23         5.98        11.41        26.76 
TCGA-DU-A76O TCGA-DU-A7T8 TCGA-DU-A7TG TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 
        7.13       124.50        44.42        67.46        41.13        79.99 
TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 
       57.93       134.27        78.21        95.57       130.78        14.33 
TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 
        0.23         0.20        47.77        17.98        34.36        32.19 
TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 
       18.77        14.93        24.99        23.97        13.58        15.35 
TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 
       17.88        22.55        20.61        20.09        12.95        13.68 
TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 
       14.24        16.01        20.09        14.96        22.52        15.52 
TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J 
       38.27        10.72         5.26        18.71        23.70        14.76 
TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A70Y TCGA-FG-A70Z 
       17.82        16.41        15.02        16.44        28.54        10.78 
TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 
       22.95        43.69         5.23         7.43         5.72         0.13 
TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 
        0.10         6.67         7.82         0.13         0.03        16.54 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7479 TCGA-HT-7480 
        3.75        17.42         6.54        24.26         7.10        75.19 
TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 
       59.18        60.03       154.19         4.01         5.03        29.85 
TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 
       23.18       107.93         4.57        17.29         3.16        22.06 
TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 
       45.99        56.09        57.60         0.23        14.27         0.16 
TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7687 TCGA-HT-7688 
       16.24         0.76        44.68         6.05         0.10        31.69 
TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 
       14.96         0.10         0.10         2.96        17.52         6.90 
TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 
       14.53        39.48        19.23        39.09         0.23        50.63 
TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 
        0.49        23.61        37.15         0.33         0.13         3.68 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 
        5.33         2.93         1.71        11.28        31.43         1.64 
TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 
       16.24         9.40        63.55         0.10        21.50        33.01 
TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8107 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 
       12.23         6.25         0.46         3.95         4.70         0.23 
TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV 
       29.59         3.88        16.04        15.72         0.23        10.49 
TCGA-HT-A5R5 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 
        0.13         0.07        14.70         0.10         5.33         2.70 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A74O TCGA-HW-7486 
       13.02         1.81        16.14         5.33         0.10        29.92 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 
       13.45         8.32        19.23        40.18        35.90         4.31 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
       21.70        21.60        19.59        17.82        20.35         7.89 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 
       20.81        20.71        19.00        42.77         5.23         4.73 
TCGA-P5-A5EV TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 
        0.23         1.64         2.37         2.30         4.11         5.88 
TCGA-P5-A5F2 TCGA-P5-A5F6 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X 
        7.63         1.28         5.75         2.53         4.83         7.79 
TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CX TCGA-QH-A6CY 
        4.11         4.18        14.83        14.53        12.23         2.20 
TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 
        3.16         0.59         6.31         3.91         4.73         1.91 
TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML 
        0.23         5.03         3.48         0.07        88.83        94.03 
TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW 
       32.65        59.38        62.17        69.07        18.77        37.84 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U2 TCGA-S9-A6U5 
       34.49        31.33        21.63        16.37        23.64        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
        9.86        94.62        83.70         5.85       106.39        62.37 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM 
       72.59        80.12        32.45        84.99        10.88        19.86 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
       15.91         7.59        15.16        14.07        14.27         7.92 
TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 
       19.63        12.59         4.21         9.37         8.19         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 
        8.12         3.58         4.04        28.37        13.02       164.38 
TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89Z TCGA-TM-A7C3 
       10.39        99.06        83.80        31.59         5.00        49.45 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
       48.33        49.32        34.78        48.39        12.00        15.09 
TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L 
       50.76        34.36        24.26        19.36        17.49        40.83 
TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T 
       16.50        29.92        18.90         9.44         4.57        12.00 
TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE 
       33.07        30.08        13.51         0.10         7.89        26.79 
TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-W9-A837 
       10.95        27.06         7.04        23.21        45.07 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              0.10               0.03 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             77.98             211.17 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             13.30              16.01 
[1] "0.1 - 78.0 (13.3)"  "0.0 - 211.2 (16.0)"
[1] "hr=" "1.2"
D62V2, continuous
D62V3, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    11  10
  12P LOSS WILD-TYPE 179 230
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     11   10
  12P LOSS WILD-TYPE  179  230
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE               11                179
  MALE                 10                230
[1] 2 2
[1] FALSE
D62V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  12P LOSS MUTATED            12                4                 5
  12P LOSS WILD-TYPE         147              103               159
D62V5, multiclass
                   clus
vv                  12P LOSS MUTATED 12P LOSS WILD-TYPE
  ASTROCYTOMA                     12                147
  OLIGOASTROCYTOMA                 4                103
  OLIGODENDROGLIOMA                5                159
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V6, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     5  16
  12P LOSS WILD-TYPE  84 325
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      5   16
  12P LOSS WILD-TYPE   84  325
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  NO                 5                 84
  YES               16                325
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12P LOSS MUTATED                                  0     0
  12P LOSS WILD-TYPE                                1     6
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12P LOSS MUTATED                           0    20
  12P LOSS WILD-TYPE                        14   380
D62V7, multiclass
                                  clus
vv                                 12P LOSS MUTATED 12P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  6
  BLACK OR AFRICAN AMERICAN                       0                 14
  WHITE                                          20                380
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V8, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     0  20
  12P LOSS WILD-TYPE  16 367
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      0   20
  12P LOSS WILD-TYPE   16  367
                        clus
vv                       12P LOSS MUTATED 12P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 16
  NOT HISPANIC OR LATINO               20                367
[1] 2 2
[1] FALSE

Clustering(63) Variable = 12Q LOSS MUTATION ANALYSIS
D63V1, survival
                    sevent
clus2                  0   1
  12Q LOSS MUTATED    35   4
  12Q LOSS WILD-TYPE 317  71
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                39                388 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 4                 71 
$`12Q LOSS MUTATED`
TCGA-CS-6665 TCGA-DB-5275 TCGA-DB-5277 TCGA-DB-5279 TCGA-DB-A4XH TCGA-DH-A66B 
       12.43        47.93        46.65        44.52        12.59        42.05 
TCGA-DU-5871 TCGA-DU-6401 TCGA-DU-6542 TCGA-DU-8167 TCGA-DU-A5TU TCGA-DU-A6S6 
       18.94        87.45         7.73        15.48         3.65        77.98 
TCGA-DU-A76R TCGA-E1-5302 TCGA-FG-6689 TCGA-HT-7470 TCGA-HT-7474 TCGA-HT-7478 
       21.30        50.14        14.93         8.81         3.75         6.38 
TCGA-HT-7686 TCGA-HT-7688 TCGA-HT-7690 TCGA-HT-7902 TCGA-HT-8018 TCGA-HT-8106 
       42.74        31.69         0.10        31.43        21.50         0.10 
TCGA-HT-8108 TCGA-HT-A5R7 TCGA-HT-A618 TCGA-P5-A5EW TCGA-P5-A5EZ TCGA-P5-A5F4 
        2.50        14.01         5.33         6.71         2.30         0.76 
TCGA-S9-A6TV TCGA-S9-A6U1 TCGA-S9-A6WQ TCGA-S9-A7QX TCGA-S9-A7R4 TCGA-S9-A7R7 
       18.77        17.62        14.07         4.04        17.42        83.80 
TCGA-S9-A89V TCGA-TM-A84I TCGA-VM-A8C8 
       18.71        19.36        33.07 

$`12Q LOSS WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 
       23.84        17.95         8.48         7.56         8.02         7.40 
TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5276 TCGA-DB-5278 
        6.61       122.73        81.96        75.25        72.92        50.17 
TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC 
       36.56        78.28        30.08        10.29        12.72        27.62 
TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A64L TCGA-DB-A64O 
       27.02        18.84        18.38        72.95        11.01        18.84 
TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V 
       16.80         5.98        16.08        15.42        27.81        14.73 
TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O 
       13.64        10.92         7.40         6.44        10.29        30.74 
TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 
        3.81        19.96        31.82        30.31        14.40         8.02 
TCGA-DH-A669 TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       30.21        27.81        17.19        17.19        54.25        10.22 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
        6.58         3.45         6.21        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5872 
        6.74        13.38         8.45         6.81       182.33        17.49 
TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       15.16       211.17        52.11        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 
       46.06        65.75         1.22         7.04        11.64       133.74 
TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-7006 
       19.89        16.83        94.52       114.08         7.96        11.47 
TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 
       62.96       156.23       138.28        14.99       105.21         6.54 
TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 
        8.84       117.40        90.77        30.67        26.30        10.36 
TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 
        7.96        94.32        18.94        44.02        62.01        25.91 
TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 
       60.30        23.31        41.98         2.76         5.10        23.74 
TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8168 
        3.98        20.68        21.40        19.13        16.96        14.17 
TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TW TCGA-DU-A5TY 
       14.24        12.59        15.12         4.96         5.65        12.20 
TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L 
        8.65         2.70         7.23         5.98        11.41        26.76 
TCGA-DU-A76O TCGA-DU-A7T8 TCGA-DU-A7TG TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 
        7.13       124.50        44.42        67.46        41.13        79.99 
TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 
       57.93       134.27        78.21        95.57       130.78        14.33 
TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 
        0.23         0.20        47.77        17.98        34.36        32.19 
TCGA-FG-6688 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 
       18.77        24.99        23.97        13.58        15.35        17.88 
TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 
       22.55        20.61        20.09        12.95        13.68        14.24 
TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT 
       16.01        20.09        14.96        22.52        15.52        38.27 
TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K 
       10.72         5.26        18.71        23.70        14.76        17.82 
TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z 
       16.41        15.02        16.44        10.59        28.54        10.78 
TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 
       22.95        43.69         5.23         7.43         5.72         0.13 
TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 
        0.10         6.67         7.82         0.13         0.03        16.54 
TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 
       17.42         6.54        24.26         7.10        75.19        59.18 
TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 
       60.03       154.19         4.01         5.03        29.85        23.18 
TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 
      107.93         4.57        17.29         3.16        22.06        45.99 
TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 
       56.09        57.60         0.23        14.27         0.16        16.24 
TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7687 TCGA-HT-7689 TCGA-HT-7691 
        0.76        44.68         6.05         0.10        14.96         0.10 
TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 
        2.96        17.52         6.90        14.53        39.48        19.23 
TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 
       39.09         0.23        50.63         0.49        23.61        37.15 
TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 
        0.33         0.13         3.68         5.33         2.93         1.71 
TCGA-HT-7884 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 
       11.28         1.64        16.24         9.40        63.55         0.10 
TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8107 TCGA-HT-8109 TCGA-HT-8110 
       33.01        12.23         6.25         0.46         3.95         4.70 
TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS 
        0.23        29.59         3.88        16.04        15.72         0.23 
TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC 
       10.49         0.13         0.07        14.70         0.10         5.33 
TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A74O TCGA-HW-7486 
        2.70        13.02         1.81        16.14         0.10        29.92 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 
       13.45         8.32        19.23        40.18        35.90         4.31 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
       21.70        21.60        19.59        17.82        20.35         7.89 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 
       20.81        20.71        19.00        42.77         5.23         4.73 
TCGA-P5-A5EV TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 
        0.23         1.64         2.37         4.11         5.88         7.63 
TCGA-P5-A5F6 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z 
        1.28         5.75         2.53         4.83         7.79         4.11 
TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ 
        4.18        14.83        14.53        12.23         2.20         3.16 
TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA 
        0.59         6.31         3.91         4.73         1.91         0.23 
TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO 
        5.03         3.48         0.07        88.83        94.03        32.65 
TCGA-R8-A73M TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY 
       59.38        62.17        69.07        37.84        34.49        31.33 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       21.63        16.37        23.64        32.61         9.86        94.62 
TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG 
       83.70         5.85       106.39        62.37        72.59        80.12 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO 
       32.45        84.99        10.88        19.86        15.91         7.59 
TCGA-S9-A6WP TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ 
       15.16        14.27         7.92        19.63        12.59         4.21 
TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QY 
        9.37         8.19         2.04         8.12         3.58        28.37 
TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R8 TCGA-S9-A89Z 
       13.02       164.38        10.39        99.06        31.59         5.00 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B 
       49.45        48.33        49.32        34.78        48.39        12.00 
TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84J TCGA-TM-A84L 
       15.09        50.76        34.36        24.26        17.49        40.83 
TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T 
       16.50        29.92        18.90         9.44         4.57        12.00 
TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH 
       30.08        13.51         0.10         7.89        26.79        10.95 
TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-W9-A837 
       27.06         7.04        23.21        45.07 

  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
              0.10               0.03 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             87.45             211.17 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
            17.420             15.815 
[1] "0.1 - 87.5 (17.4)"  "0.0 - 211.2 (15.8)"
[1] "hr=" "1.5"
D63V2, continuous
D63V3, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    19  21
  12Q LOSS WILD-TYPE 171 219
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     19   21
  12Q LOSS WILD-TYPE  171  219
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FEMALE               19                171
  MALE                 21                219
[1] 2 2
[1] FALSE
D63V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  12Q LOSS MUTATED            20               12                 8
  12Q LOSS WILD-TYPE         139               95               156
D63V5, multiclass
                   clus
vv                  12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  ASTROCYTOMA                     20                139
  OLIGOASTROCYTOMA                12                 95
  OLIGODENDROGLIOMA                8                156
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V6, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    10  30
  12Q LOSS WILD-TYPE  79 311
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     10   30
  12Q LOSS WILD-TYPE   79  311
     clus
vv    12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  NO                10                 79
  YES               30                311
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12Q LOSS MUTATED                                  0     0
  12Q LOSS WILD-TYPE                                1     6
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12Q LOSS MUTATED                           0    39
  12Q LOSS WILD-TYPE                        14   361
D63V7, multiclass
                                  clus
vv                                 12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  6
  BLACK OR AFRICAN AMERICAN                       0                 14
  WHITE                                          39                361
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V8, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     0  38
  12Q LOSS WILD-TYPE  16 349
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      0   38
  12Q LOSS WILD-TYPE   16  349
                        clus
vv                       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 16
  NOT HISPANIC OR LATINO               38                349
[1] 2 2
[1] FALSE

Clustering(64) Variable = 13Q LOSS MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                  0   1
  13Q LOSS MUTATED    73  24
  13Q LOSS WILD-TYPE 279  51
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                97                330 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                24                 51 
$`13Q LOSS MUTATED`
TCGA-CS-4943 TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6670 TCGA-DB-5275 TCGA-DB-5277 
       18.15        17.95         8.48         6.61        47.93        46.65 
TCGA-DB-A4XA TCGA-DB-A4XE TCGA-DB-A64X TCGA-DH-5140 TCGA-DH-5142 TCGA-DH-A669 
       10.29        18.84        10.92        19.96        30.31        30.21 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A7UU TCGA-DU-5847 TCGA-DU-5853 TCGA-DU-6392 
       27.81        17.19         3.45        18.02        13.38       211.17 
TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-7006 TCGA-DU-7008 
       65.75         1.22        94.52       114.08        11.47       156.23 
TCGA-DU-7010 TCGA-DU-7290 TCGA-DU-7299 TCGA-DU-7301 TCGA-DU-8158 TCGA-DU-8165 
       14.99        10.36        44.02        25.91         5.10        19.13 
TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TS TCGA-DU-A6S3 TCGA-DU-A6S7 TCGA-DU-A76R 
       15.48        14.17        15.12         2.70         7.23        21.30 
TCGA-DU-A7T8 TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5307 TCGA-E1-5322 
      124.50        50.14        67.46        41.13        57.93       130.78 
TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-6689 TCGA-FG-6692 TCGA-FG-7641 
       47.77        17.98        34.36        14.93        13.58        20.61 
TCGA-FG-8188 TCGA-FG-A60J TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J3 TCGA-FG-A70Z 
       14.96        14.76        16.41        15.02        10.59        10.78 
TCGA-FG-A87Q TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7476 TCGA-HT-7477 
        5.72         7.82         8.81         0.13         6.54        24.26 
TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7688 
       60.03       154.19       107.93         4.57        17.29        31.69 
TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7692 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7902 
       14.96         0.10         2.96        39.09         0.23        31.43 
TCGA-HT-8106 TCGA-HT-8564 TCGA-HT-A617 TCGA-HW-7489 TCGA-HW-7491 TCGA-KT-A74X 
        0.10        15.72        16.14         8.32        40.18         5.23 
TCGA-P5-A5EZ TCGA-P5-A5F4 TCGA-QH-A65Z TCGA-QH-A6CV TCGA-QH-A6CY TCGA-QH-A6X8 
        2.30         0.76         4.11        14.53         2.20         4.73 
TCGA-S9-A6UA TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7J0 TCGA-S9-A7J3 TCGA-S9-A89V 
        5.85        19.63        12.59         9.37         8.12        18.71 
TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A84F TCGA-TM-A84I TCGA-TM-A84R TCGA-TM-A84S 
        5.00        49.45        50.76        19.36         9.44         4.57 
TCGA-VM-A8CD 
        7.89 

$`13Q LOSS WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5393 
        4.70         7.69        43.89        10.62        64.64        40.18 
TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
        0.10        21.01         9.96         6.38        17.69        23.84 
TCGA-CS-6665 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-DB-5270 TCGA-DB-5273 
       12.43         7.56         8.02         7.40       122.73        81.96 
TCGA-DB-5274 TCGA-DB-5276 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       75.25        72.92        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XF TCGA-DB-A4XG 
       30.08        12.72        27.62        27.02        18.38        72.95 
TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R 
       12.59        11.01        18.84        16.80         5.98        16.08 
TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A75K TCGA-DB-A75L 
       15.42        27.81        14.73        13.64         7.40         6.44 
TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5141 TCGA-DH-5143 TCGA-DH-5144 
       10.29        30.74         3.81        31.82        14.40         8.02 
TCGA-DH-A66B TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UV 
       42.05        17.19        54.25        10.22         6.58         6.21 
TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 
       14.56        17.46         6.74         8.45         6.81       182.33 
TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 
       18.94        17.49        15.16        52.11        22.42        49.02 
TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 
       75.16        46.06        87.45         7.04        11.64       133.74 
TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7007 TCGA-DU-7009 
       19.89        16.83         7.96         7.73        62.96       138.28 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 
      105.21         6.54         8.84       117.40        90.77        30.67 
TCGA-DU-7019 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7300 TCGA-DU-7302 
       26.30         7.96        94.32        18.94        62.01        60.30 
TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 
       23.31        41.98         2.76        23.74         3.98        20.68 
TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TT TCGA-DU-A5TU 
       21.40        16.96        14.24        12.59         4.96         3.65 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S6 TCGA-DU-A6S8 TCGA-DU-A76K 
        5.65        12.20         8.65        77.98         5.98        11.41 
TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A7TG TCGA-E1-5305 TCGA-E1-5311 TCGA-E1-5318 
       26.76         7.13        44.42        79.99       134.27        78.21 
TCGA-E1-5319 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5965 TCGA-FG-6688 
       95.57        14.33         0.23         0.20        32.19        18.77 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7643 
       24.99        23.97        15.35        17.88        22.55        20.09 
TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8189 
       12.95        13.68        14.24        16.01        20.09        22.52 
TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY 
       15.52        38.27        10.72         5.26        18.71        23.70 
TCGA-FG-A60K TCGA-FG-A6J1 TCGA-FG-A70Y TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 
       17.82        16.44        28.54        22.95        43.69         5.23 
TCGA-FG-A87N TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7472 TCGA-HT-7473 
        7.43         0.13         0.10         6.67         0.03        16.54 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 
        3.75        17.42         6.38         7.10        75.19        59.18 
TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7607 TCGA-HT-7608 
        4.01         5.03        29.85        23.18         3.16        22.06 
TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 
       45.99        56.09        57.60         0.23        14.27         0.16 
TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 
       16.24         0.76        44.68         6.05        42.74         0.10 
TCGA-HT-7691 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 
        0.10        17.52         6.90        14.53        39.48        19.23 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
       50.63         0.49        23.61        37.15         0.33         0.13 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-8010 
        3.68         5.33         2.93         1.71        11.28         1.64 
TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 
       16.24         9.40        63.55         0.10        21.50        33.01 
TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 
       12.23         6.25         0.46         2.50         3.95         4.70 
TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-A4DS TCGA-HT-A4DV 
        0.23        29.59         3.88        16.04         0.23        10.49 
TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC 
        0.13        14.01         0.07        14.70         0.10         5.33 
TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A618 TCGA-HT-A74O TCGA-HW-7486 
        2.70        13.02         1.81         5.33         0.10        29.92 
TCGA-HW-7487 TCGA-HW-7490 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 
       13.45        19.23        35.90         4.31        21.70        21.60 
TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM 
       19.59        17.82        20.35         7.89        20.81        20.71 
TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX 
       19.00        42.77         4.73         0.23         6.71         1.64 
TCGA-P5-A5EY TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F6 TCGA-QH-A65R 
        2.37         4.11         5.88         7.63         1.28         5.75 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CX 
        2.53         4.83         7.79         4.18        14.83        12.23 
TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X9 TCGA-QH-A6XA 
        3.16         0.59         6.31         3.91         1.91         0.23 
TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO 
        5.03         3.48         0.07        88.83        94.03        32.65 
TCGA-R8-A73M TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX 
       59.38        62.17        69.07        18.77        37.84        34.49 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       31.33        21.63        16.37        17.62        23.64        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE 
        9.86        94.62        83.70       106.39        62.37        72.59 
TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN 
       80.12        32.45        84.99        10.88        19.86        15.91 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IZ 
        7.59        15.16        14.07        14.27         7.92         4.21 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ 
        8.19         2.04         3.58         4.04        28.37        13.02 
TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 
      164.38        10.39        99.06        17.42        83.80        31.59 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
       48.33        49.32        34.78        48.39        12.00        15.09 
TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O 
       34.36        24.26        17.49        40.83        16.50        29.92 
TCGA-TM-A84Q TCGA-TM-A84T TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB 
       18.90        12.00        33.07        30.08        13.51         0.10 
TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-W9-A837 
       26.79        10.95        27.06         7.04        23.21        45.07 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              0.10               0.03 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            211.17             182.33 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             15.12              16.06 
[1] "0.1 - 211.2 (15.1)" "0.0 - 182.3 (16.1)"
[1] "hr=" "1.4"
D64V2, continuous
D64V3, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    36  62
  13Q LOSS WILD-TYPE 154 178
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     36   62
  13Q LOSS WILD-TYPE  154  178
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE               36                154
  MALE                 62                178
[1] 2 2
[1] FALSE
D64V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  13Q LOSS MUTATED            41               22                35
  13Q LOSS WILD-TYPE         118               85               129
D64V5, multiclass
                   clus
vv                  13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  ASTROCYTOMA                     41                118
  OLIGOASTROCYTOMA                22                 85
  OLIGODENDROGLIOMA               35                129
[1] 3 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
  13Q LOSS MUTATED    29  69
  13Q LOSS WILD-TYPE  60 272
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     29   69
  13Q LOSS WILD-TYPE   60  272
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  NO                29                 60
  YES               69                272
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  13Q LOSS MUTATED                                  1     1
  13Q LOSS WILD-TYPE                                0     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  13Q LOSS MUTATED                           3    92
  13Q LOSS WILD-TYPE                        11   308
D64V7, multiclass
                                  clus
vv                                 13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           1                  5
  BLACK OR AFRICAN AMERICAN                       3                 11
  WHITE                                          92                308
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V8, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED     2  91
  13Q LOSS WILD-TYPE  14 296
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      2   91
  13Q LOSS WILD-TYPE   14  296
                        clus
vv                       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                 14
  NOT HISPANIC OR LATINO               91                296
[1] 2 2
[1] FALSE

Clustering(65) Variable = 14Q LOSS MUTATION ANALYSIS
D65V1, survival
                    sevent
clus2                  0   1
  14Q LOSS MUTATED    41  22
  14Q LOSS WILD-TYPE 311  53
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                63                364 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                22                 53 
$`14Q LOSS MUTATED`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-6668 TCGA-DB-5279 TCGA-DB-A4XA 
        4.70         7.69        43.89         8.02        44.52        10.29 
TCGA-DB-A64L TCGA-DB-A64O TCGA-DH-5140 TCGA-DH-5142 TCGA-DH-5143 TCGA-DU-5847 
       11.01        18.84        19.96        30.31        14.40        18.02 
TCGA-DU-5852 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6542 TCGA-DU-7007 TCGA-DU-7010 
        6.74        46.06        65.75         7.73        62.96        14.99 
TCGA-DU-7012 TCGA-DU-7290 TCGA-DU-7302 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8165 
        6.54        10.36        60.30         5.10        23.74        19.13 
TCGA-DU-A6S8 TCGA-DU-A76L TCGA-DU-A76R TCGA-E1-5305 TCGA-E1-5322 TCGA-EZ-7264 
        5.98        26.76        21.30        79.99       130.78        14.33 
TCGA-FG-7643 TCGA-FG-8191 TCGA-FG-A6J3 TCGA-HT-7477 TCGA-HT-7616 TCGA-HT-7688 
       20.09        15.52        10.59        24.26         0.23        31.69 
TCGA-HT-7689 TCGA-HT-7902 TCGA-HT-8110 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A617 
       14.96        31.43         4.70        15.72         0.23        16.14 
TCGA-HT-A618 TCGA-HW-7489 TCGA-HW-A5KK TCGA-IK-8125 TCGA-P5-A5EX TCGA-P5-A5EZ 
        5.33         8.32         7.89        42.77         1.64         2.30 
TCGA-QH-A6CS TCGA-QH-A6CV TCGA-QH-A6CZ TCGA-S9-A6TS TCGA-S9-A6WM TCGA-S9-A7IX 
        4.18        14.53         3.16        62.17        19.86        19.63 
TCGA-S9-A7QZ TCGA-S9-A7R2 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-TM-A7C3 TCGA-TM-A84I 
       13.02        10.39        31.59        18.71        49.45        19.36 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VV-A829 
        0.10         7.89        27.06 

$`14Q LOSS WILD-TYPE`
TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 
       18.15        10.62        64.64        40.18         0.10        21.01 
TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 
        9.96         6.38        17.69        23.84        17.95        12.43 
TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 
        8.48         7.56         7.40         6.61       122.73        81.96 
TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5280 
       75.25        47.93        72.92        46.65        50.17        36.56 
TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       78.28        30.08        12.72        27.62        27.02        18.84 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R 
       18.38        72.95        12.59        16.80         5.98        16.08 
TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K 
       15.42        27.81        14.73        13.64        10.92         7.40 
TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5141 TCGA-DH-5144 
        6.44        10.29        30.74         3.81        31.82         8.02 
TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR 
       30.21        42.05        27.81        17.19        17.19        54.25 
TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5849 TCGA-DU-5851 
       10.22         6.58         3.45         6.21        14.56        17.46 
TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 
       13.38         8.45         6.81       182.33        18.94        17.49 
TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       15.16       211.17        52.11        22.42        49.02        75.16 
TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 
        1.22        87.45         7.04        11.64       133.74        19.89 
TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-7006 TCGA-DU-7008 
       16.83        94.52       114.08         7.96        11.47       156.23 
TCGA-DU-7009 TCGA-DU-7011 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 
      138.28       105.21         8.84       117.40        90.77        30.67 
TCGA-DU-7019 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 
       26.30         7.96        94.32        18.94        44.02        62.01 
TCGA-DU-7301 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8162 TCGA-DU-8163 
       25.91        23.31        41.98         2.76         3.98        20.68 
TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR 
       21.40        16.96        15.48        14.17        14.24        12.59 
TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 
       15.12         4.96         3.65         5.65        12.20         8.65 
TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A76K TCGA-DU-A76O TCGA-DU-A7T8 
        2.70        77.98         7.23        11.41         7.13       124.50 
TCGA-DU-A7TG TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5307 TCGA-E1-5311 
       44.42        50.14        67.46        41.13        57.93       134.27 
TCGA-E1-5318 TCGA-E1-5319 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 
       78.21        95.57         0.23         0.20        47.77        17.98 
TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 
       34.36        32.19        18.77        14.93        24.99        23.97 
TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-8181 
       13.58        15.35        17.88        22.55        20.61        12.95 
TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 
       13.68        14.24        16.01        20.09        14.96        22.52 
TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J 
       38.27        10.72         5.26        18.71        23.70        14.76 
TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A70Y TCGA-FG-A70Z 
       17.82        16.41        15.02        16.44        28.54        10.78 
TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 
       22.95        43.69         5.23         7.43         5.72         0.13 
TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 
        0.10         6.67         7.82         8.81         0.13         0.03 
TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7478 TCGA-HT-7479 
       16.54         3.75        17.42         6.54         6.38         7.10 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
       75.19        59.18        60.03       154.19         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 
       29.85        23.18       107.93         4.57        17.29         3.16 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7620 TCGA-HT-7676 
       22.06        45.99        56.09        57.60        14.27         0.16 
TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 
       16.24         0.76        44.68         6.05        42.74         0.10 
TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 
        0.10         0.10         2.96        17.52         6.90        14.53 
TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 
       39.48        19.23        39.09         0.23        50.63         0.49 
TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 
       23.61        37.15         0.33         0.13         3.68         5.33 
TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 
        2.93         1.71        11.28         1.64        16.24         9.40 
TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 
       63.55         0.10        21.50        33.01        12.23         6.25 
TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8111 TCGA-HT-8113 
        0.10         0.46         2.50         3.95         0.23        29.59 
TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 
        3.88        16.04        10.49         0.13        14.01         0.07 
TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 
       14.70         0.10         5.33         2.70        13.02         1.81 
TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 
        0.10        29.92        13.45        19.23        40.18        35.90 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
        4.31        21.70        21.60        19.59        17.82        20.35 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV 
       20.81        20.71        19.00         5.23         4.73         0.23 
TCGA-P5-A5EW TCGA-P5-A5EY TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 
        6.71         2.37         4.11         5.88         7.63         0.76 
TCGA-P5-A5F6 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z 
        1.28         5.75         2.53         4.83         7.79         4.11 
TCGA-QH-A6CU TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 
       14.83        12.23         2.20         0.59         6.31         3.91 
TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 
        4.73         1.91         0.23         5.03         3.48         0.07 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TU TCGA-S9-A6TV 
       88.83        94.03        32.65        59.38        69.07        18.77 
TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 
       37.84        34.49        31.33        21.63        16.37        17.62 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA 
       23.64        32.61         9.86        94.62        83.70         5.85 
TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI 
      106.39        62.37        72.59        80.12        32.45        84.99 
TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ 
       10.88        15.91         7.59        15.16        14.07        14.27 
TCGA-S9-A7IS TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 
        7.92        12.59         4.21         9.37         8.19         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7R1 TCGA-S9-A7R3 
        8.12         3.58         4.04        28.37       164.38        99.06 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A89Z TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA 
       17.42        83.80         5.00        48.33        49.32        34.78 
TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H 
       48.39        12.00        15.09        50.76        34.36        24.26 
TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R 
       17.49        40.83        16.50        29.92        18.90         9.44 
TCGA-TM-A84S TCGA-TM-A84T TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CE 
        4.57        12.00        33.07        30.08        13.51        26.79 
TCGA-VM-A8CH TCGA-VV-A86M TCGA-VW-A7QS TCGA-W9-A837 
       10.95         7.04        23.21        45.07 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              0.10               0.03 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            130.78             211.17 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            15.520             16.025 
[1] "0.1 - 130.8 (15.5)" "0.0 - 211.2 (16.0)"
[1] "hr=" "3.1"
D65V2, continuous
D65V3, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    28  37
  14Q LOSS WILD-TYPE 162 203
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     28   37
  14Q LOSS WILD-TYPE  162  203
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE               28                162
  MALE                 37                203
[1] 2 2
[1] FALSE
D65V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  14Q LOSS MUTATED            30               16                19
  14Q LOSS WILD-TYPE         129               91               145
D65V5, multiclass
                   clus
vv                  14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  ASTROCYTOMA                     30                129
  OLIGOASTROCYTOMA                16                 91
  OLIGODENDROGLIOMA               19                145
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V6, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    11  54
  14Q LOSS WILD-TYPE  78 287
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     11   54
  14Q LOSS WILD-TYPE   78  287
     clus
vv    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  NO                11                 78
  YES               54                287
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  14Q LOSS MUTATED                                  1     1
  14Q LOSS WILD-TYPE                                0     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  14Q LOSS MUTATED                           2    59
  14Q LOSS WILD-TYPE                        12   341
D65V7, multiclass
                                  clus
vv                                 14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           1                  5
  BLACK OR AFRICAN AMERICAN                       2                 12
  WHITE                                          59                341
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V8, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED     1  58
  14Q LOSS WILD-TYPE  15 329
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      1   58
  14Q LOSS WILD-TYPE   15  329
                        clus
vv                       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 15
  NOT HISPANIC OR LATINO               58                329
[1] 2 2
[1] FALSE

Clustering(66) Variable = 15Q LOSS MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                  0   1
  15Q LOSS MUTATED    27  11
  15Q LOSS WILD-TYPE 325  64
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                38                389 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                11                 64 
$`15Q LOSS MUTATED`
TCGA-DB-5274 TCGA-DB-5279 TCGA-DB-A4XA TCGA-DB-A4XH TCGA-DH-5140 TCGA-DH-5142 
       75.25        44.52        10.29        12.59        19.96        30.31 
TCGA-DH-A669 TCGA-DH-A7UT TCGA-DU-6393 TCGA-DU-6400 TCGA-DU-7007 TCGA-DU-8158 
       30.21         6.58        52.11         1.22        62.96         5.10 
TCGA-DU-A6S3 TCGA-DU-A76R TCGA-E1-5311 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-A4MW 
        2.70        21.30       134.27        15.35        17.88         5.26 
TCGA-FG-A6J3 TCGA-HT-7468 TCGA-HT-7480 TCGA-HT-7606 TCGA-HT-7609 TCGA-HT-7616 
       10.59         6.67        75.19        17.29        45.99         0.23 
TCGA-HT-8012 TCGA-HT-A618 TCGA-P5-A5EZ TCGA-QH-A65S TCGA-QH-A6X8 TCGA-S9-A6TS 
        9.40         5.33         2.30         2.53         4.73        62.17 
TCGA-S9-A6U2 TCGA-S9-A6WD TCGA-S9-A6WI TCGA-S9-A7QZ TCGA-S9-A89Z TCGA-TM-A7C5 
       23.64        62.37        84.99        13.02         5.00        49.32 
TCGA-VV-A86M TCGA-W9-A837 
        7.04        45.07 

$`15Q LOSS WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5275 TCGA-DB-5276 
        7.40         6.61       122.73        81.96        47.93        72.92 
TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XB 
       46.65        50.17        36.56        78.28        30.08        12.72 
TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A64L 
       27.62        27.02        18.84        18.38        72.95        11.01 
TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U 
       18.84        16.80         5.98        16.08        15.42        27.81 
TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M 
       14.73        13.64        10.92         7.40         6.44        10.29 
TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5141 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A66B 
       30.74         3.81        31.82        14.40         8.02        42.05 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UU 
       27.81        17.19        17.19        54.25        10.22         3.45 
TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 
        6.21        18.02        14.56        17.46         6.74        13.38 
TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 
        8.45         6.81       182.33        18.94        17.49        15.16 
TCGA-DU-6392 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 
      211.17        22.42        49.02        75.16        46.06        65.75 
TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 
       87.45         7.04        11.64       133.74        19.89        16.83 
TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7008 
       94.52       114.08         7.96         7.73        11.47       156.23 
TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 
      138.28        14.99       105.21         6.54         8.84       117.40 
TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 
       90.77        30.67        26.30        10.36         7.96        94.32 
TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 
       18.94        44.02        62.01        25.91        60.30        23.31 
TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 
       41.98         2.76        23.74         3.98        20.68        21.40 
TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR 
       19.13        16.96        15.48        14.17        14.24        12.59 
TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 
       15.12         4.96         3.65         5.65        12.20         8.65 
TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O 
       77.98         7.23         5.98        11.41        26.76         7.13 
TCGA-DU-A7T8 TCGA-DU-A7TG TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 
      124.50        44.42        50.14        67.46        41.13        79.99 
TCGA-E1-5307 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 TCGA-F6-A8O3 
       57.93        78.21        95.57       130.78        14.33         0.23 
TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 
        0.20        47.77        17.98        34.36        32.19        18.77 
TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7638 TCGA-FG-7641 
       14.93        24.99        23.97        13.58        22.55        20.61 
TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 
       20.09        12.95        13.68        14.24        16.01        20.09 
TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MX 
       14.96        22.52        15.52        38.27        10.72        18.71 
TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 
       23.70        14.76        17.82        16.41        15.02        16.44 
TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N 
       28.54        10.78        22.95        43.69         5.23         7.43 
TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 
        5.72         0.13         0.10         7.82         8.81         0.13 
TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 
        0.03        16.54         3.75        17.42         6.54        24.26 
TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 
        6.38         7.10        59.18        60.03       154.19         4.01 
TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7607 
        5.03        29.85        23.18       107.93         4.57         3.16 
TCGA-HT-7608 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 
       22.06        56.09        57.60        14.27         0.16        16.24 
TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 
        0.76        44.68         6.05        42.74         0.10        31.69 
TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 
       14.96         0.10         0.10         2.96        17.52         6.90 
TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 
       14.53        39.48        19.23        39.09         0.23        50.63 
TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 
        0.49        23.61        37.15         0.33         0.13         3.68 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 
        5.33         2.93         1.71        11.28        31.43         1.64 
TCGA-HT-8011 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 
       16.24        63.55         0.10        21.50        33.01        12.23 
TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 
        6.25         0.10         0.46         2.50         3.95         4.70 
TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS 
        0.23        29.59         3.88        16.04        15.72         0.23 
TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB 
       10.49         0.13        14.01         0.07        14.70         0.10 
TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A74O 
        5.33         2.70        13.02         1.81        16.14         0.10 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 
       29.92        13.45         8.32        19.23        40.18        35.90 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
        4.31        21.70        21.60        19.59        17.82        20.35 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X 
        7.89        20.81        20.71        19.00        42.77         5.23 
TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5F0 
        4.73         0.23         6.71         1.64         2.37         4.11 
TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-QH-A65R TCGA-QH-A65V 
        5.88         7.63         0.76         1.28         5.75         4.83 
TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CX 
        7.79         4.11         4.18        14.83        14.53        12.23 
TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X9 
        2.20         3.16         0.59         6.31         3.91         1.91 
TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML 
        0.23         5.03         3.48         0.07        88.83        94.03 
TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX 
       32.65        59.38        69.07        18.77        37.84        34.49 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U5 TCGA-S9-A6U6 
       31.33        21.63        16.37        17.62        32.61         9.86 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WE TCGA-S9-A6WG 
       94.62        83.70         5.85       106.39        72.59        80.12 
TCGA-S9-A6WH TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP 
       32.45        10.88        19.86        15.91         7.59        15.16 
TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ 
       14.07        14.27         7.92        19.63        12.59         4.21 
TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX 
        9.37         8.19         2.04         8.12         3.58         4.04 
TCGA-S9-A7QY TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 
       28.37       164.38        10.39        99.06        17.42        83.80 
TCGA-S9-A7R8 TCGA-S9-A89V TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7CA TCGA-TM-A7CF 
       31.59        18.71        49.45        48.33        34.78        48.39 
TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I 
       12.00        15.09        50.76        34.36        24.26        19.36 
TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R 
       17.49        40.83        16.50        29.92        18.90         9.44 
TCGA-TM-A84S TCGA-TM-A84T TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB 
        4.57        12.00        33.07        30.08        13.51         0.10 
TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VW-A7QS 
        7.89        26.79        10.95        27.06        23.21 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              0.23               0.03 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            134.27             211.17 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             16.32              15.91 
[1] "0.2 - 134.3 (16.3)" "0.0 - 211.2 (15.9)"
[1] "hr=" "1.6"
D66V2, continuous
D66V3, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED    15  24
  15Q LOSS WILD-TYPE 175 216
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     15   24
  15Q LOSS WILD-TYPE  175  216
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE               15                175
  MALE                 24                216
[1] 2 2
[1] FALSE
D66V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  15Q LOSS MUTATED            13                9                17
  15Q LOSS WILD-TYPE         146               98               147
D66V5, multiclass
                   clus
vv                  15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  ASTROCYTOMA                     13                146
  OLIGOASTROCYTOMA                 9                 98
  OLIGODENDROGLIOMA               17                147
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V6, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     8  31
  15Q LOSS WILD-TYPE  81 310
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      8   31
  15Q LOSS WILD-TYPE   81  310
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  NO                 8                 81
  YES               31                310
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  15Q LOSS MUTATED                                  0     0
  15Q LOSS WILD-TYPE                                1     6
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  15Q LOSS MUTATED                           0    37
  15Q LOSS WILD-TYPE                        14   363
D66V7, multiclass
                                  clus
vv                                 15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  6
  BLACK OR AFRICAN AMERICAN                       0                 14
  WHITE                                          37                363
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V8, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     1  37
  15Q LOSS WILD-TYPE  15 350
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      1   37
  15Q LOSS WILD-TYPE   15  350
                        clus
vv                       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 15
  NOT HISPANIC OR LATINO               37                350
[1] 2 2
[1] FALSE

Clustering(67) Variable = 16P LOSS MUTATION ANALYSIS
D67V1, survival
                    sevent
clus2                  0   1
  16P LOSS MUTATED     6   5
  16P LOSS WILD-TYPE 346  70
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                11                416 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 5                 70 
$`16P LOSS MUTATED`
TCGA-DB-5277 TCGA-DB-5281 TCGA-DH-A669 TCGA-DU-7018 TCGA-DU-8165 TCGA-E1-5307 
       46.65        78.28        30.21        30.67        19.13        57.93 
TCGA-FG-A4MW TCGA-HT-7477 TCGA-HT-8564 TCGA-S9-A7IX TCGA-S9-A89V 
        5.26        24.26        15.72        19.63        18.71 

$`16P LOSS WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-A4X9 TCGA-DB-A4XA 
       72.92        50.17        44.52        36.56        30.08        10.29 
TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG 
       12.72        27.62        27.02        18.84        18.38        72.95 
TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R 
       12.59        11.01        18.84        16.80         5.98        16.08 
TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K 
       15.42        27.81        14.73        13.64        10.92         7.40 
TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 
        6.44        10.29        30.74         3.81        19.96        31.82 
TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F 
       30.31        14.40         8.02        42.05        27.81        17.19 
TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV 
       17.19        54.25        10.22         6.58         3.45         6.21 
TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 
       18.02        14.56        17.46         6.74        13.38         8.45 
TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 
        6.81       182.33        18.94        17.49        15.16       211.17 
TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 
       52.11        22.42        49.02        75.16        46.06        65.75 
TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 
        1.22        87.45         7.04        11.64       133.74        19.89 
TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 
       16.83        94.52       114.08         7.96         7.73        11.47 
TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 
       62.96       156.23       138.28        14.99       105.21         6.54 
TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 
        8.84       117.40        90.77        26.30        10.36         7.96 
TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 
       94.32        18.94        44.02        62.01        25.91        60.30 
TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 
       23.31        41.98         2.76         5.10        23.74         3.98 
TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP 
       20.68        21.40        16.96        15.48        14.17        14.24 
TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY 
       12.59        15.12         4.96         3.65         5.65        12.20 
TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K 
        8.65         2.70        77.98         7.23         5.98        11.41 
TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 TCGA-DU-A7TG TCGA-E1-5302 
       26.76         7.13        21.30       124.50        44.42        50.14 
TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 
       67.46        41.13        79.99       134.27        78.21        95.57 
TCGA-E1-5322 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 
      130.78        14.33         0.23         0.20        47.77        17.98 
TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 
       34.36        32.19        18.77        14.93        24.99        23.97 
TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 
       13.58        15.35        17.88        22.55        20.61        20.09 
TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 
       12.95        13.68        14.24        16.01        20.09        14.96 
TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MX TCGA-FG-A4MY 
       22.52        15.52        38.27        10.72        18.71        23.70 
TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 
       14.76        17.82        16.41        15.02        16.44        10.59 
TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N 
       28.54        10.78        22.95        43.69         5.23         7.43 
TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 
        5.72         0.13         0.10         6.67         7.82         8.81 
TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 
        0.13         0.03        16.54         3.75        17.42         6.54 
TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 
        6.38         7.10        75.19        59.18        60.03       154.19 
TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 
        4.01         5.03        29.85        23.18       107.93         4.57 
TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 
       17.29         3.16        22.06        45.99        56.09        57.60 
TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 
        0.23        14.27         0.16        16.24         0.76        44.68 
TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 
        6.05        42.74         0.10        31.69        14.96         0.10 
TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 
        0.10         2.96        17.52         6.90        14.53        39.48 
TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 
       19.23        39.09         0.23        50.63         0.49        23.61 
TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 
       37.15         0.33         0.13         3.68         5.33         2.93 
TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 
        1.71        11.28        31.43         1.64        16.24         9.40 
TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 
       63.55         0.10        21.50        33.01        12.23         6.25 
TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 
        0.10         0.46         2.50         3.95         4.70         0.23 
TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
       29.59         3.88        16.04         0.23        10.49         0.13 
TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 
       14.01         0.07        14.70         0.10         5.33         2.70 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A74O TCGA-HW-7486 
       13.02         1.81        16.14         5.33         0.10        29.92 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 
       13.45         8.32        19.23        40.18        35.90         4.31 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
       21.70        21.60        19.59        17.82        20.35         7.89 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 
       20.81        20.71        19.00        42.77         5.23         4.73 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 
        0.23         6.71         1.64         2.37         2.30         4.11 
TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-QH-A65R TCGA-QH-A65S 
        5.88         7.63         0.76         1.28         5.75         2.53 
TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV 
        4.83         7.79         4.11         4.18        14.83        14.53 
TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 
       12.23         2.20         3.16         0.59         6.31         3.91 
TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 
        4.73         1.91         0.23         5.03         3.48         0.07 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TS TCGA-S9-A6TU 
       88.83        94.03        32.65        59.38        62.17        69.07 
TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 
       18.77        37.84        34.49        31.33        21.63        16.37 
TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
       17.62        23.64        32.61         9.86        94.62        83.70 
TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH 
        5.85       106.39        62.37        72.59        80.12        32.45 
TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP 
       84.99        10.88        19.86        15.91         7.59        15.16 
TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 
       14.07        14.27         7.92        12.59         4.21         9.37 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY 
        8.19         2.04         8.12         3.58         4.04        28.37 
TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 
       13.02       164.38        10.39        99.06        17.42        83.80 
TCGA-S9-A7R8 TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA 
       31.59         5.00        49.45        48.33        49.32        34.78 
TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H 
       48.39        12.00        15.09        50.76        34.36        24.26 
TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q 
       19.36        17.49        40.83        16.50        29.92        18.90 
TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA 
        9.44         4.57        12.00        33.07        30.08        13.51 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M 
        0.10         7.89        26.79        10.95        27.06         7.04 
TCGA-VW-A7QS TCGA-W9-A837 
       23.21        45.07 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              5.26               0.03 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             78.28             211.17 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
            24.260             15.385 
[1] "5.3 - 78.3 (24.3)"  "0.0 - 211.2 (15.4)"
[1] "hr=" "2.3"
D67V2, continuous
D67V3, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     3   8
  16P LOSS WILD-TYPE 187 232
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      3    8
  16P LOSS WILD-TYPE  187  232
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE                3                187
  MALE                  8                232
[1] 2 2
[1] FALSE
D67V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  16P LOSS MUTATED             6                2                 3
  16P LOSS WILD-TYPE         153              105               161
D67V5, multiclass
                   clus
vv                  16P LOSS MUTATED 16P LOSS WILD-TYPE
  ASTROCYTOMA                      6                153
  OLIGOASTROCYTOMA                 2                105
  OLIGODENDROGLIOMA                3                161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V6, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     2   9
  16P LOSS WILD-TYPE  87 332
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      2    9
  16P LOSS WILD-TYPE   87  332
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  NO                 2                 87
  YES                9                332
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16P LOSS MUTATED                                  0     0
  16P LOSS WILD-TYPE                                1     6
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16P LOSS MUTATED                           0    11
  16P LOSS WILD-TYPE                        14   389
D67V7, multiclass
                                  clus
vv                                 16P LOSS MUTATED 16P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  6
  BLACK OR AFRICAN AMERICAN                       0                 14
  WHITE                                          11                389
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V8, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     1  10
  16P LOSS WILD-TYPE  15 377
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      1   10
  16P LOSS WILD-TYPE   15  377
                        clus
vv                       16P LOSS MUTATED 16P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 15
  NOT HISPANIC OR LATINO               10                377
[1] 2 2
[1] FALSE

Clustering(68) Variable = 16Q LOSS MUTATION ANALYSIS
D68V1, survival
                    sevent
clus2                  0   1
  16Q LOSS MUTATED    11   8
  16Q LOSS WILD-TYPE 341  67
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                19                408 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 8                 67 
$`16Q LOSS MUTATED`
TCGA-DB-5277 TCGA-DB-5281 TCGA-DH-A669 TCGA-DU-5847 TCGA-DU-7012 TCGA-DU-7014 
       46.65        78.28        30.21        18.02         6.54       117.40 
TCGA-DU-7018 TCGA-DU-8165 TCGA-DU-8167 TCGA-E1-5307 TCGA-FG-A4MW TCGA-HT-7469 
       30.67        19.13        15.48        57.93         5.26         7.82 
TCGA-HT-8564 TCGA-HT-A4DS TCGA-S9-A6U9 TCGA-S9-A6WH TCGA-S9-A7IX TCGA-S9-A89V 
       15.72         0.23        83.70        32.45        19.63        18.71 
TCGA-S9-A89Z 
        5.00 

$`16Q LOSS WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-A4X9 TCGA-DB-A4XA 
       72.92        50.17        44.52        36.56        30.08        10.29 
TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG 
       12.72        27.62        27.02        18.84        18.38        72.95 
TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R 
       12.59        11.01        18.84        16.80         5.98        16.08 
TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K 
       15.42        27.81        14.73        13.64        10.92         7.40 
TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5141 
        6.44        10.29        30.74         3.81        19.96        31.82 
TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F 
       30.31        14.40         8.02        42.05        27.81        17.19 
TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV 
       17.19        54.25        10.22         6.58         3.45         6.21 
TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 
       14.56        17.46         6.74        13.38         8.45         6.81 
TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 
      182.33        18.94        17.49        15.16       211.17        52.11 
TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 
       22.42        49.02        75.16        46.06        65.75         1.22 
TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 
       87.45         7.04        11.64       133.74        19.89        16.83 
TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 
       94.52       114.08         7.96         7.73        11.47        62.96 
TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7013 TCGA-DU-7015 
      156.23       138.28        14.99       105.21         8.84        90.77 
TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 
       26.30        10.36         7.96        94.32        18.94        44.02 
TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 
       62.01        25.91        60.30        23.31        41.98         2.76 
TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8166 
        5.10        23.74         3.98        20.68        21.40        16.96 
TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU 
       14.17        14.24        12.59        15.12         4.96         3.65 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
        5.65        12.20         8.65         2.70        77.98         7.23 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 
        5.98        11.41        26.76         7.13        21.30       124.50 
TCGA-DU-A7TG TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5311 
       44.42        50.14        67.46        41.13        79.99       134.27 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 
       78.21        95.57       130.78        14.33         0.23         0.20 
TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 
       47.77        17.98        34.36        32.19        18.77        14.93 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 
       24.99        23.97        13.58        15.35        17.88        22.55 
TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 
       20.61        20.09        12.95        13.68        14.24        16.01 
TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU 
       20.09        14.96        22.52        15.52        38.27        10.72 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ 
       18.71        23.70        14.76        17.82        16.41        15.02 
TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 
       16.44        10.59        28.54        10.78        22.95        43.69 
TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 
        5.23         7.43         5.72         0.13         0.10         6.67 
TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 
        8.81         0.13         0.03        16.54         3.75        17.42 
TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 
        6.54        24.26         6.38         7.10        75.19        59.18 
TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 
       60.03       154.19         4.01         5.03        29.85        23.18 
TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 
      107.93         4.57        17.29         3.16        22.06        45.99 
TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 
       56.09        57.60         0.23        14.27         0.16        16.24 
TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 
        0.76        44.68         6.05        42.74         0.10        31.69 
TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 
       14.96         0.10         0.10         2.96        17.52         6.90 
TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 
       14.53        39.48        19.23        39.09         0.23        50.63 
TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 
        0.49        23.61        37.15         0.33         0.13         3.68 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 
        5.33         2.93         1.71        11.28        31.43         1.64 
TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 
       16.24         9.40        63.55         0.10        21.50        33.01 
TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 
       12.23         6.25         0.10         0.46         2.50         3.95 
TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-A4DV 
        4.70         0.23        29.59         3.88        16.04        10.49 
TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC 
        0.13        14.01         0.07        14.70         0.10         5.33 
TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A74O 
        2.70        13.02         1.81        16.14         5.33         0.10 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 
       29.92        13.45         8.32        19.23        40.18        35.90 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
        4.31        21.70        21.60        19.59        17.82        20.35 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X 
        7.89        20.81        20.71        19.00        42.77         5.23 
TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ 
        4.73         0.23         6.71         1.64         2.37         2.30 
TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-QH-A65R 
        4.11         5.88         7.63         0.76         1.28         5.75 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU 
        2.53         4.83         7.79         4.11         4.18        14.83 
TCGA-QH-A6CV TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
       14.53        12.23         2.20         3.16         0.59         6.31 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X 
        3.91         4.73         1.91         0.23         5.03         3.48 
TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TS 
        0.07        88.83        94.03        32.65        59.38        62.17 
TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ 
       69.07        18.77        37.84        34.49        31.33        21.63 
TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       16.37        17.62        23.64        32.61         9.86        94.62 
TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WI 
        5.85       106.39        62.37        72.59        80.12        84.99 
TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ 
       10.88        19.86        15.91         7.59        15.16        14.07 
TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 
       14.27         7.92        12.59         4.21         9.37         8.19 
TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ 
        2.04         8.12         3.58         4.04        28.37        13.02 
TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 
      164.38        10.39        99.06        17.42        83.80        31.59 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B 
       49.45        48.33        49.32        34.78        48.39        12.00 
TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J 
       15.09        50.76        34.36        24.26        19.36        17.49 
TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S 
       40.83        16.50        29.92        18.90         9.44         4.57 
TCGA-TM-A84T TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD 
       12.00        33.07        30.08        13.51         0.10         7.89 
TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-W9-A837 
       26.79        10.95        27.06         7.04        23.21        45.07 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              0.23               0.03 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
            117.40             211.17 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
            19.130             15.385 
[1] "0.2 - 117.4 (19.1)" "0.0 - 211.2 (15.4)"
[1] "hr=" "2"  
D68V2, continuous
D68V3, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED     8  11
  16Q LOSS WILD-TYPE 182 229
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      8   11
  16Q LOSS WILD-TYPE  182  229
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE                8                182
  MALE                 11                229
[1] 2 2
[1] FALSE
D68V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  16Q LOSS MUTATED            10                4                 5
  16Q LOSS WILD-TYPE         149              103               159
D68V5, multiclass
                   clus
vv                  16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  ASTROCYTOMA                     10                149
  OLIGOASTROCYTOMA                 4                103
  OLIGODENDROGLIOMA                5                159
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V6, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED     5  14
  16Q LOSS WILD-TYPE  84 327
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      5   14
  16Q LOSS WILD-TYPE   84  327
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  NO                 5                 84
  YES               14                327
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16Q LOSS MUTATED                                  0     0
  16Q LOSS WILD-TYPE                                1     6
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16Q LOSS MUTATED                           1    18
  16Q LOSS WILD-TYPE                        13   382
D68V7, multiclass
                                  clus
vv                                 16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  6
  BLACK OR AFRICAN AMERICAN                       1                 13
  WHITE                                          18                382
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V8, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED     1  18
  16Q LOSS WILD-TYPE  15 369
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      1   18
  16Q LOSS WILD-TYPE   15  369
                        clus
vv                       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 15
  NOT HISPANIC OR LATINO               18                369
[1] 2 2
[1] FALSE

Clustering(69) Variable = 17P LOSS MUTATION ANALYSIS
D69V1, survival
                    sevent
clus2                  0   1
  17P LOSS MUTATED     9   3
  17P LOSS WILD-TYPE 343  72
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                12                415 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 3                 72 
$`17P LOSS MUTATED`
TCGA-DU-6400 TCGA-DU-7010 TCGA-DU-8161 TCGA-DU-8165 TCGA-DU-A5TP TCGA-FG-A4MY 
        1.22        14.99        23.74        19.13        14.24        23.70 
TCGA-HT-7689 TCGA-HT-8106 TCGA-HT-8564 TCGA-HT-A4DS TCGA-P5-A5EZ TCGA-P5-A5F6 
       14.96         0.10        15.72         0.23         2.30         1.28 

$`17P LOSS WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        46.65        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       30.08        10.29        12.72        27.62        27.02        18.84 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       18.38        72.95        12.59        11.01        18.84        16.80 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        16.08        15.42        27.81        14.73        13.64 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       10.92         7.40         6.44        10.29        30.74         3.81 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       42.05        27.81        17.19        17.19        54.25        10.22 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
        6.58         3.45         6.21        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
        6.74        13.38         8.45         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 
       17.49        15.16       211.17        52.11        22.42        49.02 
TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       75.16        46.06        65.75        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 
      133.74        19.89        16.83        94.52       114.08         7.96 
TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7011 
        7.73        11.47        62.96       156.23       138.28       105.21 
TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 
        6.54         8.84       117.40        90.77        30.67        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 
       10.36         7.96        94.32        18.94        44.02        62.01 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 
       25.91        60.30        23.31        41.98         2.76         5.10 
TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 
        3.98        20.68        21.40        16.96        15.48        14.17 
TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY 
       12.59        15.12         4.96         3.65         5.65        12.20 
TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K 
        8.65         2.70        77.98         7.23         5.98        11.41 
TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 TCGA-DU-A7TG TCGA-E1-5302 
       26.76         7.13        21.30       124.50        44.42        50.14 
TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 
       67.46        41.13        79.99        57.93       134.27        78.21 
TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 
       95.57       130.78        14.33         0.23         0.20        47.77 
TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 
       17.98        34.36        32.19        18.77        14.93        24.99 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 
       23.97        13.58        15.35        17.88        22.55        20.61 
TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 
       20.09        12.95        13.68        14.24        16.01        20.09 
TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW 
       14.96        22.52        15.52        38.27        10.72         5.26 
TCGA-FG-A4MX TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 
       18.71        14.76        17.82        16.41        15.02        16.44 
TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 
       10.59        28.54        10.78        22.95        43.69         5.23 
TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 
        7.43         5.72         0.13         0.10         6.67         7.82 
TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 
        8.81         0.13         0.03        16.54         3.75        17.42 
TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 
        6.54        24.26         6.38         7.10        75.19        59.18 
TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 
       60.03       154.19         4.01         5.03        29.85        23.18 
TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 
      107.93         4.57        17.29         3.16        22.06        45.99 
TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 
       56.09        57.60         0.23        14.27         0.16        16.24 
TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 
        0.76        44.68         6.05        42.74         0.10        31.69 
TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 
        0.10         0.10         2.96        17.52         6.90        14.53 
TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 
       39.48        19.23        39.09         0.23        50.63         0.49 
TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 
       23.61        37.15         0.33         0.13         3.68         5.33 
TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 
        2.93         1.71        11.28        31.43         1.64        16.24 
TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 
        9.40        63.55         0.10        21.50        33.01        12.23 
TCGA-HT-8105 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 
        6.25         0.46         2.50         3.95         4.70         0.23 
TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 
       29.59         3.88        16.04        10.49         0.13        14.01 
TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 
        0.07        14.70         0.10         5.33         2.70        13.02 
TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 
        1.81        16.14         5.33         0.10        29.92        13.45 
TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 
        8.32        19.23        40.18        35.90         4.31        21.70 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
       21.60        19.59        17.82        20.35         7.89        20.81 
TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV 
       20.71        19.00        42.77         5.23         4.73         0.23 
TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 
        6.71         1.64         2.37         4.11         5.88         7.63 
TCGA-P5-A5F4 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z 
        0.76         5.75         2.53         4.83         7.79         4.11 
TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ 
        4.18        14.83        14.53        12.23         2.20         3.16 
TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA 
        0.59         6.31         3.91         4.73         1.91         0.23 
TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO 
        5.03         3.48         0.07        88.83        94.03        32.65 
TCGA-R8-A73M TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX 
       59.38        62.17        69.07        18.77        37.84        34.49 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       31.33        21.63        16.37        17.62        23.64        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
        9.86        94.62        83.70         5.85       106.39        62.37 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM 
       72.59        80.12        32.45        84.99        10.88        19.86 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
       15.91         7.59        15.16        14.07        14.27         7.92 
TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 
       19.63        12.59         4.21         9.37         8.19         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 
        8.12         3.58         4.04        28.37        13.02       164.38 
TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V 
       10.39        99.06        17.42        83.80        31.59        18.71 
TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF 
        5.00        49.45        48.33        49.32        34.78        48.39 
TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I 
       12.00        15.09        50.76        34.36        24.26        19.36 
TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R 
       17.49        40.83        16.50        29.92        18.90         9.44 
TCGA-TM-A84S TCGA-TM-A84T TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB 
        4.57        12.00        33.07        30.08        13.51         0.10 
TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS 
        7.89        26.79        10.95        27.06         7.04        23.21 
TCGA-W9-A837 
       45.07 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              0.10               0.03 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             23.74             211.17 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             14.60              16.08 
[1] "0.1 - 23.7 (14.6)"  "0.0 - 211.2 (16.1)"
[1] "hr=" "3.9"
D69V2, continuous
D69V3, binary
                    cls
clus                   0   1
  17P LOSS MUTATED     7   5
  17P LOSS WILD-TYPE 183 235
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      7    5
  17P LOSS WILD-TYPE  183  235
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE                7                183
  MALE                  5                235
[1] 2 2
[1] FALSE
D69V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  17P LOSS MUTATED             6                2                 4
  17P LOSS WILD-TYPE         153              105               160
D69V5, multiclass
                   clus
vv                  17P LOSS MUTATED 17P LOSS WILD-TYPE
  ASTROCYTOMA                      6                153
  OLIGOASTROCYTOMA                 2                105
  OLIGODENDROGLIOMA                4                160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V6, binary
                    cls
clus                   0   1
  17P LOSS MUTATED     1  11
  17P LOSS WILD-TYPE  88 330
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      1   11
  17P LOSS WILD-TYPE   88  330
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  NO                 1                 88
  YES               11                330
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17P LOSS MUTATED                                  0     0
  17P LOSS WILD-TYPE                                1     6
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17P LOSS MUTATED                           0    12
  17P LOSS WILD-TYPE                        14   388
D69V7, multiclass
                                  clus
vv                                 17P LOSS MUTATED 17P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  6
  BLACK OR AFRICAN AMERICAN                       0                 14
  WHITE                                          12                388
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V8, binary
                    cls
clus                   0   1
  17P LOSS MUTATED     2  10
  17P LOSS WILD-TYPE  14 377
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      2   10
  17P LOSS WILD-TYPE   14  377
                        clus
vv                       17P LOSS MUTATED 17P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                 14
  NOT HISPANIC OR LATINO               10                377
[1] 2 2
[1] FALSE

Clustering(70) Variable = 17Q LOSS MUTATION ANALYSIS
D70V1, survival
                    sevent
clus2                  0   1
  17Q LOSS MUTATED     7   1
  17Q LOSS WILD-TYPE 345  74
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 8                419 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 1                 74 
$`17Q LOSS MUTATED`
TCGA-DU-6400 TCGA-DU-8165 TCGA-FG-A4MY TCGA-HT-7689 TCGA-HT-8106 TCGA-HT-8564 
        1.22        19.13        23.70        14.96         0.10        15.72 
TCGA-P5-A5EZ TCGA-P5-A5F6 
        2.30         1.28 

$`17Q LOSS WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
       72.92        46.65        50.17        44.52        36.56        78.28 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
       30.08        10.29        12.72        27.62        27.02        18.84 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
       18.38        72.95        12.59        11.01        18.84        16.80 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        16.08        15.42        27.81        14.73        13.64 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       10.92         7.40         6.44        10.29        30.74         3.81 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       19.96        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       42.05        27.81        17.19        17.19        54.25        10.22 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
        6.58         3.45         6.21        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
        6.74        13.38         8.45         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 
       17.49        15.16       211.17        52.11        22.42        49.02 
TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       75.16        46.06        65.75        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 
      133.74        19.89        16.83        94.52       114.08         7.96 
TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 
        7.73        11.47        62.96       156.23       138.28        14.99 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 
      105.21         6.54         8.84       117.40        90.77        30.67 
TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 
       26.30        10.36         7.96        94.32        18.94        44.02 
TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 
       62.01        25.91        60.30        23.31        41.98         2.76 
TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8166 
        5.10        23.74         3.98        20.68        21.40        16.96 
TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT 
       15.48        14.17        14.24        12.59        15.12         4.96 
TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
        3.65         5.65        12.20         8.65         2.70        77.98 
TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R 
        7.23         5.98        11.41        26.76         7.13        21.30 
TCGA-DU-A7T8 TCGA-DU-A7TG TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 
      124.50        44.42        50.14        67.46        41.13        79.99 
TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 
       57.93       134.27        78.21        95.57       130.78        14.33 
TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 
        0.23         0.20        47.77        17.98        34.36        32.19 
TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 
       18.77        14.93        24.99        23.97        13.58        15.35 
TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 
       17.88        22.55        20.61        20.09        12.95        13.68 
TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 
       14.24        16.01        20.09        14.96        22.52        15.52 
TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A60J TCGA-FG-A60K 
       38.27        10.72         5.26        18.71        14.76        17.82 
TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z 
       16.41        15.02        16.44        10.59        28.54        10.78 
TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 
       22.95        43.69         5.23         7.43         5.72         0.13 
TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 
        0.10         6.67         7.82         8.81         0.13         0.03 
TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 
       16.54         3.75        17.42         6.54        24.26         6.38 
TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 
        7.10        75.19        59.18        60.03       154.19         4.01 
TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 
        5.03        29.85        23.18       107.93         4.57        17.29 
TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 
        3.16        22.06        45.99        56.09        57.60         0.23 
TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 
       14.27         0.16        16.24         0.76        44.68         6.05 
TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 
       42.74         0.10        31.69         0.10         0.10         2.96 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 
       17.52         6.90        14.53        39.48        19.23        39.09 
TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 
        0.23        50.63         0.49        23.61        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 
        0.13         3.68         5.33         2.93         1.71        11.28 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 
       31.43         1.64        16.24         9.40        63.55         0.10 
TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8107 TCGA-HT-8108 
       21.50        33.01        12.23         6.25         0.46         2.50 
TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 
        3.95         4.70         0.23        29.59         3.88        16.04 
TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA 
        0.23        10.49         0.13        14.01         0.07        14.70 
TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 
        0.10         5.33         2.70        13.02         1.81        16.14 
TCGA-HT-A618 TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 
        5.33         0.10        29.92        13.45         8.32        19.23 
TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 
       40.18        35.90         4.31        21.70        21.60        19.59 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 
       17.82        20.35         7.89        20.81        20.71        19.00 
TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX 
       42.77         5.23         4.73         0.23         6.71         1.64 
TCGA-P5-A5EY TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-QH-A65R 
        2.37         4.11         5.88         7.63         0.76         5.75 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU 
        2.53         4.83         7.79         4.11         4.18        14.83 
TCGA-QH-A6CV TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
       14.53        12.23         2.20         3.16         0.59         6.31 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X 
        3.91         4.73         1.91         0.23         5.03         3.48 
TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TS 
        0.07        88.83        94.03        32.65        59.38        62.17 
TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ 
       69.07        18.77        37.84        34.49        31.33        21.63 
TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       16.37        17.62        23.64        32.61         9.86        94.62 
TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG 
       83.70         5.85       106.39        62.37        72.59        80.12 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO 
       32.45        84.99        10.88        19.86        15.91         7.59 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY 
       15.16        14.07        14.27         7.92        19.63        12.59 
TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW 
        4.21         9.37         8.19         2.04         8.12         3.58 
TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 
        4.04        28.37        13.02       164.38        10.39        99.06 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 
       17.42        83.80        31.59        18.71         5.00        49.45 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
       48.33        49.32        34.78        48.39        12.00        15.09 
TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L 
       50.76        34.36        24.26        19.36        17.49        40.83 
TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T 
       16.50        29.92        18.90         9.44         4.57        12.00 
TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE 
       33.07        30.08        13.51         0.10         7.89        26.79 
TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-W9-A837 
       10.95        27.06         7.04        23.21        45.07 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              0.10               0.03 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             23.70             211.17 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              8.63              16.04 
[1] "0.1 - 23.7 (8.6)"   "0.0 - 211.2 (16.0)"
[1] "hr=" "2.1"
D70V2, continuous
D70V3, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     4   4
  17Q LOSS WILD-TYPE 186 236
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      4    4
  17Q LOSS WILD-TYPE  186  236
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE                4                186
  MALE                  4                236
[1] 2 2
[1] FALSE
D70V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  17Q LOSS MUTATED             3                1                 4
  17Q LOSS WILD-TYPE         156              106               160
D70V5, multiclass
                   clus
vv                  17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  ASTROCYTOMA                      3                156
  OLIGOASTROCYTOMA                 1                106
  OLIGODENDROGLIOMA                4                160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V6, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     1   7
  17Q LOSS WILD-TYPE  88 334
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      1    7
  17Q LOSS WILD-TYPE   88  334
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  NO                 1                 88
  YES                7                334
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17Q LOSS MUTATED                                  0     0
  17Q LOSS WILD-TYPE                                1     6
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17Q LOSS MUTATED                           0     8
  17Q LOSS WILD-TYPE                        14   392
D70V7, multiclass
                                  clus
vv                                 17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  6
  BLACK OR AFRICAN AMERICAN                       0                 14
  WHITE                                           8                392
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V8, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     2   6
  17Q LOSS WILD-TYPE  14 381
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      2    6
  17Q LOSS WILD-TYPE   14  381
                        clus
vv                       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                 14
  NOT HISPANIC OR LATINO                6                381
[1] 2 2
[1] FALSE

Clustering(71) Variable = 18P LOSS MUTATION ANALYSIS
D71V1, survival
                    sevent
clus2                  0   1
  18P LOSS MUTATED    46  13
  18P LOSS WILD-TYPE 306  62
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                59                368 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                13                 62 
$`18P LOSS MUTATED`
TCGA-CS-4943 TCGA-CS-5396 TCGA-DB-5275 TCGA-DB-5279 TCGA-DB-A4XD TCGA-DB-A4XG 
       18.15         9.96        47.93        44.52        27.02        72.95 
TCGA-DB-A4XH TCGA-DB-A64L TCGA-DH-5140 TCGA-DH-5142 TCGA-DH-A669 TCGA-DH-A66B 
       12.59        11.01        19.96        30.31        30.21        42.05 
TCGA-DU-5849 TCGA-DU-6393 TCGA-DU-6407 TCGA-DU-7009 TCGA-DU-7014 TCGA-DU-7300 
       14.56        52.11        94.52       138.28       117.40        62.01 
TCGA-DU-8158 TCGA-DU-A5TR TCGA-DU-A5TT TCGA-E1-5307 TCGA-FG-8188 TCGA-HT-7476 
        5.10        12.59         4.96        57.93        14.96         6.54 
TCGA-HT-7477 TCGA-HT-7480 TCGA-HT-7609 TCGA-HT-7616 TCGA-HT-7688 TCGA-HT-7692 
       24.26        75.19        45.99         0.23        31.69         2.96 
TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-8564 TCGA-HT-A5RB TCGA-HT-A616 TCGA-HT-A617 
        0.23        50.63        15.72         0.10         1.81        16.14 
TCGA-HW-7491 TCGA-HW-8320 TCGA-HW-A5KK TCGA-P5-A5EX TCGA-P5-A5EZ TCGA-QH-A65R 
       40.18        21.60         7.89         1.64         2.30         5.75 
TCGA-QH-A65Z TCGA-S9-A6TS TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6UA TCGA-S9-A6WD 
        4.11        62.17        37.84        34.49         5.85        62.37 
TCGA-S9-A6WH TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WP TCGA-S9-A7QY 
       32.45        10.88        19.86        15.91        15.16        28.37 
TCGA-S9-A7R2 TCGA-S9-A89V TCGA-TM-A84G TCGA-TM-A84I TCGA-VM-A8CA 
       10.39        18.71        34.36        19.36        13.51 

$`18P LOSS WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5393 
        4.70         7.69        43.89        10.62        64.64        40.18 
TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6290 
        0.10        21.01         6.38        17.69        23.84        17.95 
TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 
       12.43         8.48         7.56         8.02         7.40         6.61 
TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 
      122.73        81.96        75.25        72.92        46.65        50.17 
TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC 
       36.56        78.28        30.08        10.29        12.72        27.62 
TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R 
       18.84        18.38        18.84        16.80         5.98        16.08 
TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K 
       15.42        27.81        14.73        13.64        10.92         7.40 
TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5141 TCGA-DH-5143 
        6.44        10.29        30.74         3.81        31.82        14.40 
TCGA-DH-5144 TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
        8.02        27.81        17.19        17.19        54.25        10.22 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5851 TCGA-DU-5852 
        6.58         3.45         6.21        18.02        17.46         6.74 
TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 
       13.38         8.45         6.81       182.33        18.94        17.49 
TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 
       15.16       211.17        22.42        49.02        75.16        46.06 
TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 
       65.75         1.22        87.45         7.04        11.64       133.74 
TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 
       19.89        16.83       114.08         7.96         7.73        11.47 
TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 
       62.96       156.23        14.99       105.21         6.54         8.84 
TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 
       90.77        30.67        26.30        10.36         7.96        94.32 
TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 
       18.94        44.02        25.91        60.30        23.31        41.98 
TCGA-DU-7309 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 
        2.76        23.74         3.98        20.68        21.40        19.13 
TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TS TCGA-DU-A5TU 
       16.96        15.48        14.17        14.24        15.12         3.65 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
        5.65        12.20         8.65         2.70        77.98         7.23 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 
        5.98        11.41        26.76         7.13        21.30       124.50 
TCGA-DU-A7TG TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5311 
       44.42        50.14        67.46        41.13        79.99       134.27 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 
       78.21        95.57       130.78        14.33         0.23         0.20 
TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 
       47.77        17.98        34.36        32.19        18.77        14.93 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 
       24.99        23.97        13.58        15.35        17.88        22.55 
TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 
       20.61        20.09        12.95        13.68        14.24        16.01 
TCGA-FG-8187 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW 
       20.09        22.52        15.52        38.27        10.72         5.26 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ 
       18.71        23.70        14.76        17.82        16.41        15.02 
TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 
       16.44        10.59        28.54        10.78        22.95        43.69 
TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 
        5.23         7.43         5.72         0.13         0.10         6.67 
TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 
        7.82         8.81         0.13         0.03        16.54         3.75 
TCGA-HT-7475 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 
       17.42         6.38         7.10        59.18        60.03       154.19 
TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 
        4.01         5.03        29.85        23.18       107.93         4.57 
TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7620 
       17.29         3.16        22.06        56.09        57.60        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 
        0.16        16.24         0.76        44.68         6.05        42.74 
TCGA-HT-7687 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7693 TCGA-HT-7694 
        0.10        14.96         0.10         0.10        17.52         6.90 
TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7860 TCGA-HT-7873 
       14.53        39.48        19.23        39.09         0.49        23.61 
TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 
       37.15         0.33         0.13         3.68         5.33         2.93 
TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 
        1.71        11.28        31.43         1.64        16.24         9.40 
TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 
       63.55         0.10        21.50        33.01        12.23         6.25 
TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 
        0.10         0.46         2.50         3.95         4.70         0.23 
TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
       29.59         3.88        16.04         0.23        10.49         0.13 
TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 
       14.01         0.07        14.70         5.33         2.70        13.02 
TCGA-HT-A618 TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 
        5.33         0.10        29.92        13.45         8.32        19.23 
TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
       35.90         4.31        21.70        19.59        17.82        20.35 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 
       20.81        20.71        19.00        42.77         5.23         4.73 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EY TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 
        0.23         6.71         2.37         4.11         5.88         7.63 
TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A6CS 
        0.76         1.28         2.53         4.83         7.79         4.18 
TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
       14.83        14.53        12.23         2.20         3.16         0.59 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC 
        6.31         3.91         4.73         1.91         0.23         5.03 
TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
        3.48         0.07        88.83        94.03        32.65        59.38 
TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 
       69.07        18.77        31.33        21.63        16.37        17.62 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UB 
       23.64        32.61         9.86        94.62        83.70       106.39 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WI TCGA-S9-A6WO TCGA-S9-A6WQ TCGA-S9-A7IQ 
       72.59        80.12        84.99         7.59        14.07        14.27 
TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 
        7.92        19.63        12.59         4.21         9.37         8.19 
TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QZ TCGA-S9-A7R1 
        2.04         8.12         3.58         4.04        13.02       164.38 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89Z TCGA-TM-A7C3 
       99.06        17.42        83.80        31.59         5.00        49.45 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
       48.33        49.32        34.78        48.39        12.00        15.09 
TCGA-TM-A84F TCGA-TM-A84H TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O 
       50.76        24.26        17.49        40.83        16.50        29.92 
TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-VM-A8C8 TCGA-VM-A8C9 
       18.90         9.44         4.57        12.00        33.07        30.08 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M 
        0.10         7.89        26.79        10.95        27.06         7.04 
TCGA-VW-A7QS TCGA-W9-A837 
       23.21        45.07 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              0.10               0.03 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            138.28             211.17 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            19.360             15.255 
[1] "0.1 - 138.3 (19.4)" "0.0 - 211.2 (15.3)"
[1] "hr=" "1.1"
D71V2, continuous
D71V3, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    19  40
  18P LOSS WILD-TYPE 171 200
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     19   40
  18P LOSS WILD-TYPE  171  200
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE               19                171
  MALE                 40                200
[1] 2 2
[1] FALSE
D71V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  18P LOSS MUTATED            24               10                25
  18P LOSS WILD-TYPE         135               97               139
D71V5, multiclass
                   clus
vv                  18P LOSS MUTATED 18P LOSS WILD-TYPE
  ASTROCYTOMA                     24                135
  OLIGOASTROCYTOMA                10                 97
  OLIGODENDROGLIOMA               25                139
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V6, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    11  48
  18P LOSS WILD-TYPE  78 293
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     11   48
  18P LOSS WILD-TYPE   78  293
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  NO                11                 78
  YES               48                293
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18P LOSS MUTATED                                  1     0
  18P LOSS WILD-TYPE                                0     6
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18P LOSS MUTATED                           0    56
  18P LOSS WILD-TYPE                        14   344
D71V7, multiclass
                                  clus
vv                                 18P LOSS MUTATED 18P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           0                  6
  BLACK OR AFRICAN AMERICAN                       0                 14
  WHITE                                          56                344
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V8, binary
                    cls
clus                   0   1
  18P LOSS MUTATED     3  50
  18P LOSS WILD-TYPE  13 337
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      3   50
  18P LOSS WILD-TYPE   13  337
                        clus
vv                       18P LOSS MUTATED 18P LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                 13
  NOT HISPANIC OR LATINO               50                337
[1] 2 2
[1] FALSE

Clustering(72) Variable = 18Q LOSS MUTATION ANALYSIS
D72V1, survival
                    sevent
clus2                  0   1
  18Q LOSS MUTATED    43  11
  18Q LOSS WILD-TYPE 309  64
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                54                373 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                11                 64 
$`18Q LOSS MUTATED`
TCGA-CS-5396 TCGA-DB-5275 TCGA-DB-5279 TCGA-DB-A4XD TCGA-DB-A4XG TCGA-DB-A4XH 
        9.96        47.93        44.52        27.02        72.95        12.59 
TCGA-DB-A64L TCGA-DH-5140 TCGA-DH-5142 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A7UT 
       11.01        19.96        30.31        30.21        42.05         6.58 
TCGA-DU-5849 TCGA-DU-5870 TCGA-DU-6393 TCGA-DU-6407 TCGA-DU-7009 TCGA-DU-7014 
       14.56       182.33        52.11        94.52       138.28       117.40 
TCGA-DU-7300 TCGA-DU-8158 TCGA-DU-A5TT TCGA-E1-5307 TCGA-FG-8188 TCGA-HT-7476 
       62.01         5.10         4.96        57.93        14.96         6.54 
TCGA-HT-7477 TCGA-HT-7480 TCGA-HT-7606 TCGA-HT-7609 TCGA-HT-7616 TCGA-HT-7688 
       24.26        75.19        17.29        45.99         0.23        31.69 
TCGA-HT-7692 TCGA-HT-7857 TCGA-HT-8564 TCGA-HT-A5RB TCGA-HT-A617 TCGA-HW-7491 
        2.96         0.23        15.72         0.10        16.14        40.18 
TCGA-HW-8320 TCGA-P5-A5EX TCGA-QH-A65R TCGA-QH-A65Z TCGA-S9-A6TS TCGA-S9-A6TW 
       21.60         1.64         5.75         4.11        62.17        37.84 
TCGA-S9-A6TX TCGA-S9-A6WD TCGA-S9-A6WH TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN 
       34.49        62.37        32.45        10.88        19.86        15.91 
TCGA-S9-A6WP TCGA-S9-A7QY TCGA-S9-A7R2 TCGA-TM-A84G TCGA-TM-A84I TCGA-VM-A8CA 
       15.16        28.37        10.39        34.36        19.36        13.51 

$`18Q LOSS WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
       40.18         0.10        21.01         6.38        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 
       17.95        12.43         8.48         7.56         8.02         7.40 
TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5276 TCGA-DB-5277 
        6.61       122.73        81.96        75.25        72.92        46.65 
TCGA-DB-5278 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB 
       50.17        36.56        78.28        30.08        10.29        12.72 
TCGA-DB-A4XC TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q 
       27.62        18.84        18.38        18.84        16.80         5.98 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X 
       16.08        15.42        27.81        14.73        13.64        10.92 
TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5141 
        7.40         6.44        10.29        30.74         3.81        31.82 
TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR 
       14.40         8.02        27.81        17.19        17.19        54.25 
TCGA-DH-A7US TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5851 TCGA-DU-5852 
       10.22         3.45         6.21        18.02        17.46         6.74 
TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 
       13.38         8.45         6.81        18.94        17.49        15.16 
TCGA-DU-6392 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 
      211.17        22.42        49.02        75.16        46.06        65.75 
TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 
        1.22        87.45         7.04        11.64       133.74        19.89 
TCGA-DU-6406 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 
       16.83       114.08         7.96         7.73        11.47        62.96 
TCGA-DU-7008 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 
      156.23        14.99       105.21         6.54         8.84        90.77 
TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 
       30.67        26.30        10.36         7.96        94.32        18.94 
TCGA-DU-7299 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 
       44.02        25.91        60.30        23.31        41.98         2.76 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 
       23.74         3.98        20.68        21.40        19.13        16.96 
TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TU 
       15.48        14.17        14.24        12.59        15.12         3.65 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
        5.65        12.20         8.65         2.70        77.98         7.23 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 
        5.98        11.41        26.76         7.13        21.30       124.50 
TCGA-DU-A7TG TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5311 
       44.42        50.14        67.46        41.13        79.99       134.27 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 
       78.21        95.57       130.78        14.33         0.23         0.20 
TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 
       47.77        17.98        34.36        32.19        18.77        14.93 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 
       24.99        23.97        13.58        15.35        17.88        22.55 
TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 
       20.61        20.09        12.95        13.68        14.24        16.01 
TCGA-FG-8187 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW 
       20.09        22.52        15.52        38.27        10.72         5.26 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ 
       18.71        23.70        14.76        17.82        16.41        15.02 
TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 
       16.44        10.59        28.54        10.78        22.95        43.69 
TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 
        5.23         7.43         5.72         0.13         0.10         6.67 
TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 
        7.82         8.81         0.13         0.03        16.54         3.75 
TCGA-HT-7475 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 
       17.42         6.38         7.10        59.18        60.03       154.19 
TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 
        4.01         5.03        29.85        23.18       107.93         4.57 
TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7620 TCGA-HT-7676 
        3.16        22.06        56.09        57.60        14.27         0.16 
TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 
       16.24         0.76        44.68         6.05        42.74         0.10 
TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 
       14.96         0.10         0.10        17.52         6.90        14.53 
TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 
       39.48        19.23        39.09        50.63         0.49        23.61 
TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 
       37.15         0.33         0.13         3.68         5.33         2.93 
TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 
        1.71        11.28        31.43         1.64        16.24         9.40 
TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 
       63.55         0.10        21.50        33.01        12.23         6.25 
TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 
        0.10         0.46         2.50         3.95         4.70         0.23 
TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
       29.59         3.88        16.04         0.23        10.49         0.13 
TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 
       14.01         0.07        14.70         5.33         2.70        13.02 
TCGA-HT-A616 TCGA-HT-A618 TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 
        1.81         5.33         0.10        29.92        13.45         8.32 
TCGA-HW-7490 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8321 TCGA-HW-8322 
       19.23        35.90         4.31        21.70        19.59        17.82 
TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 
       20.35         7.89        20.81        20.71        19.00        42.77 
TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EY TCGA-P5-A5EZ 
        5.23         4.73         0.23         6.71         2.37         2.30 
TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-QH-A65S 
        4.11         5.88         7.63         0.76         1.28         2.53 
TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CX 
        4.83         7.79         4.18        14.83        14.53        12.23 
TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 
        2.20         3.16         0.59         6.31         3.91         4.73 
TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK 
        1.91         0.23         5.03         3.48         0.07        88.83 
TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TY 
       94.03        32.65        59.38        69.07        18.77        31.33 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       21.63        16.37        17.62        23.64        32.61         9.86 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WE TCGA-S9-A6WG 
       94.62        83.70         5.85       106.39        72.59        80.12 
TCGA-S9-A6WI TCGA-S9-A6WO TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX 
       84.99         7.59        14.07        14.27         7.92        19.63 
TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       12.59         4.21         9.37         8.19         2.04         8.12 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R3 TCGA-S9-A7R4 
        3.58         4.04        13.02       164.38        99.06        17.42 
TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 
       83.80        31.59        18.71         5.00        49.45        48.33 
TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F 
       49.32        34.78        48.39        12.00        15.09        50.76 
TCGA-TM-A84H TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q 
       24.26        17.49        40.83        16.50        29.92        18.90 
TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CB 
        9.44         4.57        12.00        33.07        30.08         0.10 
TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS 
        7.89        26.79        10.95        27.06         7.04        23.21 
TCGA-W9-A837 
       45.07 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              0.10               0.03 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            182.33             211.17 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             20.78              15.12 
[1] "0.1 - 182.3 (20.8)" "0.0 - 211.2 (15.1)"
[1] "hr=" "1.2"
D72V2, continuous
D72V3, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED    20  34
  18Q LOSS WILD-TYPE 170 206
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     20   34
  18Q LOSS WILD-TYPE  170  206
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE               20                170
  MALE                 34                206
[1] 2 2
[1] FALSE
D72V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  18Q LOSS MUTATED            19                9                26
  18Q LOSS WILD-TYPE         140               98               138
D72V5, multiclass
                   clus
vv                  18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  ASTROCYTOMA                     19                140
  OLIGOASTROCYTOMA                 9                 98
  OLIGODENDROGLIOMA               26                138
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V6, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED    11  43
  18Q LOSS WILD-TYPE  78 298
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     11   43
  18Q LOSS WILD-TYPE   78  298
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  NO                11                 78
  YES               43                298
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18Q LOSS MUTATED                                  1     0
  18Q LOSS WILD-TYPE                                0     6
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18Q LOSS MUTATED                           0    51
  18Q LOSS WILD-TYPE                        14   349
D72V7, multiclass
                                  clus
vv                                 18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           0                  6
  BLACK OR AFRICAN AMERICAN                       0                 14
  WHITE                                          51                349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V8, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED     3  47
  18Q LOSS WILD-TYPE  13 340
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      3   47
  18Q LOSS WILD-TYPE   13  340
                        clus
vv                       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                 13
  NOT HISPANIC OR LATINO               47                340
[1] 2 2
[1] FALSE

Clustering(73) Variable = 19P LOSS MUTATION ANALYSIS
D73V1, survival
                    sevent
clus2                  0   1
  19P LOSS MUTATED    14   5
  19P LOSS WILD-TYPE 338  70
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                19                408 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 5                 70 
$`19P LOSS MUTATED`
TCGA-CS-4942 TCGA-DB-5277 TCGA-DH-5140 TCGA-DH-5142 TCGA-DH-5144 TCGA-DH-A66B 
       43.89        46.65        19.96        30.31         8.02        42.05 
TCGA-DU-5855 TCGA-DU-A5TS TCGA-E1-5318 TCGA-HT-7688 TCGA-HT-7857 TCGA-HT-8111 
        6.81        15.12        78.21        31.69         0.23         0.23 
TCGA-HT-8564 TCGA-P5-A5F6 TCGA-R8-A6MO TCGA-S9-A6TX TCGA-S9-A6WI TCGA-S9-A7IS 
       15.72         1.28        32.65        34.49        84.99         7.92 
TCGA-TM-A84M 
       16.50 

$`19P LOSS WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5393 
        4.70         7.69        18.15        10.62        64.64        40.18 
TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
        0.10        21.01         9.96         6.38        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 
       17.95        12.43         8.48         7.56         8.02         7.40 
TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 
        6.61       122.73        81.96        75.25        47.93        72.92 
TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA 
       50.17        44.52        36.56        78.28        30.08        10.29 
TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG 
       12.72        27.62        27.02        18.84        18.38        72.95 
TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R 
       12.59        11.01        18.84        16.80         5.98        16.08 
TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K 
       15.42        27.81        14.73        13.64        10.92         7.40 
TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5141 TCGA-DH-5143 
        6.44        10.29        30.74         3.81        31.82        14.40 
TCGA-DH-A669 TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US 
       30.21        27.81        17.19        17.19        54.25        10.22 
TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
        6.58         3.45         6.21        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 
        6.74        13.38         8.45       182.33        18.94        17.49 
TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       15.16       211.17        52.11        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       46.06        65.75         1.22        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 
      133.74        19.89        16.83        94.52       114.08         7.96 
TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 
        7.73        11.47        62.96       156.23       138.28        14.99 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 
      105.21         6.54         8.84       117.40        90.77        30.67 
TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 
       26.30        10.36         7.96        94.32        18.94        44.02 
TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 
       62.01        25.91        60.30        23.31        41.98         2.76 
TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 
        5.10        23.74         3.98        20.68        21.40        19.13 
TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TT 
       16.96        15.48        14.17        14.24        12.59         4.96 
TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
        3.65         5.65        12.20         8.65         2.70        77.98 
TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R 
        7.23         5.98        11.41        26.76         7.13        21.30 
TCGA-DU-A7T8 TCGA-DU-A7TG TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 
      124.50        44.42        50.14        67.46        41.13        79.99 
TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 TCGA-F6-A8O3 
       57.93       134.27        95.57       130.78        14.33         0.23 
TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 
        0.20        47.77        17.98        34.36        32.19        18.77 
TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 
       14.93        24.99        23.97        13.58        15.35        17.88 
TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 
       22.55        20.61        20.09        12.95        13.68        14.24 
TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT 
       16.01        20.09        14.96        22.52        15.52        38.27 
TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K 
       10.72         5.26        18.71        23.70        14.76        17.82 
TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z 
       16.41        15.02        16.44        10.59        28.54        10.78 
TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 
       22.95        43.69         5.23         7.43         5.72         0.13 
TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 
        0.10         6.67         7.82         8.81         0.13         0.03 
TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 
       16.54         3.75        17.42         6.54        24.26         6.38 
TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 
        7.10        75.19        59.18        60.03       154.19         4.01 
TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 
        5.03        29.85        23.18       107.93         4.57        17.29 
TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 
        3.16        22.06        45.99        56.09        57.60         0.23 
TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 
       14.27         0.16        16.24         0.76        44.68         6.05 
TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 
       42.74         0.10        14.96         0.10         0.10         2.96 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 
       17.52         6.90        14.53        39.48        19.23        39.09 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
       50.63         0.49        23.61        37.15         0.33         0.13 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 
        3.68         5.33         2.93         1.71        11.28        31.43 
TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 
        1.64        16.24         9.40        63.55         0.10        21.50 
TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 
       33.01        12.23         6.25         0.10         0.46         2.50 
TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-A4DS 
        3.95         4.70        29.59         3.88        16.04         0.23 
TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB 
       10.49         0.13        14.01         0.07        14.70         0.10 
TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 
        5.33         2.70        13.02         1.81        16.14         5.33 
TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 
        0.10        29.92        13.45         8.32        19.23        40.18 
TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 
       35.90         4.31        21.70        21.60        19.59        17.82 
TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 
       20.35         7.89        20.81        20.71        19.00        42.77 
TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY 
        5.23         4.73         0.23         6.71         1.64         2.37 
TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-QH-A65R 
        2.30         4.11         5.88         7.63         0.76         5.75 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU 
        2.53         4.83         7.79         4.11         4.18        14.83 
TCGA-QH-A6CV TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
       14.53        12.23         2.20         3.16         0.59         6.31 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X 
        3.91         4.73         1.91         0.23         5.03         3.48 
TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A73M TCGA-S9-A6TS TCGA-S9-A6TU 
        0.07        88.83        94.03        59.38        62.17        69.07 
TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 
       18.77        37.84        31.33        21.63        16.37        17.62 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA 
       23.64        32.61         9.86        94.62        83.70         5.85 
TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WL 
      106.39        62.37        72.59        80.12        32.45        10.88 
TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ 
       19.86        15.91         7.59        15.16        14.07        14.27 
TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 
       19.63        12.59         4.21         9.37         8.19         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 
        8.12         3.58         4.04        28.37        13.02       164.38 
TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V 
       10.39        99.06        17.42        83.80        31.59        18.71 
TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF 
        5.00        49.45        48.33        49.32        34.78        48.39 
TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I 
       12.00        15.09        50.76        34.36        24.26        19.36 
TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S 
       17.49        40.83        29.92        18.90         9.44         4.57 
TCGA-TM-A84T TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD 
       12.00        33.07        30.08        13.51         0.10         7.89 
TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-W9-A837 
       26.79        10.95        27.06         7.04        23.21        45.07 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              0.23               0.03 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             84.99             211.17 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             19.96              15.50 
[1] "0.2 - 85.0 (20.0)"  "0.0 - 211.2 (15.5)"
[1] "hr=" "1.5"
D73V2, continuous
D73V3, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     9  10
  19P LOSS WILD-TYPE 181 230
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      9   10
  19P LOSS WILD-TYPE  181  230
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE                9                181
  MALE                 10                230
[1] 2 2
[1] FALSE
D73V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  19P LOSS MUTATED             7                4                 8
  19P LOSS WILD-TYPE         152              103               156
D73V5, multiclass
                   clus
vv                  19P LOSS MUTATED 19P LOSS WILD-TYPE
  ASTROCYTOMA                      7                152
  OLIGOASTROCYTOMA                 4                103
  OLIGODENDROGLIOMA                8                156
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V6, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     7  12
  19P LOSS WILD-TYPE  82 329
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      7   12
  19P LOSS WILD-TYPE   82  329
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  NO                 7                 82
  YES               12                329
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19P LOSS MUTATED                                  0     1
  19P LOSS WILD-TYPE                                1     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19P LOSS MUTATED                           2    16
  19P LOSS WILD-TYPE                        12   384
D73V7, multiclass
                                  clus
vv                                 19P LOSS MUTATED 19P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  5
  BLACK OR AFRICAN AMERICAN                       2                 12
  WHITE                                          16                384
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V8, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     1  16
  19P LOSS WILD-TYPE  15 371
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      1   16
  19P LOSS WILD-TYPE   15  371
                        clus
vv                       19P LOSS MUTATED 19P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 15
  NOT HISPANIC OR LATINO               16                371
[1] 2 2
[1] FALSE

Clustering(74) Variable = 19Q LOSS MUTATION ANALYSIS
D74V1, survival
                    sevent
clus2                  0   1
  19Q LOSS MUTATED   151  25
  19Q LOSS WILD-TYPE 201  50
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
               176                251 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                25                 50 
$`19Q LOSS MUTATED`
TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-5390 TCGA-CS-5396 TCGA-CS-6668 TCGA-CS-6670 
       43.89        18.15        64.64         9.96         8.02         6.61 
TCGA-DB-5274 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-A4XA TCGA-DB-A4XG 
       75.25        46.65        50.17        44.52        10.29        72.95 
TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64U 
       12.59        11.01        16.80         5.98        16.08        27.81 
TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A75K TCGA-DB-A75L TCGA-DH-5140 TCGA-DH-5141 
       14.73        13.64         7.40         6.44        19.96        31.82 
TCGA-DH-5142 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F 
       30.31         8.02        30.21        42.05        27.81        17.19 
TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DU-5849 TCGA-DU-5855 TCGA-DU-5870 
       17.19        54.25        10.22        14.56         6.81       182.33 
TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6397 TCGA-DU-6400 TCGA-DU-6408 
       15.16        52.11        22.42        46.06         1.22       114.08 
TCGA-DU-6410 TCGA-DU-7009 TCGA-DU-7014 TCGA-DU-7018 TCGA-DU-7294 TCGA-DU-7298 
        7.96       138.28       117.40        30.67        94.32        18.94 
TCGA-DU-7300 TCGA-DU-7302 TCGA-DU-8164 TCGA-DU-8168 TCGA-DU-A5TS TCGA-DU-A6S2 
       62.01        60.30        21.40        14.17        15.12         8.65 
TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S8 TCGA-DU-A76R TCGA-DU-A7TG TCGA-E1-5304 
        2.70        77.98         5.98        21.30        44.42        41.13 
TCGA-E1-5305 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 
       79.99       134.27        78.21        95.57       130.78        14.33 
TCGA-F6-A8O3 TCGA-FG-5962 TCGA-FG-5964 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 
        0.23        47.77        34.36        15.35        17.88        22.55 
TCGA-FG-7641 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-A4MT TCGA-FG-A60K 
       20.61        16.01        20.09        14.96        38.27        17.82 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A710 TCGA-FG-A713 TCGA-HT-7467 TCGA-HT-7468 
       15.02        16.44        22.95         5.23         0.10         6.67 
TCGA-HT-7469 TCGA-HT-7471 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7605 TCGA-HT-7607 
        7.82         0.13        75.19        59.18         4.57         3.16 
TCGA-HT-7608 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7677 TCGA-HT-7681 TCGA-HT-7687 
       22.06         0.23        14.27        16.24        44.68         0.10 
TCGA-HT-7688 TCGA-HT-7692 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7856 TCGA-HT-7857 
       31.69         2.96         6.90        14.53        39.09         0.23 
TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7881 TCGA-HT-8010 TCGA-HT-8012 
       37.15         0.33         0.13         2.93         1.64         9.40 
TCGA-HT-8105 TCGA-HT-8109 TCGA-HT-8111 TCGA-HT-8564 TCGA-HT-A4DV TCGA-HT-A5R9 
        6.25         3.95         0.23        15.72        10.49         0.07 
TCGA-HT-A615 TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8322 
       13.02        29.92        13.45        40.18         4.31        17.82 
TCGA-HW-A5KJ TCGA-IK-8125 TCGA-KT-A74X TCGA-P5-A5EX TCGA-P5-A5F0 TCGA-P5-A5F6 
       20.35        42.77         5.23         1.64         4.11         1.28 
TCGA-QH-A65R TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CU TCGA-QH-A6CY 
        5.75         4.83         7.79         4.11        14.83         2.20 
TCGA-QH-A6CZ TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A86X TCGA-R8-A6MK 
        3.16         6.31         3.91         4.73         3.48        88.83 
TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY 
       94.03        32.65        59.38        37.84        34.49        31.33 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WH 
       23.64        32.61       106.39        62.37        72.59        32.45 
TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WP TCGA-S9-A7IQ TCGA-S9-A7IS 
       84.99        10.88        15.91        15.16        14.27         7.92 
TCGA-S9-A7IY TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QY TCGA-S9-A7QZ 
       12.59         8.19         2.04         8.12        28.37        13.02 
TCGA-S9-A7R1 TCGA-TM-A7C5 TCGA-TM-A84G TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84R 
      164.38        49.32        34.36        16.50        29.92         9.44 
TCGA-TM-A84S TCGA-VM-A8C8 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CE TCGA-VV-A829 
        4.57        33.07        13.51         0.10        26.79        27.06 
TCGA-VW-A7QS TCGA-W9-A837 
       23.21        45.07 

$`19Q LOSS WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4944 TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 
        4.70         7.69        10.62        40.18         0.10        21.01 
TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 
        6.38        17.69        23.84        17.95        12.43         8.48 
TCGA-CS-6667 TCGA-CS-6669 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5275 TCGA-DB-5276 
        7.56         7.40       122.73        81.96        47.93        72.92 
TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD 
       36.56        78.28        30.08        12.72        27.62        27.02 
TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A64O TCGA-DB-A64S TCGA-DB-A64X TCGA-DB-A75M 
       18.84        18.38        18.84        15.42        10.92        10.29 
TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5143 TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV 
       30.74         3.81        14.40         6.58         3.45         6.21 
TCGA-DU-5847 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5871 
       18.02        17.46         6.74        13.38         8.45        18.94 
TCGA-DU-5872 TCGA-DU-6392 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6399 TCGA-DU-6401 
       17.49       211.17        49.02        75.16        65.75        87.45 
TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 
        7.04        11.64       133.74        19.89        16.83        94.52 
TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7010 TCGA-DU-7011 
        7.73        11.47        62.96       156.23        14.99       105.21 
TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 
        6.54         8.84        90.77        26.30        10.36         7.96 
TCGA-DU-7299 TCGA-DU-7301 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 
       44.02        25.91        23.31        41.98         2.76         5.10 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 
       23.74         3.98        20.68        19.13        16.96        15.48 
TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY 
       14.24        12.59         4.96         3.65         5.65        12.20 
TCGA-DU-A6S7 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A7T8 TCGA-E1-5302 
        7.23        11.41        26.76         7.13       124.50        50.14 
TCGA-E1-5303 TCGA-E1-5307 TCGA-F6-A8O4 TCGA-FG-5963 TCGA-FG-5965 TCGA-FG-6688 
       67.46        57.93         0.20        17.98        32.19        18.77 
TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7643 TCGA-FG-8181 
       14.93        24.99        23.97        13.58        20.09        12.95 
TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MU TCGA-FG-A4MW 
       13.68        14.24        22.52        15.52        10.72         5.26 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60L TCGA-FG-A6J3 TCGA-FG-A70Y 
       18.71        23.70        14.76        16.41        10.59        28.54 
TCGA-FG-A70Z TCGA-FG-A711 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7470 
       10.78        43.69         7.43         5.72         0.13         8.81 
TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 
        0.03        16.54         3.75        17.42         6.54        24.26 
TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
        6.38         7.10        60.03       154.19         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7606 TCGA-HT-7609 TCGA-HT-7610 
       29.85        23.18       107.93        17.29        45.99        56.09 
TCGA-HT-7611 TCGA-HT-7676 TCGA-HT-7680 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7689 
       57.60         0.16         0.76         6.05        42.74        14.96 
TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7693 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7858 
        0.10         0.10        17.52        39.48        19.23        50.63 
TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7882 TCGA-HT-7884 
        0.49        23.61         3.68         5.33         1.71        11.28 
TCGA-HT-7902 TCGA-HT-8011 TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 
       31.43        16.24        63.55         0.10        21.50        33.01 
TCGA-HT-8104 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8110 TCGA-HT-8113 
       12.23         0.10         0.46         2.50         4.70        29.59 
TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-A4DS TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5RA 
        3.88        16.04         0.23         0.13        14.01        14.70 
TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 
        0.10         5.33         2.70         1.81        16.14         5.33 
TCGA-HT-A74O TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7493 TCGA-HW-8319 TCGA-HW-8320 
        0.10         8.32        19.23        35.90        21.70        21.60 
TCGA-HW-8321 TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-KT-A7W1 
       19.59         7.89        20.81        20.71        19.00         4.73 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F1 TCGA-P5-A5F2 
        0.23         6.71         2.37         2.30         5.88         7.63 
TCGA-P5-A5F4 TCGA-QH-A65S TCGA-QH-A6CS TCGA-QH-A6CV TCGA-QH-A6CX TCGA-QH-A6X3 
        0.76         2.53         4.18        14.53        12.23         0.59 
TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A870 TCGA-S9-A6TS TCGA-S9-A6TU 
        1.91         0.23         5.03         0.07        62.17        69.07 
TCGA-S9-A6TV TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U6 TCGA-S9-A6U8 
       18.77        21.63        16.37        17.62         9.86        94.62 
TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6WG TCGA-S9-A6WM TCGA-S9-A6WO TCGA-S9-A6WQ 
       83.70         5.85        80.12        19.86         7.59        14.07 
TCGA-S9-A7IX TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7R2 
       19.63         4.21         9.37         3.58         4.04        10.39 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z 
       99.06        17.42        83.80        31.59        18.71         5.00 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
       49.45        48.33        34.78        48.39        12.00        15.09 
TCGA-TM-A84F TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84Q 
       50.76        24.26        19.36        17.49        40.83        18.90 
TCGA-TM-A84T TCGA-VM-A8C9 TCGA-VM-A8CD TCGA-VM-A8CH TCGA-VV-A86M 
       12.00        30.08         7.89        10.95         7.04 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              0.07               0.03 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
            182.33             211.17 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             16.34              15.09 
[1] "0.1 - 182.3 (16.3)" "0.0 - 211.2 (15.1)"
[1] "hr=" "1.7"
D74V2, continuous
D74V3, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    78  99
  19Q LOSS WILD-TYPE 112 141
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     78   99
  19Q LOSS WILD-TYPE  112  141
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE               78                112
  MALE                 99                141
[1] 2 2
[1] FALSE
D74V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  19Q LOSS MUTATED            18               35               124
  19Q LOSS WILD-TYPE         141               72                40
D74V5, multiclass
                   clus
vv                  19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  ASTROCYTOMA                     18                141
  OLIGOASTROCYTOMA                35                 72
  OLIGODENDROGLIOMA              124                 40
[1] 3 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
  19Q LOSS MUTATED    31 146
  19Q LOSS WILD-TYPE  58 195
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     31  146
  19Q LOSS WILD-TYPE   58  195
     clus
vv    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  NO                31                 58
  YES              146                195
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19Q LOSS MUTATED                                  0     3
  19Q LOSS WILD-TYPE                                1     3
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19Q LOSS MUTATED                           6   163
  19Q LOSS WILD-TYPE                         8   237
D74V7, multiclass
                                  clus
vv                                 19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           3                  3
  BLACK OR AFRICAN AMERICAN                       6                  8
  WHITE                                         163                237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V8, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED     7 157
  19Q LOSS WILD-TYPE   9 230
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      7  157
  19Q LOSS WILD-TYPE    9  230
                        clus
vv                       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    7                  9
  NOT HISPANIC OR LATINO              157                230
[1] 2 2
[1] FALSE

Clustering(75) Variable = 20P LOSS MUTATION ANALYSIS
D75V1, survival
                    sevent
clus2                  0   1
  20P LOSS MUTATED     4   1
  20P LOSS WILD-TYPE 348  74
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 5                422 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 1                 74 
$`20P LOSS MUTATED`
TCGA-DB-5277 TCGA-DU-8166 TCGA-FG-A87N TCGA-HT-7693 TCGA-S9-A89V 
       46.65        16.96         7.43        17.52        18.71 

$`20P LOSS WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
       23.84        17.95        12.43         8.48         7.56         8.02 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
        7.40         6.61       122.73        81.96        75.25        47.93 
TCGA-DB-5276 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 
       72.92        50.17        44.52        36.56        78.28        30.08 
TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF 
       10.29        12.72        27.62        27.02        18.84        18.38 
TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q 
       72.95        12.59        11.01        18.84        16.80         5.98 
TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X 
       16.08        15.42        27.81        14.73        13.64        10.92 
TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 
        7.40         6.44        10.29        30.74         3.81        19.96 
TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B 
       31.82        30.31        14.40         8.02        30.21        42.05 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT 
       27.81        17.19        17.19        54.25        10.22         6.58 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
        3.45         6.21        18.02        14.56        17.46         6.74 
TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 
       13.38         8.45         6.81       182.33        18.94        17.49 
TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       15.16       211.17        52.11        22.42        49.02        75.16 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       46.06        65.75         1.22        87.45         7.04        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 
      133.74        19.89        16.83        94.52       114.08         7.96 
TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 
        7.73        11.47        62.96       156.23       138.28        14.99 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 
      105.21         6.54         8.84       117.40        90.77        30.67 
TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 
       26.30        10.36         7.96        94.32        18.94        44.02 
TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 
       62.01        25.91        60.30        23.31        41.98         2.76 
TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 
        5.10        23.74         3.98        20.68        21.40        19.13 
TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT 
       15.48        14.17        14.24        12.59        15.12         4.96 
TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
        3.65         5.65        12.20         8.65         2.70        77.98 
TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R 
        7.23         5.98        11.41        26.76         7.13        21.30 
TCGA-DU-A7T8 TCGA-DU-A7TG TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 
      124.50        44.42        50.14        67.46        41.13        79.99 
TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 
       57.93       134.27        78.21        95.57       130.78        14.33 
TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 
        0.23         0.20        47.77        17.98        34.36        32.19 
TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 
       18.77        14.93        24.99        23.97        13.58        15.35 
TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 
       17.88        22.55        20.61        20.09        12.95        13.68 
TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 
       14.24        16.01        20.09        14.96        22.52        15.52 
TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J 
       38.27        10.72         5.26        18.71        23.70        14.76 
TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y 
       17.82        16.41        15.02        16.44        10.59        28.54 
TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87Q TCGA-FN-7833 
       10.78        22.95        43.69         5.23         5.72         0.13 
TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 
        0.10         6.67         7.82         8.81         0.13         0.03 
TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 
       16.54         3.75        17.42         6.54        24.26         6.38 
TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 
        7.10        75.19        59.18        60.03       154.19         4.01 
TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 
        5.03        29.85        23.18       107.93         4.57        17.29 
TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 
        3.16        22.06        45.99        56.09        57.60         0.23 
TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 
       14.27         0.16        16.24         0.76        44.68         6.05 
TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 
       42.74         0.10        31.69        14.96         0.10         0.10 
TCGA-HT-7692 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 
        2.96         6.90        14.53        39.48        19.23        39.09 
TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 
        0.23        50.63         0.49        23.61        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 
        0.13         3.68         5.33         2.93         1.71        11.28 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 
       31.43         1.64        16.24         9.40        63.55         0.10 
TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 
       21.50        33.01        12.23         6.25         0.10         0.46 
TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 
        2.50         3.95         4.70         0.23        29.59         3.88 
TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 
       16.04        15.72         0.23        10.49         0.13        14.01 
TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 
        0.07        14.70         0.10         5.33         2.70        13.02 
TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 
        1.81        16.14         5.33         0.10        29.92        13.45 
TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 
        8.32        19.23        40.18        35.90         4.31        21.70 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
       21.60        19.59        17.82        20.35         7.89        20.81 
TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV 
       20.71        19.00        42.77         5.23         4.73         0.23 
TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 
        6.71         1.64         2.37         2.30         4.11         5.88 
TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V 
        7.63         0.76         1.28         5.75         2.53         4.83 
TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CX 
        7.79         4.11         4.18        14.83        14.53        12.23 
TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 
        2.20         3.16         0.59         6.31         3.91         4.73 
TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK 
        1.91         0.23         5.03         3.48         0.07        88.83 
TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV 
       94.03        32.65        59.38        62.17        69.07        18.77 
TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 
       37.84        34.49        31.33        21.63        16.37        17.62 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA 
       23.64        32.61         9.86        94.62        83.70         5.85 
TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI 
      106.39        62.37        72.59        80.12        32.45        84.99 
TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ 
       10.88        19.86        15.91         7.59        15.16        14.07 
TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 
       14.27         7.92        19.63        12.59         4.21         9.37 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY 
        8.19         2.04         8.12         3.58         4.04        28.37 
TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 
       13.02       164.38        10.39        99.06        17.42        83.80 
TCGA-S9-A7R8 TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA 
       31.59         5.00        49.45        48.33        49.32        34.78 
TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H 
       48.39        12.00        15.09        50.76        34.36        24.26 
TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q 
       19.36        17.49        40.83        16.50        29.92        18.90 
TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA 
        9.44         4.57        12.00        33.07        30.08        13.51 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M 
        0.10         7.89        26.79        10.95        27.06         7.04 
TCGA-VW-A7QS TCGA-W9-A837 
       23.21        45.07 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
              7.43               0.03 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             46.65             211.17 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             17.52              15.62 
[1] "7.4 - 46.6 (17.5)"  "0.0 - 211.2 (15.6)"
[1] "hr=" "1.6"
D75V2, continuous
D75V3, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     3   2
  20P LOSS WILD-TYPE 187 238
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      3    2
  20P LOSS WILD-TYPE  187  238
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  FEMALE                3                187
  MALE                  2                238
[1] 2 2
[1] FALSE
D75V4, continuous
[1] "Remove cluster labels:" "20P LOSS MUTATED"      
clus
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 2                247 
        TCGA-CS-4938         TCGA-CS-4941         TCGA-CS-4942 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CS-4943         TCGA-CS-4944         TCGA-CS-5390 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CS-5393         TCGA-CS-5395         TCGA-CS-5396 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CS-5397         TCGA-CS-6186         TCGA-CS-6188 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CS-6290         TCGA-CS-6665         TCGA-CS-6666 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CS-6667         TCGA-CS-6668         TCGA-CS-6669 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DB-5274         TCGA-DB-A4XE         TCGA-DB-A64L 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DB-A64Q         TCGA-DB-A64R         TCGA-DB-A64S 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DB-A64U         TCGA-DB-A64V         TCGA-DB-A64W 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DB-A64X         TCGA-DB-A75L         TCGA-DB-A75O 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DH-5140         TCGA-DH-5142         TCGA-DH-5143 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DH-5144         TCGA-DH-A66B         TCGA-DH-A66D 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DH-A66F         TCGA-DH-A66G         TCGA-DH-A7UR 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DH-A7UU         TCGA-DH-A7UV         TCGA-DU-5851 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DU-5852         TCGA-DU-5853         TCGA-DU-5854 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DU-5855         TCGA-DU-5870         TCGA-DU-5871 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DU-5874         TCGA-DU-6396         TCGA-DU-6403 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DU-6404         TCGA-DU-6405         TCGA-DU-6407 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DU-6408         TCGA-DU-6410         TCGA-DU-7011 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DU-7013         TCGA-DU-7014         TCGA-DU-7015 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DU-7018         TCGA-DU-7019         TCGA-DU-7294 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DU-7298         TCGA-DU-7299         TCGA-DU-7300 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DU-7301         TCGA-DU-7302         TCGA-DU-7304 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DU-7306         TCGA-DU-7309         TCGA-DU-8158 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DU-8161         TCGA-DU-8162         TCGA-DU-8163 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DU-8165         TCGA-DU-8167         TCGA-DU-8168 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DU-A5TP         TCGA-DU-A5TR         TCGA-DU-A5TS 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DU-A5TU         TCGA-DU-A5TW         TCGA-DU-A6S2 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DU-A6S6         TCGA-DU-A6S7         TCGA-DU-A6S8 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DU-A76R         TCGA-DU-A7T8         TCGA-DU-A7TG 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-E1-5302         TCGA-E1-5303         TCGA-E1-5304 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-E1-5305         TCGA-E1-5307         TCGA-E1-5311 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-E1-5318         TCGA-E1-5319         TCGA-E1-5322 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FG-5963         TCGA-FG-5965         TCGA-FG-6688 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FG-6689         TCGA-FG-6690         TCGA-FG-6691 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FG-7636         TCGA-FG-7638         TCGA-FG-8181 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FG-8185         TCGA-FG-8186         TCGA-FG-8187 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FG-8188         TCGA-FG-8189         TCGA-FG-A4MT 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FG-A4MW         TCGA-FG-A4MX         TCGA-FG-A60J 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FG-A60L         TCGA-FG-A6J1         TCGA-FG-A6J3 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FG-A711         TCGA-FG-A713         TCGA-FG-A87Q 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-HT-7468         TCGA-HT-7470         TCGA-HT-7475 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-HT-7477         TCGA-HT-7485         TCGA-HT-7607 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-HT-7609         TCGA-HT-7611         TCGA-HT-7689 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-HT-7692         TCGA-HT-7694         TCGA-HT-7854 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-HT-7875         TCGA-HT-7884         TCGA-HT-8564 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-HT-A4DV         TCGA-HT-A5R7         TCGA-HT-A5RA 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-HT-A5RC         TCGA-HT-A615         TCGA-HT-A617 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-HT-A618         TCGA-IK-7675         TCGA-KT-A74X 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-KT-A7W1         TCGA-P5-A5EU         TCGA-P5-A5EV 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-P5-A5EW         TCGA-P5-A5EX         TCGA-P5-A5F0 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-P5-A5F2         TCGA-P5-A5F4         TCGA-P5-A5F6 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-QH-A65R         TCGA-QH-A65S         TCGA-QH-A65V 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-QH-A65X         TCGA-QH-A65Z         TCGA-QH-A6CS 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-QH-A6CU         TCGA-QH-A6CV         TCGA-QH-A6CW 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-QH-A6CX         TCGA-QH-A6CY         TCGA-QH-A6CZ 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-QH-A6X3         TCGA-QH-A6X4         TCGA-QH-A6X5 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-QH-A6X8         TCGA-QH-A6X9         TCGA-QH-A6XA 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-QH-A6XC         TCGA-QH-A86X         TCGA-QH-A870 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-S9-A6TS         TCGA-S9-A6TU         TCGA-S9-A6TV 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-S9-A6TW         TCGA-S9-A6TX         TCGA-S9-A6TY 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-S9-A6TZ         TCGA-S9-A6U0         TCGA-S9-A6U1 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-S9-A6U2         TCGA-S9-A6U5         TCGA-S9-A6U6 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-S9-A6U8         TCGA-S9-A6UA         TCGA-S9-A6UB 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-S9-A6WD         TCGA-S9-A6WE         TCGA-S9-A6WG 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-S9-A6WH         TCGA-S9-A6WI         TCGA-S9-A6WL 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-S9-A6WM         TCGA-S9-A6WN         TCGA-S9-A6WO 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-S9-A6WP         TCGA-S9-A6WQ         TCGA-S9-A7IQ 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-S9-A7IS         TCGA-S9-A7IX         TCGA-S9-A7IY 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-S9-A7IZ         TCGA-S9-A7J0         TCGA-S9-A7J1 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-S9-A7J2         TCGA-S9-A7J3         TCGA-S9-A7QW 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-S9-A7QX         TCGA-S9-A7QY         TCGA-S9-A7QZ 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-S9-A7R1         TCGA-S9-A7R2         TCGA-S9-A7R3 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-S9-A7R4         TCGA-S9-A7R7         TCGA-S9-A7R8 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-S9-A89Z         TCGA-TM-A7C3         TCGA-TM-A7C4 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-TM-A7C5         TCGA-TM-A7CA         TCGA-TM-A7CF 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-TM-A84B         TCGA-TM-A84C         TCGA-TM-A84F 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-TM-A84G         TCGA-TM-A84H         TCGA-TM-A84I 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-TM-A84J         TCGA-TM-A84L         TCGA-TM-A84M 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-TM-A84O         TCGA-TM-A84Q         TCGA-TM-A84R 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-TM-A84S         TCGA-TM-A84T         TCGA-VM-A8C8 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-VM-A8CA         TCGA-VM-A8CD         TCGA-VM-A8CE 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-VM-A8CH 
"20P LOSS WILD-TYPE" 
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  20P LOSS MUTATED             3                1                 1
  20P LOSS WILD-TYPE         156              106               163
D75V5, multiclass
                   clus
vv                  20P LOSS MUTATED 20P LOSS WILD-TYPE
  ASTROCYTOMA                      3                156
  OLIGOASTROCYTOMA                 1                106
  OLIGODENDROGLIOMA                1                163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V6, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     1   4
  20P LOSS WILD-TYPE  88 337
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      1    4
  20P LOSS WILD-TYPE   88  337
     clus
vv    20P LOSS MUTATED 20P LOSS WILD-TYPE
  NO                 1                 88
  YES                4                337
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20P LOSS MUTATED                                  0     1
  20P LOSS WILD-TYPE                                1     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20P LOSS MUTATED                           0     4
  20P LOSS WILD-TYPE                        14   396
D75V7, multiclass
                                  clus
vv                                 20P LOSS MUTATED 20P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  5
  BLACK OR AFRICAN AMERICAN                       0                 14
  WHITE                                           4                396
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V8, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     0   5
  20P LOSS WILD-TYPE  16 382
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      0    5
  20P LOSS WILD-TYPE   16  382
                        clus
vv                       20P LOSS MUTATED 20P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 16
  NOT HISPANIC OR LATINO                5                382
[1] 2 2
[1] FALSE

Clustering(76) Variable = 21Q LOSS MUTATION ANALYSIS
D76V1, survival
                    sevent
clus2                  0   1
  21Q LOSS MUTATED    23   3
  21Q LOSS WILD-TYPE 329  72
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                26                401 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 3                 72 
$`21Q LOSS MUTATED`
TCGA-CS-4943 TCGA-DB-5279 TCGA-DB-A75L TCGA-DH-5140 TCGA-DH-5142 TCGA-DU-5871 
       18.15        44.52         6.44        19.96        30.31        18.94 
TCGA-DU-7010 TCGA-DU-8165 TCGA-DU-8167 TCGA-DU-A5TU TCGA-E1-5307 TCGA-FG-7636 
       14.99        19.13        15.48         3.65        57.93        17.88 
TCGA-FG-A60J TCGA-HT-7689 TCGA-HT-7857 TCGA-HT-7902 TCGA-HT-8106 TCGA-HT-8564 
       14.76        14.96         0.23        31.43         0.10        15.72 
TCGA-HW-7490 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EZ TCGA-P5-A5F4 TCGA-P5-A5F6 
       19.23         0.23         6.71         2.30         0.76         1.28 
TCGA-S9-A89Z TCGA-TM-A84Q 
        5.00        18.90 

$`21Q LOSS WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5393 
        4.70         7.69        43.89        10.62        64.64        40.18 
TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 
        0.10        21.01         9.96         6.38        17.69        23.84 
TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 
       17.95        12.43         8.48         7.56         8.02         7.40 
TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 
        6.61       122.73        81.96        75.25        47.93        72.92 
TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA 
       46.65        50.17        36.56        78.28        30.08        10.29 
TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG 
       12.72        27.62        27.02        18.84        18.38        72.95 
TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R 
       12.59        11.01        18.84        16.80         5.98        16.08 
TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K 
       15.42        27.81        14.73        13.64        10.92         7.40 
TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5141 TCGA-DH-5143 TCGA-DH-5144 
       10.29        30.74         3.81        31.82        14.40         8.02 
TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR 
       30.21        42.05        27.81        17.19        17.19        54.25 
TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5849 
       10.22         6.58         3.45         6.21        18.02        14.56 
TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 
       17.46         6.74        13.38         8.45         6.81       182.33 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 
       17.49        15.16       211.17        52.11        22.42        49.02 
TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 
       75.16        46.06        65.75         1.22        87.45         7.04 
TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 
       11.64       133.74        19.89        16.83        94.52       114.08 
TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 
        7.96         7.73        11.47        62.96       156.23       138.28 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 
      105.21         6.54         8.84       117.40        90.77        30.67 
TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 
       26.30        10.36         7.96        94.32        18.94        44.02 
TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 
       62.01        25.91        60.30        23.31        41.98         2.76 
TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8166 
        5.10        23.74         3.98        20.68        21.40        16.96 
TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TW 
       14.17        14.24        12.59        15.12         4.96         5.65 
TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 
       12.20         8.65         2.70        77.98         7.23         5.98 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 TCGA-DU-A7TG 
       11.41        26.76         7.13        21.30       124.50        44.42 
TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5311 TCGA-E1-5318 
       50.14        67.46        41.13        79.99       134.27        78.21 
TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 
       95.57       130.78        14.33         0.23         0.20        47.77 
TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 
       17.98        34.36        32.19        18.77        14.93        24.99 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 
       23.97        13.58        15.35        22.55        20.61        20.09 
TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 
       12.95        13.68        14.24        16.01        20.09        14.96 
TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX 
       22.52        15.52        38.27        10.72         5.26        18.71 
TCGA-FG-A4MY TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 
       23.70        17.82        16.41        15.02        16.44        10.59 
TCGA-FG-A70Y TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N 
       28.54        10.78        22.95        43.69         5.23         7.43 
TCGA-FG-A87Q TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 
        5.72         0.13         0.10         6.67         7.82         8.81 
TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 
        0.13         0.03        16.54         3.75        17.42         6.54 
TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 
       24.26         6.38         7.10        75.19        59.18        60.03 
TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 
      154.19         4.01         5.03        29.85        23.18       107.93 
TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 
        4.57        17.29         3.16        22.06        45.99        56.09 
TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 
       57.60         0.23        14.27         0.16        16.24         0.76 
TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7690 
       44.68         6.05        42.74         0.10        31.69         0.10 
TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 
        0.10         2.96        17.52         6.90        14.53        39.48 
TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 
       19.23        39.09        50.63         0.49        23.61        37.15 
TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 
        0.33         0.13         3.68         5.33         2.93         1.71 
TCGA-HT-7884 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 
       11.28         1.64        16.24         9.40        63.55         0.10 
TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8107 TCGA-HT-8108 
       21.50        33.01        12.23         6.25         0.46         2.50 
TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 
        3.95         4.70         0.23        29.59         3.88        16.04 
TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA 
        0.23        10.49         0.13        14.01         0.07        14.70 
TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 
        0.10         5.33         2.70        13.02         1.81        16.14 
TCGA-HT-A618 TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7491 
        5.33         0.10        29.92        13.45         8.32        40.18 
TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 
       35.90         4.31        21.70        21.60        19.59        17.82 
TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 
       20.35         7.89        20.81        20.71        19.00        42.77 
TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5F0 TCGA-P5-A5F1 
        5.23         4.73         1.64         2.37         4.11         5.88 
TCGA-P5-A5F2 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z 
        7.63         5.75         2.53         4.83         7.79         4.11 
TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ 
        4.18        14.83        14.53        12.23         2.20         3.16 
TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA 
        0.59         6.31         3.91         4.73         1.91         0.23 
TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO 
        5.03         3.48         0.07        88.83        94.03        32.65 
TCGA-R8-A73M TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX 
       59.38        62.17        69.07        18.77        37.84        34.49 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       31.33        21.63        16.37        17.62        23.64        32.61 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD 
        9.86        94.62        83.70         5.85       106.39        62.37 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM 
       72.59        80.12        32.45        84.99        10.88        19.86 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
       15.91         7.59        15.16        14.07        14.27         7.92 
TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 
       19.63        12.59         4.21         9.37         8.19         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 
        8.12         3.58         4.04        28.37        13.02       164.38 
TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V 
       10.39        99.06        17.42        83.80        31.59        18.71 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B 
       49.45        48.33        49.32        34.78        48.39        12.00 
TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J 
       15.09        50.76        34.36        24.26        19.36        17.49 
TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T 
       40.83        16.50        29.92         9.44         4.57        12.00 
TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE 
       33.07        30.08        13.51         0.10         7.89        26.79 
TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-W9-A837 
       10.95        27.06         7.04        23.21        45.07 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              0.10               0.03 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             57.93             211.17 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            15.235             16.040 
[1] "0.1 - 57.9 (15.2)"  "0.0 - 211.2 (16.0)"
[1] "hr=" "1.3"
D76V2, continuous
D76V3, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    14  12
  21Q LOSS WILD-TYPE 176 228
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     14   12
  21Q LOSS WILD-TYPE  176  228
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE               14                176
  MALE                 12                228
[1] 2 2
[1] FALSE
D76V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  21Q LOSS MUTATED            16                5                 5
  21Q LOSS WILD-TYPE         143              102               159
D76V5, multiclass
                   clus
vv                  21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  ASTROCYTOMA                     16                143
  OLIGOASTROCYTOMA                 5                102
  OLIGODENDROGLIOMA                5                159
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V6, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED     4  22
  21Q LOSS WILD-TYPE  85 319
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      4   22
  21Q LOSS WILD-TYPE   85  319
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  NO                 4                 85
  YES               22                319
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  21Q LOSS MUTATED                                  0     0
  21Q LOSS WILD-TYPE                                1     6
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  21Q LOSS MUTATED                           0    25
  21Q LOSS WILD-TYPE                        14   375
D76V7, multiclass
                                  clus
vv                                 21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  6
  BLACK OR AFRICAN AMERICAN                       0                 14
  WHITE                                          25                375
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V8, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED     1  23
  21Q LOSS WILD-TYPE  15 364
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      1   23
  21Q LOSS WILD-TYPE   15  364
                        clus
vv                       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 15
  NOT HISPANIC OR LATINO               23                364
[1] 2 2
[1] FALSE

Clustering(77) Variable = 22Q LOSS MUTATION ANALYSIS
D77V1, survival
                    sevent
clus2                  0   1
  22Q LOSS MUTATED    28  18
  22Q LOSS WILD-TYPE 324  57
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                46                381 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                18                 57 
$`22Q LOSS MUTATED`
TCGA-CS-4943 TCGA-CS-5397 TCGA-CS-6186 TCGA-DB-5277 TCGA-DB-A64L TCGA-DB-A64O 
       18.15         6.38        17.69        46.65        11.01        18.84 
TCGA-DH-A669 TCGA-DU-5847 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-6399 TCGA-DU-7008 
       30.21        18.02         6.74        13.38        65.75       156.23 
TCGA-DU-7290 TCGA-DU-7298 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8165 TCGA-DU-8167 
       10.36        18.94         5.10        23.74        19.13        15.48 
TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TY TCGA-DU-A76K TCGA-DU-A76L TCGA-E1-5304 
        4.96         3.65        12.20        11.41        26.76        41.13 
TCGA-E1-5322 TCGA-FG-7643 TCGA-FG-A4MY TCGA-HT-7477 TCGA-HT-7686 TCGA-HT-7688 
      130.78        20.09        23.70        24.26        42.74        31.69 
TCGA-HT-7690 TCGA-HT-7860 TCGA-HT-A614 TCGA-HT-A617 TCGA-HT-A618 TCGA-HW-A5KK 
        0.10         0.49         2.70        16.14         5.33         7.89 
TCGA-P5-A5F6 TCGA-QH-A6CS TCGA-S9-A6TS TCGA-S9-A6UA TCGA-S9-A7IX TCGA-S9-A7J0 
        1.28         4.18        62.17         5.85        19.63         9.37 
TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A84G TCGA-VM-A8CD 
       18.71         5.00        34.36         7.89 

$`22Q LOSS WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5393 
        4.70         7.69        43.89        10.62        64.64        40.18 
TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 
        0.10        21.01         9.96        23.84        17.95        12.43 
TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 
        8.48         7.56         8.02         7.40         6.61       122.73 
TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5278 TCGA-DB-5279 
       81.96        75.25        47.93        72.92        50.17        44.52 
TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC 
       36.56        78.28        30.08        10.29        12.72        27.62 
TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64P 
       27.02        18.84        18.38        72.95        12.59        16.80 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
        5.98        16.08        15.42        27.81        14.73        13.64 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       10.92         7.40         6.44        10.29        30.74         3.81 
TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A66B 
       19.96        31.82        30.31        14.40         8.02        42.05 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT 
       27.81        17.19        17.19        54.25        10.22         6.58 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5854 TCGA-DU-5855 
        3.45         6.21        14.56        17.46         8.45         6.81 
TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 
      182.33        18.94        17.49        15.16       211.17        52.11 
TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6400 TCGA-DU-6401 
       22.42        49.02        75.16        46.06         1.22        87.45 
TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 
        7.04        11.64       133.74        19.89        16.83        94.52 
TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7009 
      114.08         7.96         7.73        11.47        62.96       138.28 
TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 
       14.99       105.21         6.54         8.84       117.40        90.77 
TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7299 TCGA-DU-7300 
       30.67        26.30         7.96        94.32        44.02        62.01 
TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8162 
       25.91        60.30        23.31        41.98         2.76         3.98 
TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR 
       20.68        21.40        16.96        14.17        14.24        12.59 
TCGA-DU-A5TS TCGA-DU-A5TW TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
       15.12         5.65         8.65         2.70        77.98         7.23 
TCGA-DU-A6S8 TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 TCGA-DU-A7TG TCGA-E1-5302 
        5.98         7.13        21.30       124.50        44.42        50.14 
TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 
       67.46        79.99        57.93       134.27        78.21        95.57 
TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 
       14.33         0.23         0.20        47.77        17.98        34.36 
TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 
       32.19        18.77        14.93        24.99        23.97        13.58 
TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-8181 TCGA-FG-8182 
       15.35        17.88        22.55        20.61        12.95        13.68 
TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 
       14.24        16.01        20.09        14.96        22.52        15.52 
TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A60J TCGA-FG-A60K 
       38.27        10.72         5.26        18.71        14.76        17.82 
TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z 
       16.41        15.02        16.44        10.59        28.54        10.78 
TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 
       22.95        43.69         5.23         7.43         5.72         0.13 
TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 
        0.10         6.67         7.82         8.81         0.13         0.03 
TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7478 TCGA-HT-7479 
       16.54         3.75        17.42         6.54         6.38         7.10 
TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
       75.19        59.18        60.03       154.19         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 
       29.85        23.18       107.93         4.57        17.29         3.16 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
       22.06        45.99        56.09        57.60         0.23        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7687 
        0.16        16.24         0.76        44.68         6.05         0.10 
TCGA-HT-7689 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 
       14.96         0.10         2.96        17.52         6.90        14.53 
TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7873 
       39.48        19.23        39.09         0.23        50.63        23.61 
TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 
       37.15         0.33         0.13         3.68         5.33         2.93 
TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 
        1.71        11.28        31.43         1.64        16.24         9.40 
TCGA-HT-8013 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 
       63.55         0.10        21.50        33.01        12.23         6.25 
TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 
        0.10         0.46         2.50         3.95         4.70         0.23 
TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV 
       29.59         3.88        16.04        15.72         0.23        10.49 
TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC 
        0.13        14.01         0.07        14.70         0.10         5.33 
TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 
       13.02         1.81         0.10        29.92        13.45         8.32 
TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 
       19.23        40.18        35.90         4.31        21.70        21.60 
TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 
       19.59        17.82        20.35        20.81        20.71        19.00 
TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX 
       42.77         5.23         4.73         0.23         6.71         1.64 
TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 
        2.37         2.30         4.11         5.88         7.63         0.76 
TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CU 
        5.75         2.53         4.83         7.79         4.11        14.83 
TCGA-QH-A6CV TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
       14.53        12.23         2.20         3.16         0.59         6.31 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X 
        3.91         4.73         1.91         0.23         5.03         3.48 
TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TU 
        0.07        88.83        94.03        32.65        59.38        69.07 
TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 
       18.77        37.84        34.49        31.33        21.63        16.37 
TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
       17.62        23.64        32.61         9.86        94.62        83.70 
TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI 
      106.39        62.37        72.59        80.12        32.45        84.99 
TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ 
       10.88        19.86        15.91         7.59        15.16        14.07 
TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J1 TCGA-S9-A7J2 
       14.27         7.92        12.59         4.21         8.19         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 
        8.12         3.58         4.04        28.37        13.02       164.38 
TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-TM-A7C3 
       10.39        99.06        17.42        83.80        31.59        49.45 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
       48.33        49.32        34.78        48.39        12.00        15.09 
TCGA-TM-A84F TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M 
       50.76        24.26        19.36        17.49        40.83        16.50 
TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-VM-A8C8 
       29.92        18.90         9.44         4.57        12.00        33.07 
TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A829 
       30.08        13.51         0.10        26.79        10.95        27.06 
TCGA-VV-A86M TCGA-VW-A7QS TCGA-W9-A837 
        7.04        23.21        45.07 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              0.10               0.03 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            156.23             211.17 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            16.915             15.720 
[1] "0.1 - 156.2 (16.9)" "0.0 - 211.2 (15.7)"
[1] "hr=" "3"  
D77V2, continuous
D77V3, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    22  24
  22Q LOSS WILD-TYPE 168 216
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     22   24
  22Q LOSS WILD-TYPE  168  216
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE               22                168
  MALE                 24                216
[1] 2 2
[1] FALSE
D77V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  22Q LOSS MUTATED            22               11                13
  22Q LOSS WILD-TYPE         137               96               151
D77V5, multiclass
                   clus
vv                  22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  ASTROCYTOMA                     22                137
  OLIGOASTROCYTOMA                11                 96
  OLIGODENDROGLIOMA               13                151
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V6, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED     9  37
  22Q LOSS WILD-TYPE  80 304
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      9   37
  22Q LOSS WILD-TYPE   80  304
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  NO                 9                 80
  YES               37                304
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  22Q LOSS MUTATED                                  1     0
  22Q LOSS WILD-TYPE                                0     6
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  22Q LOSS MUTATED                           1    44
  22Q LOSS WILD-TYPE                        13   356
D77V7, multiclass
                                  clus
vv                                 22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           0                  6
  BLACK OR AFRICAN AMERICAN                       1                 13
  WHITE                                          44                356
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V8, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED     1  41
  22Q LOSS WILD-TYPE  15 346
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      1   41
  22Q LOSS WILD-TYPE   15  346
                        clus
vv                       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 15
  NOT HISPANIC OR LATINO               41                346
[1] 2 2
[1] FALSE

Clustering(78) Variable = XQ LOSS MUTATION ANALYSIS
D78V1, survival
                   sevent
clus2                 0   1
  XQ LOSS MUTATED    40  15
  XQ LOSS WILD-TYPE 312  60
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               55               372 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               15                60 
$`XQ LOSS MUTATED`
TCGA-CS-6667 TCGA-DB-5275 TCGA-DB-5277 TCGA-DB-5279 TCGA-DB-A4XH TCGA-DB-A64W 
        7.56        47.93        46.65        44.52        12.59        13.64 
TCGA-DH-5140 TCGA-DU-5847 TCGA-DU-6404 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 
       19.96        18.02       133.74         7.96         7.73        11.47 
TCGA-DU-7018 TCGA-DU-7294 TCGA-DU-7299 TCGA-DU-7302 TCGA-DU-8158 TCGA-DU-8168 
       30.67        94.32        44.02        60.30         5.10        14.17 
TCGA-DU-A6S8 TCGA-DU-A76R TCGA-E1-5302 TCGA-E1-5311 TCGA-EZ-7264 TCGA-F6-A8O3 
        5.98        21.30        50.14       134.27        14.33         0.23 
TCGA-FG-5964 TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-HT-7469 TCGA-HT-7471 TCGA-HT-7477 
       34.36        15.02        16.44         7.82         0.13        24.26 
TCGA-HT-7616 TCGA-HT-7690 TCGA-HT-7692 TCGA-HT-7855 TCGA-HT-8104 TCGA-HT-8564 
        0.23         0.10         2.96        19.23        12.23        15.72 
TCGA-HW-7491 TCGA-HW-8321 TCGA-IK-7675 TCGA-KT-A74X TCGA-P5-A5EZ TCGA-P5-A5F6 
       40.18        19.59        19.00         5.23         2.30         1.28 
TCGA-QH-A65Z TCGA-QH-A6X4 TCGA-QH-A6X8 TCGA-S9-A6TV TCGA-S9-A6WP TCGA-S9-A7IS 
        4.11         6.31         4.73        18.77        15.16         7.92 
TCGA-S9-A7QW TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C5 TCGA-TM-A84I TCGA-VM-A8CD 
        3.58        18.71         5.00        49.32        19.36         7.89 
TCGA-VV-A829 
       27.06 

$`XQ LOSS WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6668 TCGA-CS-6669 
       23.84        17.95        12.43         8.48         8.02         7.40 
TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5276 TCGA-DB-5278 
        6.61       122.73        81.96        75.25        72.92        50.17 
TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC 
       36.56        78.28        30.08        10.29        12.72        27.62 
TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A64L TCGA-DB-A64O 
       27.02        18.84        18.38        72.95        11.01        18.84 
TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V 
       16.80         5.98        16.08        15.42        27.81        14.73 
TCGA-DB-A64X TCGA-DB-A75K TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P 
       10.92         7.40         6.44        10.29        30.74         3.81 
TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B 
       31.82        30.31        14.40         8.02        30.21        42.05 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DH-A7UT 
       27.81        17.19        17.19        54.25        10.22         6.58 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 
        3.45         6.21        14.56        17.46         6.74        13.38 
TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 
        8.45         6.81       182.33        18.94        17.49        15.16 
TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 
      211.17        52.11        22.42        49.02        75.16        46.06 
TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6405 
       65.75         1.22        87.45         7.04        11.64        19.89 
TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 
       16.83        94.52       114.08        62.96       156.23       138.28 
TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 
       14.99       105.21         6.54         8.84       117.40        90.77 
TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7298 TCGA-DU-7300 TCGA-DU-7301 
       26.30        10.36         7.96        18.94        62.01        25.91 
TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 
       23.31        41.98         2.76        23.74         3.98        20.68 
TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-A5TP TCGA-DU-A5TR 
       21.40        19.13        16.96        15.48        14.24        12.59 
TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 
       15.12         4.96         3.65         5.65        12.20         8.65 
TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O 
        2.70        77.98         7.23        11.41        26.76         7.13 
TCGA-DU-A7T8 TCGA-DU-A7TG TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 
      124.50        44.42        67.46        41.13        79.99        57.93 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5963 
       78.21        95.57       130.78         0.20        47.77        17.98 
TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 
       32.19        18.77        14.93        24.99        23.97        13.58 
TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 
       15.35        17.88        22.55        20.61        20.09        12.95 
TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 
       13.68        14.24        16.01        20.09        14.96        22.52 
TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY 
       15.52        38.27        10.72         5.26        18.71        23.70 
TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FG-A70Z 
       14.76        17.82        16.41        10.59        28.54        10.78 
TCGA-FG-A710 TCGA-FG-A711 TCGA-FG-A713 TCGA-FG-A87N TCGA-FG-A87Q TCGA-FN-7833 
       22.95        43.69         5.23         7.43         5.72         0.13 
TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7470 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 
        0.10         6.67         8.81         0.03        16.54         3.75 
TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 
       17.42         6.54         6.38         7.10        75.19        59.18 
TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 
       60.03       154.19         4.01         5.03        29.85        23.18 
TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 
      107.93         4.57        17.29         3.16        22.06        45.99 
TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 
       56.09        57.60        14.27         0.16        16.24         0.76 
TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 
       44.68         6.05        42.74         0.10        31.69        14.96 
TCGA-HT-7691 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7856 
        0.10        17.52         6.90        14.53        39.48        39.09 
TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 
        0.23        50.63         0.49        23.61        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 
        0.13         3.68         5.33         2.93         1.71        11.28 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8015 
       31.43         1.64        16.24         9.40        63.55         0.10 
TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 
       21.50        33.01         6.25         0.10         0.46         2.50 
TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 
        3.95         4.70         0.23        29.59         3.88        16.04 
TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RA 
        0.23        10.49         0.13        14.01         0.07        14.70 
TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 
        0.10         5.33         2.70        13.02         1.81        16.14 
TCGA-HT-A618 TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 
        5.33         0.10        29.92        13.45         8.32        19.23 
TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8322 TCGA-HW-A5KJ 
       35.90         4.31        21.70        21.60        17.82        20.35 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-8125 TCGA-KT-A7W1 TCGA-P5-A5EV 
        7.89        20.81        20.71        42.77         4.73         0.23 
TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 
        6.71         1.64         2.37         4.11         5.88         7.63 
TCGA-P5-A5F4 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A6CS 
        0.76         5.75         2.53         4.83         7.79         4.18 
TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
       14.83        14.53        12.23         2.20         3.16         0.59 
TCGA-QH-A6X5 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-QH-A86X TCGA-QH-A870 
        3.91         1.91         0.23         5.03         3.48         0.07 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TS TCGA-S9-A6TU 
       88.83        94.03        32.65        59.38        62.17        69.07 
TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 
       37.84        34.49        31.33        21.63        16.37        17.62 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA 
       23.64        32.61         9.86        94.62        83.70         5.85 
TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI 
      106.39        62.37        72.59        80.12        32.45        84.99 
TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WQ TCGA-S9-A7IQ 
       10.88        19.86        15.91         7.59        14.07        14.27 
TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 
       19.63        12.59         4.21         9.37         8.19         2.04 
TCGA-S9-A7J3 TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R2 
        8.12         4.04        28.37        13.02       164.38        10.39 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-TM-A7C3 TCGA-TM-A7C4 
       99.06        17.42        83.80        31.59        49.45        48.33 
TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G 
       34.78        48.39        12.00        15.09        50.76        34.36 
TCGA-TM-A84H TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q 
       24.26        17.49        40.83        16.50        29.92        18.90 
TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA 
        9.44         4.57        12.00        33.07        30.08        13.51 
TCGA-VM-A8CB TCGA-VM-A8CE TCGA-VM-A8CH TCGA-VV-A86M TCGA-VW-A7QS TCGA-W9-A837 
        0.10        26.79        10.95         7.04        23.21        45.07 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             0.10              0.03 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           134.27            211.17 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            15.02             16.06 
[1] "0.1 - 134.3 (15.0)" "0.0 - 211.2 (16.1)"
[1] "hr=" "1.9"
D78V2, continuous
D78V3, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    20  36
  XQ LOSS WILD-TYPE 170 204
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     20   36
  XQ LOSS WILD-TYPE  170  204
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE              20               170
  MALE                36               204
[1] 2 2
[1] FALSE
D78V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  XQ LOSS MUTATED            20               13                23
  XQ LOSS WILD-TYPE         139               94               141
D78V5, multiclass
                   clus
vv                  XQ LOSS MUTATED XQ LOSS WILD-TYPE
  ASTROCYTOMA                    20               139
  OLIGOASTROCYTOMA               13                94
  OLIGODENDROGLIOMA              23               141
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V6, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    12  44
  XQ LOSS WILD-TYPE  77 297
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     12   44
  XQ LOSS WILD-TYPE   77  297
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  NO               12                77
  YES              44               297
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XQ LOSS MUTATED                                  0     1
  XQ LOSS WILD-TYPE                                1     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XQ LOSS MUTATED                           0    54
  XQ LOSS WILD-TYPE                        14   346
D78V7, multiclass
                                  clus
vv                                 XQ LOSS MUTATED XQ LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 5
  BLACK OR AFRICAN AMERICAN                      0                14
  WHITE                                         54               346
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V8, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     2  51
  XQ LOSS WILD-TYPE  14 336
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      2   51
  XQ LOSS WILD-TYPE   14  336
                        clus
vv                       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                14
  NOT HISPANIC OR LATINO              51               336
[1] 2 2
[1] FALSE
