[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/10005995/LGG-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LGG-TP/10013775/transformed.cor.cli.txt"

nPatients in clinical file=403, in cluster file=512, common to both=400
[1] "Reduce the number of clustering variables from 80 to 78."
[1]  78 400
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               11               389 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               11               389 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               18               382 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               18               382 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               10               390 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               10               390 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                9               391 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                9               391 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               11               389 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               11               389 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                8               392 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                8               392 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                9               391 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                9               391 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                3               397 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                3               397 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                8               392 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                8               392 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                5               395 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                5               395 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                7               393 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                7               393 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               92               308 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               92               308 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              121               279 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              121               279 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               37               363 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               37               363 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               44               356 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               44               356 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               14               386 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               14               386 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               19               381 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               19               381 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                38                362 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                38                362 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 7                393 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 7                393 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                27                373 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                27                373 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                47                353 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                47                353 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                27                373 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                27                373 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                13                387 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                13                387 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 5                395 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 5                395 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 3                397 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 3                397 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 8                392 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 8                392 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                14                386 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                14                386 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                17                383 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                17                383 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                17                383 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                17                383 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                19                381 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                19                381 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                12                388 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                12                388 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 9                391 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 9                391 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                79                321 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                79                321 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                20                380 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                20                380 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                36                364 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                36                364 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                37                363 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                37                363 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                21                379 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                21                379 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                14                386 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                14                386 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               28               372 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               28               372 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
              147               253 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
              147               253 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               18               382 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               18               382 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               14               386 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               14               386 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               13               387 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               13               387 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               19               381 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               19               381 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               23               377 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               23               377 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               56               344 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               56               344 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               72               328 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               72               328 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               28               372 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               28               372 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               28               372 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               28               372 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               24               376 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               24               376 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               47               353 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               47               353 
[1] "7P LOSS MUTATION ANALYSIS"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                3               397 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                3               397 
[1] "7Q LOSS MUTATION ANALYSIS"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                3               397 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                3               397 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               13               387 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               13               387 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                9               391 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                9               391 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               86               314 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               86               314 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               34               366 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               34               366 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                66                334 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                66                334 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                77                323 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                77                323 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                49                351 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                49                351 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                17                383 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                17                383 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                18                382 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                18                382 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                37                363 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                37                363 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                94                306 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                94                306 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                63                337 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                63                337 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                36                364 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                36                364 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                10                390 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                10                390 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                18                382 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                18                382 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                12                388 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                12                388 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 8                392 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 8                392 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                58                342 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                58                342 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                53                347 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                53                347 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                18                382 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                18                382 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
               166                234 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
               166                234 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 3                397 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 3                397 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                24                376 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                24                376 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                45                355 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                45                355 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               53               347 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               53               347 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDESEASE"                  
 [6] "DCCUPLOADDATE"                         
 [7] "GENDER"                                
 [8] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
 [9] "DAYSTOLASTKNOWNALIVE"                  
[10] "RADIATIONTHERAPY"                      
[11] "KARNOFSKYPERFORMANCESCORE"             
[12] "HISTOLOGICALTYPE"                      
[13] "RADIATIONS.RADIATION.REGIMENINDICATION"
[14] "RACE"                                  
[15] "ETHNICITY"                             
[16] "BATCHNUMBER"                           

Input Data has 16 rows and 400 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-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 
         332           NA          968          922          438          244 
TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DU-5847 
          NA          901          479          237          117          548 
TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 
         443          531           NA          407          257          207 
TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 
        5546          576          532          461         6423         1585 
TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 
         682         1491         2286         1401           NA           37 
TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 
        2660          214           NA           NA          605           NA 
TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 
          NA         3470          242          235           NA           NA 
TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 
        4752         4206           NA           NA           NA           NA 
TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 
          NA         2761           NA          800           NA           NA 
TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 
        2869           NA           NA           NA           NA         1834 
TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 
          NA         1277           84           NA           NA          121 
TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 
         629          651          582          516          471          431 
TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW 
         433          383          460          151          111          172 
TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 
         371          263           82         2372          220          182 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 TCGA-E1-5302 
          NA           NA          217           NA         3787         1525 
TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 
        2052         1251         2433         1762         4084         2379 
TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 
        2907         3978          436         1453          547         1045 
TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 
         979          571          454          760          729          413 
TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 
         467          544          686          627          611          394 
TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 
         416          433          487          611          455          361 
TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY 
         472          744           18          160          113          294 
TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 
         214          202          214          128          124          322 
TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A713 TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 
         328          698          159            4            3          203 
TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 
         238          268            4            1          503          114 
TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 
         530          199          738          194          216         2287 
TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 
        1800         1826         4690          122          153          908 
TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 
         705         3283          139          526           NA          671 
TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 
        1399         1706         1752           NA          434            5 
TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 
         494           23         1359          184         1300            3 
TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 
         964          455            3            3           90          533 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 
         210          442         1201          585         1189            7 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
        1540           15          718         1130           10            4 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 
         112          162           89           52          343          956 
TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8018 TCGA-HT-8019 
          50          494          286           NA          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-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB 
           7          319            4            2          447            3 
TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 
          NA           82          396           55          491          162 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 
         910          409          253          585         1222         1092 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
         131          262          272          596          542          321 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X 
         240          294          201           NA         1301          159 
TCGA-KT-A7W1 TCGA-P5-A5ET TCGA-P5-A5EU TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX 
         144           NA           NA            7          204           50 
TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F6 TCGA-QH-A65R 
          72           70          125          179           39          175 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU 
          77          147          237          125          127           NA 
TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
          90           NA           NA           67           96           18 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC 
         192          119          144           58            7          153 
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          860          856          684          658          498 
TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
         344          475          610          300         2878         2546 
TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH 
          NA         3156         1897         2208         2146          697 
TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP 
        2149          331          283          275          231          187 
TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ 
         103          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-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 
         554          396           NA         2649          530         2549 
TCGA-S9-A7R8 TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA 
          NA          152         1504         1093          770          687 
TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H 
        1472          365          459         1544         1045          738 
TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q 
         589          532           NA          502          910          575 
TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA 
         287          139          365         1006          915          411 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH 
           3           NA          815          333 
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=71,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=300,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 7:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=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=17,	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 400 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 317  67
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               11               384 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                4                67 
$`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         9.30        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-DH-5140 
       15.42        27.81        14.73        13.64        10.92        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        29.62 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       15.75         7.79         3.85        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-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-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-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-E1-5302 
       11.41        26.76         7.13        21.30       124.50        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-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 
      130.78        14.33        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        11.87        15.52 
TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J 
       24.46         0.59         5.26         3.72         9.67         7.04 
TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Z 
        6.64         7.04         4.21         4.08        10.59        10.78 
TCGA-FG-A710 TCGA-FG-A713 TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 
       22.95         5.23         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-7687 TCGA-HT-7688 TCGA-HT-7689 
        0.76        44.68         6.05         0.10        31.69        14.96 
TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 
        0.10         0.10         2.96        17.52         6.90        14.53 
TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 
       39.48        19.23        39.09         0.23        50.63         0.49 
TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 
       23.61        37.15         0.33         0.13         3.68         5.33 
TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 
        2.93         1.71        11.28        31.43         1.64        16.24 
TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 
        9.40        63.55        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-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-HW-7486 TCGA-HW-7487 TCGA-HW-7489 
        1.81        16.14         5.33        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         8.61         8.94 
TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM 
       19.59        17.82        10.55         7.89         9.67         6.61 
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-A5F6 
        1.64         2.37         2.30         4.11         5.88         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-A6CV TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 
        2.96         2.20         3.16         0.59         6.31         3.91 
TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-R8-A6MK TCGA-R8-A6ML 
        4.73         1.91         0.23         5.03        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        28.27 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 
       28.14        22.49        21.63        16.37        11.31        15.62 
TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB 
       20.05         9.86        94.62        83.70         5.85       103.76 
TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL 
       62.37        72.59        70.55        22.92        70.65        10.88 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
        9.04         7.59         6.15         3.39        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-A7R2 
        8.12         3.58         4.04        18.21        13.02        10.39 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89Z TCGA-TM-A7C3 
       87.09        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 
       35.93        25.32        22.59        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 

  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 
           12.430            15.025 
[1] "0.2 - 42.7 (12.4)"  "0.0 - 211.2 (15.0)"
[1] "hr=" "3.9"
D1V2, continuous
D1V3, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     7   4
  1P GAIN WILD-TYPE 169 220
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      7    4
  1P GAIN WILD-TYPE  169  220
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE               7               169
  MALE                 4               220
[1] 2 2
[1] FALSE
D1V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  1P GAIN MUTATED             9                0                 2
  1P GAIN WILD-TYPE         134              104               151
D1V5, multiclass
                   clus
vv                  1P GAIN MUTATED 1P GAIN WILD-TYPE
  ASTROCYTOMA                     9               134
  OLIGOASTROCYTOMA                0               104
  OLIGODENDROGLIOMA               2               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"
D1V6, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     3   8
  1P GAIN WILD-TYPE  86 303
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      3    8
  1P GAIN WILD-TYPE   86  303
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  NO                3                86
  YES               8               303
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1P GAIN MUTATED                                  0     0
  1P GAIN WILD-TYPE                                1     2
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1P GAIN MUTATED                           0    11
  1P GAIN WILD-TYPE                        14   365
D1V7, multiclass
                                  clus
vv                                 1P GAIN MUTATED 1P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 2
  BLACK OR AFRICAN AMERICAN                      0                14
  WHITE                                         11               365
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V8, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     0  11
  1P GAIN WILD-TYPE  15 348
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      0   11
  1P GAIN WILD-TYPE   15  348
                        clus
vv                       1P GAIN MUTATED 1P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                15
  NOT HISPANIC OR LATINO              11               348
[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 311  66
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               18               377 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                5                66 
$`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         9.30        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-DH-5140 TCGA-DH-5141 
       27.81        14.73        13.64        10.92        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        29.62        15.75 
TCGA-DH-A66F TCGA-DH-A66G TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
        7.79         3.85        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-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 
       15.16        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-7018 TCGA-DU-7019 TCGA-DU-7292 TCGA-DU-7294 
        8.84       117.40        30.67        26.30         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-8163 TCGA-DU-8164 
       41.98         2.76         5.10        23.74        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-A76O TCGA-DU-A76R 
        7.23         5.98        11.41        26.76         7.13        21.30 
TCGA-DU-A7T8 TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 
      124.50        50.14        67.46        79.99        57.93       134.27 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 TCGA-FG-5962 TCGA-FG-5963 
       78.21        95.57       130.78        14.33        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 
       11.87        15.52        24.46         0.59         5.26         3.72 
TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 
        9.67         7.04         6.64         7.04         4.21         4.08 
TCGA-FG-A6J3 TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A713 TCGA-FN-7833 TCGA-HT-7467 
       10.59        10.78        22.95         5.23         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-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 
        3.75         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-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-8018 TCGA-HT-8019 TCGA-HT-8104 
       16.24         9.40        63.55        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-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-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-7493 TCGA-HW-7495 TCGA-HW-8319 
        8.32        19.23        40.18        35.90         4.31         8.61 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
        8.94        19.59        17.82        10.55         7.89         9.67 
TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV 
        6.61        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-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-A6CV TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
        4.18         2.96         2.20         3.16         0.59         6.31 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-R8-A6MK 
        3.91         4.73         1.91         0.23         5.03        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 
       28.27        28.14        22.49        21.63        16.37        11.31 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA 
       15.62        20.05         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 
      103.76        62.37        72.59        70.55        22.92        70.65 
TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ 
       10.88         9.04         7.59         6.15         3.39        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        18.21        13.02 
TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89Z 
       10.39        87.09        17.42        83.80        31.59         5.00 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84C 
       49.45        35.93        25.32        22.59        48.39        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 
       30.08         0.10         7.89        26.79        10.95 

  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 
            12.97             15.09 
[1] "0.2 - 211.2 (13.0)" "0.0 - 182.3 (15.1)"
[1] "hr=" "1.5"
D2V2, continuous
D2V3, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    10   8
  1Q GAIN WILD-TYPE 166 216
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     10    8
  1Q GAIN WILD-TYPE  166  216
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE              10               166
  MALE                 8               216
[1] 2 2
[1] FALSE
D2V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  1Q GAIN MUTATED            10                2                 6
  1Q GAIN WILD-TYPE         133              102               147
D2V5, multiclass
                   clus
vv                  1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  ASTROCYTOMA                    10               133
  OLIGOASTROCYTOMA                2               102
  OLIGODENDROGLIOMA               6               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"
D2V6, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED     5  13
  1Q GAIN WILD-TYPE  84 298
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      5   13
  1Q GAIN WILD-TYPE   84  298
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  NO                5                84
  YES              13               298
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1Q GAIN MUTATED                                  0     0
  1Q GAIN WILD-TYPE                                1     2
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1Q GAIN MUTATED                           0    17
  1Q GAIN WILD-TYPE                        14   359
D2V7, multiclass
                                  clus
vv                                 1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 2
  BLACK OR AFRICAN AMERICAN                      0                14
  WHITE                                         17               359
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V8, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED     0  17
  1Q GAIN WILD-TYPE  15 342
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      0   17
  1Q GAIN WILD-TYPE   15  342
                        clus
vv                       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                15
  NOT HISPANIC OR LATINO              17               342
[1] 2 2
[1] FALSE

Clustering(3) Variable = 2P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                 0   1
  2P GAIN MUTATED     8   2
  2P GAIN WILD-TYPE 316  69
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               10               385 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                2                69 
$`2P GAIN MUTATED`
TCGA-DB-5274 TCGA-DH-A669 TCGA-DU-8165 TCGA-E1-5304 TCGA-HT-8564 TCGA-HT-A4DS 
       75.25        30.21        19.13        41.13        15.72         0.23 
TCGA-S9-A6WM TCGA-S9-A7J0 TCGA-TM-A84Q TCGA-VM-A8CA 
        9.30         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-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        29.62 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       15.75         7.79         3.85        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-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-E1-5302 TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5307 
       21.30       124.50        50.14        67.46        79.99        57.93 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 TCGA-FG-5962 
      134.27        78.21        95.57       130.78        14.33        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        11.87        15.52        24.46         0.59         5.26 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ 
        3.72         9.67         7.04         6.64         7.04         4.21 
TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A713 TCGA-FN-7833 
        4.08        10.59        10.78        22.95         5.23         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-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-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB 
       16.04        10.49         0.13         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-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         8.61         8.94        19.59        17.82        10.55 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X 
        7.89         9.67         6.61        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-A5F6 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V 
        4.11         5.88         1.28         5.75         2.53         4.83 
TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CV TCGA-QH-A6CY TCGA-QH-A6CZ 
        7.79         4.11         4.18         2.96         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-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TS 
        5.03        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        28.27        28.14        22.49        21.63 
TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       16.37        11.31        15.62        20.05         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       103.76        62.37        72.59        70.55 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP 
       22.92        70.65        10.88         9.04         7.59         6.15 
TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ 
        3.39        14.27         7.92        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        18.21 
TCGA-S9-A7QZ TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 
       13.02        10.39        87.09        17.42        83.80        31.59 
TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF 
        5.00        49.45        35.93        25.32        22.59        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-A84R TCGA-TM-A84S 
       17.49        40.83        16.50        29.92         9.44         4.57 
TCGA-TM-A84T TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE 
       12.00        33.07        30.08         0.10         7.89        26.79 
TCGA-VM-A8CH 
       10.95 

  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 
            17.31             14.96 
[1] "0.2 - 75.2 (17.3)"  "0.0 - 211.2 (15.0)"
[1] "hr=" "1.3"
D3V2, continuous
D3V3, binary
                   cls
clus                  0   1
  2P GAIN MUTATED     5   5
  2P GAIN WILD-TYPE 171 219
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      5    5
  2P GAIN WILD-TYPE  171  219
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE               5               171
  MALE                 5               219
[1] 2 2
[1] FALSE
D3V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  2P GAIN MUTATED             5                1                 4
  2P GAIN WILD-TYPE         138              103               149
D3V5, multiclass
                   clus
vv                  2P GAIN MUTATED 2P GAIN WILD-TYPE
  ASTROCYTOMA                     5               138
  OLIGOASTROCYTOMA                1               103
  OLIGODENDROGLIOMA               4               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"
D3V6, binary
                   cls
clus                  0   1
  2P GAIN MUTATED     2   8
  2P GAIN WILD-TYPE  87 303
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      2    8
  2P GAIN WILD-TYPE   87  303
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  NO                2                87
  YES               8               303
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2P GAIN MUTATED                                  0     0
  2P GAIN WILD-TYPE                                1     2
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2P GAIN MUTATED                           0     9
  2P GAIN WILD-TYPE                        14   367
D3V7, multiclass
                                  clus
vv                                 2P GAIN MUTATED 2P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 2
  BLACK OR AFRICAN AMERICAN                      0                14
  WHITE                                          9               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"
D3V8, binary
                   cls
clus                  0   1
  2P GAIN MUTATED     1   8
  2P GAIN WILD-TYPE  14 351
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      1    8
  2P GAIN WILD-TYPE   14  351
                        clus
vv                       2P GAIN MUTATED 2P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                14
  NOT HISPANIC OR LATINO               8               351
[1] 2 2
[1] FALSE

Clustering(4) Variable = 2Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                 0   1
  2Q GAIN MUTATED     8   1
  2Q GAIN WILD-TYPE 316  70
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                9               386 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                1                70 
$`2Q GAIN MUTATED`
TCGA-DB-5274 TCGA-DU-8165 TCGA-E1-5304 TCGA-HT-8564 TCGA-HT-A4DS TCGA-S9-A6WM 
       75.25        19.13        41.13        15.72         0.23         9.30 
TCGA-S9-A7J0 TCGA-TM-A84Q TCGA-VM-A8CA 
        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-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-DU-5847 TCGA-DU-5849 
       29.62        15.75         7.79         3.85        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-6399 TCGA-DU-6400 TCGA-DU-6401 
       49.02        75.16        46.06        65.75         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-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-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-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-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-E1-5302 TCGA-E1-5303 TCGA-E1-5305 
        7.13        21.30       124.50        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-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        11.87        15.52        24.46         0.59 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
        5.26         3.72         9.67         7.04         6.64         7.04 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A713 
        4.21         4.08        10.59        10.78        22.95         5.23 
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-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 
       63.55        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-A4DV TCGA-HT-A5R5 TCGA-HT-A5R9 TCGA-HT-A5RA 
        3.88        16.04        10.49         0.13         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-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-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 
       35.90         4.31         8.61         8.94        19.59        17.82 
TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 
       10.55         7.89         9.67         6.61        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-A5F6 TCGA-QH-A65R TCGA-QH-A65S 
        2.30         4.11         5.88         1.28         5.75         2.53 
TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CV TCGA-QH-A6CY 
        4.83         7.79         4.11         4.18         2.96         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-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
        0.23         5.03        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        28.27        28.14        22.49 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       21.63        16.37        11.31        15.62        20.05         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       103.76        62.37        72.59 
TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WO 
       70.55        22.92        70.65        10.88         9.04         7.59 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY 
        6.15         3.39        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-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 
       18.21        13.02        10.39        87.09        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        35.93        25.32        22.59 
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-A84R 
       19.36        17.49        40.83        16.50        29.92         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 
       26.79        10.95 

  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 
            15.72             14.96 
[1] "0.2 - 75.2 (15.7)"  "0.0 - 211.2 (15.0)"
[1] "hr=" "1.3"
D4V2, continuous
D4V3, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED     5   4
  2Q GAIN WILD-TYPE 171 220
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      5    4
  2Q GAIN WILD-TYPE  171  220
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE               5               171
  MALE                 4               220
[1] 2 2
[1] FALSE
D4V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  2Q GAIN MUTATED             5                1                 3
  2Q GAIN WILD-TYPE         138              103               150
D4V5, multiclass
                   clus
vv                  2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  ASTROCYTOMA                     5               138
  OLIGOASTROCYTOMA                1               103
  OLIGODENDROGLIOMA               3               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"
D4V6, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED     2   7
  2Q GAIN WILD-TYPE  87 304
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      2    7
  2Q GAIN WILD-TYPE   87  304
     clus
vv    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  NO                2                87
  YES               7               304
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2Q GAIN MUTATED                                  0     0
  2Q GAIN WILD-TYPE                                1     2
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2Q GAIN MUTATED                           0     8
  2Q GAIN WILD-TYPE                        14   368
D4V7, multiclass
                                  clus
vv                                 2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 2
  BLACK OR AFRICAN AMERICAN                      0                14
  WHITE                                          8               368
[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   7
  2Q GAIN WILD-TYPE  14 352
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      1    7
  2Q GAIN WILD-TYPE   14  352
                        clus
vv                       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                14
  NOT HISPANIC OR LATINO               7               352
[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 317  67
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               11               384 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                4                67 
$`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         9.30         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-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-DU-5847 TCGA-DU-5849 
       29.62        15.75         7.79         3.85        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-6399 TCGA-DU-6401 TCGA-DU-6402 
       49.02        75.16        46.06        65.75        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-7014 TCGA-DU-7015 TCGA-DU-7018 
       14.99       105.21         6.54       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-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-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-E1-5302 TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 
      124.50        50.14        67.46        79.99        57.93       134.27 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 TCGA-FG-5963 TCGA-FG-5964 
       78.21        95.57       130.78        14.33        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        11.87 
TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY 
       15.52        24.46         0.59         5.26         3.72         9.67 
TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 
        7.04         6.64         7.04         4.21         4.08        10.59 
TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A713 TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 
       10.78        22.95         5.23         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-8018 TCGA-HT-8019 TCGA-HT-8104 
       16.24         9.40        63.55        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-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-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-7493 TCGA-HW-7495 TCGA-HW-8319 
        8.32        19.23        40.18        35.90         4.31         8.61 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
        8.94        19.59        17.82        10.55         7.89         9.67 
TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV 
        6.61        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-A5F6 
        6.71         1.64         2.37         4.11         5.88         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-A6CV TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 
        2.96         2.20         3.16         0.59         6.31         3.91 
TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-R8-A6MK TCGA-R8-A6ML 
        4.73         1.91         0.23         5.03        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        28.27 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 
       28.14        22.49        21.63        16.37        11.31        15.62 
TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB 
       20.05         9.86        94.62        83.70         5.85       103.76 
TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL 
       62.37        72.59        70.55        22.92        70.65        10.88 
TCGA-S9-A6WN TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX 
        9.04         6.15         3.39        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-A7R2 TCGA-S9-A7R3 
        3.58         4.04        18.21        13.02        10.39        87.09 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 
       17.42        83.80        31.59         5.00        49.45        35.93 
TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F 
       25.32        22.59        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 

  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            15.105 
[1] "0.2 - 47.8 (8.0)"   "0.0 - 211.2 (15.1)"
[1] "hr=" "4.7"
D5V2, continuous
D5V3, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     6   5
  3P GAIN WILD-TYPE 170 219
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      6    5
  3P GAIN WILD-TYPE  170  219
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE               6               170
  MALE                 5               219
[1] 2 2
[1] FALSE
D5V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  3P GAIN MUTATED             8                0                 3
  3P GAIN WILD-TYPE         135              104               150
D5V5, multiclass
                   clus
vv                  3P GAIN MUTATED 3P GAIN WILD-TYPE
  ASTROCYTOMA                     8               135
  OLIGOASTROCYTOMA                0               104
  OLIGODENDROGLIOMA               3               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"
D5V6, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     3   8
  3P GAIN WILD-TYPE  86 303
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      3    8
  3P GAIN WILD-TYPE   86  303
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  NO                3                86
  YES               8               303
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3P GAIN MUTATED                                  0     0
  3P GAIN WILD-TYPE                                1     2
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3P GAIN MUTATED                           0    11
  3P GAIN WILD-TYPE                        14   365
D5V7, multiclass
                                  clus
vv                                 3P GAIN MUTATED 3P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 2
  BLACK OR AFRICAN AMERICAN                      0                14
  WHITE                                         11               365
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V8, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     0  11
  3P GAIN WILD-TYPE  15 348
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      0   11
  3P GAIN WILD-TYPE   15  348
                        clus
vv                       3P GAIN MUTATED 3P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                15
  NOT HISPANIC OR LATINO              11               348
[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 320  67
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                8               387 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                4                67 
$`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         9.30 

$`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-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 
       10.92        19.96        31.82        30.31        14.40         8.02 
TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DU-5847 
       30.21        29.62        15.75         7.79         3.85        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-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-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-7014 TCGA-DU-7015 
      138.28        14.99       105.21         6.54       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-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-E1-5302 TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5307 
       21.30       124.50        50.14        67.46        79.99        57.93 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 TCGA-FG-5963 
      134.27        78.21        95.57       130.78        14.33        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 
       11.87        15.52        24.46         0.59         5.26         3.72 
TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 
        9.67         7.04         6.64         7.04         4.21         4.08 
TCGA-FG-A6J3 TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A713 TCGA-FN-7833 TCGA-HT-7467 
       10.59        10.78        22.95         5.23         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-8018 TCGA-HT-8019 
        1.64        16.24         9.40        63.55        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-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-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-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 
        8.61         8.94        19.59        17.82        10.55         7.89 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 
        9.67         6.61        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-A5F6 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X 
        5.88         1.28         5.75         2.53         4.83         7.79 
TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CV TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
        4.11         4.18         2.96         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-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        28.27        28.14        22.49        21.63        16.37 
TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
       11.31        15.62        20.05         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       103.76        62.37        72.59        70.55        22.92 
TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ 
       70.65        10.88         9.04         7.59         6.15         3.39 
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        18.21 
TCGA-S9-A7QZ TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 
       13.02        10.39        87.09        17.42        83.80        31.59 
TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF 
        5.00        49.45        35.93        25.32        22.59        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 
        7.89        26.79        10.95 

  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 
             9.07             14.99 
[1] "0.2 - 47.8 (9.1)"   "0.0 - 211.2 (15.0)"
[1] "hr=" "5.3"
D6V2, continuous
D6V3, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED     5   3
  3Q GAIN WILD-TYPE 171 221
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      5    3
  3Q GAIN WILD-TYPE  171  221
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE               5               171
  MALE                 3               221
[1] 2 2
[1] FALSE
D6V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  3Q GAIN MUTATED             6                0                 2
  3Q GAIN WILD-TYPE         137              104               151
D6V5, multiclass
                   clus
vv                  3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  ASTROCYTOMA                     6               137
  OLIGOASTROCYTOMA                0               104
  OLIGODENDROGLIOMA               2               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"
D6V6, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED     3   5
  3Q GAIN WILD-TYPE  86 306
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      3    5
  3Q GAIN WILD-TYPE   86  306
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  NO                3                86
  YES               5               306
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3Q GAIN MUTATED                                  0     0
  3Q GAIN WILD-TYPE                                1     2
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3Q GAIN MUTATED                           0     8
  3Q GAIN WILD-TYPE                        14   368
D6V7, multiclass
                                  clus
vv                                 3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 2
  BLACK OR AFRICAN AMERICAN                      0                14
  WHITE                                          8               368
[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  15 351
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      0    8
  3Q GAIN WILD-TYPE   15  351
                        clus
vv                       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                15
  NOT HISPANIC OR LATINO               8               351
[1] 2 2
[1] FALSE

Clustering(7) Variable = 4P GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                 0   1
  4P GAIN MUTATED     9   0
  4P GAIN WILD-TYPE 315  71
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                9               386 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                0                71 
$`4P GAIN MUTATED`
TCGA-CS-4943 TCGA-CS-6665 TCGA-CS-6666 TCGA-DU-A5TS TCGA-DU-A5TT TCGA-HT-7477 
       18.15        12.43         8.48        15.12         4.96        24.26 
TCGA-HT-7857 TCGA-S9-A6TU TCGA-S9-A7J0 
        0.23        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-DH-5140 TCGA-DH-5141 
       27.81        14.73        13.64        10.92        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        29.62        15.75 
TCGA-DH-A66F TCGA-DH-A66G TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
        7.79         3.85        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-A5TU 
       16.96        15.48        14.17        14.24        12.59         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-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-FG-5962 TCGA-FG-5963 
       78.21        95.57       130.78        14.33        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 
       11.87        15.52        24.46         0.59         5.26         3.72 
TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 
        9.67         7.04         6.64         7.04         4.21         4.08 
TCGA-FG-A6J3 TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A713 TCGA-FN-7833 TCGA-HT-7467 
       10.59        10.78        22.95         5.23         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-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-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-7858 
        6.90        14.53        39.48        19.23        39.09        50.63 
TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 
        0.49        23.61        37.15         0.33         0.13         3.68 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 
        5.33         2.93         1.71        11.28        31.43         1.64 
TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 
       16.24         9.40        63.55        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-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-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 
        8.61         8.94        19.59        17.82        10.55         7.89 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 
        9.67         6.61        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-A5F6 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X 
        5.88         1.28         5.75         2.53         4.83         7.79 
TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CV TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
        4.11         4.18         2.96         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-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 
       28.27        28.14        22.49        21.63        16.37        11.31 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA 
       15.62        20.05         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 
      103.76        62.37        72.59        70.55        22.92        70.65 
TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ 
       10.88         9.30         9.04         7.59         6.15         3.39 
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        18.21        13.02 
TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89Z 
       10.39        87.09        17.42        83.80        31.59         5.00 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B 
       49.45        35.93        25.32        22.59        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 
       26.79        10.95 

  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 
           12.430            14.975 
[1] "0.2 - 69.1 (12.4)"  "0.0 - 211.2 (15.0)"
[1] "hr="     "9200000"
D7V2, continuous
D7V3, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     3   6
  4P GAIN WILD-TYPE 173 218
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      3    6
  4P GAIN WILD-TYPE  173  218
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE               3               173
  MALE                 6               218
[1] 2 2
[1] FALSE
D7V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  4P GAIN MUTATED             6                0                 3
  4P GAIN WILD-TYPE         137              104               150
D7V5, multiclass
                   clus
vv                  4P GAIN MUTATED 4P GAIN WILD-TYPE
  ASTROCYTOMA                     6               137
  OLIGOASTROCYTOMA                0               104
  OLIGODENDROGLIOMA               3               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"
D7V6, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     1   8
  4P GAIN WILD-TYPE  88 303
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      1    8
  4P GAIN WILD-TYPE   88  303
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  NO                1                88
  YES               8               303
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4P GAIN MUTATED                                  0     0
  4P GAIN WILD-TYPE                                1     2
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4P GAIN MUTATED                           1     8
  4P GAIN WILD-TYPE                        13   368
D7V7, multiclass
                                  clus
vv                                 4P GAIN MUTATED 4P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 2
  BLACK OR AFRICAN AMERICAN                      1                13
  WHITE                                          8               368
[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   8
  4P GAIN WILD-TYPE  15 351
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      0    8
  4P GAIN WILD-TYPE   15  351
                        clus
vv                       4P GAIN MUTATED 4P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                15
  NOT HISPANIC OR LATINO               8               351
[1] 2 2
[1] FALSE

Clustering(8) Variable = 4Q GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                 0   1
  4Q GAIN MUTATED     3   0
  4Q GAIN WILD-TYPE 321  71
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                3               392 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                0                71 
$`4Q GAIN MUTATED`
TCGA-DU-A5TT TCGA-HT-7477 TCGA-HT-7857 
        4.96        24.26         0.23 

$`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-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 
       10.92        19.96        31.82        30.31        14.40         8.02 
TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DU-5847 
       30.21        29.62        15.75         7.79         3.85        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-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-A5TU TCGA-DU-A5TW TCGA-DU-A5TY 
       14.24        12.59        15.12         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-E1-5302 TCGA-E1-5303 
       26.76         7.13        21.30       124.50        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-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 
      130.78        14.33        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        11.87        15.52 
TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J 
       24.46         0.59         5.26         3.72         9.67         7.04 
TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Z 
        6.64         7.04         4.21         4.08        10.59        10.78 
TCGA-FG-A710 TCGA-FG-A713 TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 
       22.95         5.23         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-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 
       63.55        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-HW-7486 TCGA-HW-7487 TCGA-HW-7489 
        1.81        16.14         5.33        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         8.61         8.94 
TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM 
       19.59        17.82        10.55         7.89         9.67         6.61 
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-A5F6 
        1.64         2.37         2.30         4.11         5.88         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-A6CV TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 
        2.96         2.20         3.16         0.59         6.31         3.91 
TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-R8-A6MK TCGA-R8-A6ML 
        4.73         1.91         0.23         5.03        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        28.27 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 
       28.14        22.49        21.63        16.37        11.31        15.62 
TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB 
       20.05         9.86        94.62        83.70         5.85       103.76 
TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL 
       62.37        72.59        70.55        22.92        70.65        10.88 
TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ 
        9.30         9.04         7.59         6.15         3.39        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        18.21        13.02 
TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89Z 
       10.39        87.09        17.42        83.80        31.59         5.00 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B 
       49.45        35.93        25.32        22.59        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 
       26.79        10.95 

  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 
            4.960            14.975 
[1] "0.2 - 24.3 (5.0)"   "0.0 - 211.2 (15.0)"
[1] "hr="     "1200000"
D8V2, continuous
D8V3, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     1   2
  4Q GAIN WILD-TYPE 175 222
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      1    2
  4Q GAIN WILD-TYPE  175  222
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE               1               175
  MALE                 2               222
[1] 2 2
[1] FALSE
D8V4, continuous
[1] "Remove cluster labels:" "4Q GAIN MUTATED"       
clus
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                1               233 
       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-DH-5140        TCGA-DH-5142        TCGA-DH-5143        TCGA-DH-5144 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DH-A66B        TCGA-DH-A66D        TCGA-DH-A66F        TCGA-DH-A66G 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DU-5851        TCGA-DU-5852        TCGA-DU-5853        TCGA-DU-5854 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DU-5855        TCGA-DU-5870        TCGA-DU-5871        TCGA-DU-5874 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DU-6396        TCGA-DU-6403        TCGA-DU-6404        TCGA-DU-6405 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DU-6407        TCGA-DU-6408        TCGA-DU-6410        TCGA-DU-7011 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DU-7013        TCGA-DU-7014        TCGA-DU-7015        TCGA-DU-7018 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DU-7019        TCGA-DU-7294        TCGA-DU-7298        TCGA-DU-7299 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DU-7300        TCGA-DU-7301        TCGA-DU-7302        TCGA-DU-7304 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DU-7306        TCGA-DU-7309        TCGA-DU-8158        TCGA-DU-8161 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DU-8162        TCGA-DU-8163        TCGA-DU-8165        TCGA-DU-8167 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DU-8168        TCGA-DU-A5TP        TCGA-DU-A5TR        TCGA-DU-A5TS 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DU-A5TU        TCGA-DU-A5TW        TCGA-DU-A6S2        TCGA-DU-A6S6 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DU-A6S7        TCGA-DU-A6S8        TCGA-DU-A76R        TCGA-DU-A7T8 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-E1-5302        TCGA-E1-5303        TCGA-E1-5304        TCGA-E1-5305 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-E1-5307        TCGA-E1-5311        TCGA-E1-5318        TCGA-E1-5319 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-E1-5322        TCGA-FG-5963        TCGA-FG-5965        TCGA-FG-6688 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-FG-6689        TCGA-FG-6690        TCGA-FG-6691        TCGA-FG-7636 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-FG-7638        TCGA-FG-8181        TCGA-FG-8185        TCGA-FG-8186 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-FG-8187        TCGA-FG-8188        TCGA-FG-8189        TCGA-FG-A4MT 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-FG-A4MW        TCGA-FG-A4MX        TCGA-FG-A60J        TCGA-FG-A60L 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-FG-A6J1        TCGA-FG-A6J3        TCGA-FG-A713        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-A5F6        TCGA-QH-A65R        TCGA-QH-A65S        TCGA-QH-A65V 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-QH-A65X        TCGA-QH-A65Z        TCGA-QH-A6CS        TCGA-QH-A6CU 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-QH-A6CV        TCGA-QH-A6CW        TCGA-QH-A6CX        TCGA-QH-A6CY 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-QH-A6CZ        TCGA-QH-A6X3        TCGA-QH-A6X4        TCGA-QH-A6X5 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-QH-A6X8        TCGA-QH-A6X9        TCGA-QH-A6XA        TCGA-QH-A6XC 
"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-A7R2 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-S9-A7R3        TCGA-S9-A7R4        TCGA-S9-A7R7        TCGA-S9-A7R8 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-S9-A89Z        TCGA-TM-A7C3        TCGA-TM-A7C4        TCGA-TM-A7C5 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-TM-A7CA        TCGA-TM-A7CF        TCGA-TM-A84B        TCGA-TM-A84C 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-TM-A84F        TCGA-TM-A84G        TCGA-TM-A84H        TCGA-TM-A84I 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-TM-A84J        TCGA-TM-A84L        TCGA-TM-A84M        TCGA-TM-A84O 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-TM-A84Q        TCGA-TM-A84R        TCGA-TM-A84S        TCGA-TM-A84T 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-VM-A8C8        TCGA-VM-A8CA        TCGA-VM-A8CD        TCGA-VM-A8CE 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-VM-A8CH 
"4Q GAIN WILD-TYPE" 
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  4Q GAIN MUTATED             2                0                 1
  4Q GAIN WILD-TYPE         141              104               152
D8V5, multiclass
                   clus
vv                  4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  ASTROCYTOMA                     2               141
  OLIGOASTROCYTOMA                0               104
  OLIGODENDROGLIOMA               1               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"
D8V6, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     0   3
  4Q GAIN WILD-TYPE  89 308
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      0    3
  4Q GAIN WILD-TYPE   89  308
     clus
vv    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  NO                0                89
  YES               3               308
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4Q GAIN MUTATED                                  0     0
  4Q GAIN WILD-TYPE                                1     2
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4Q GAIN MUTATED                           0     3
  4Q GAIN WILD-TYPE                        14   373
D8V7, multiclass
                                  clus
vv                                 4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 2
  BLACK OR AFRICAN AMERICAN                      0                14
  WHITE                                          3               373
[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   3
  4Q GAIN WILD-TYPE  15 356
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      0    3
  4Q GAIN WILD-TYPE   15  356
                        clus
vv                       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                15
  NOT HISPANIC OR LATINO               3               356
[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 318  69
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                8               387 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                2                69 
$`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         2.96        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-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 
       10.92        19.96        31.82        30.31        14.40         8.02 
TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DU-5847 
       30.21        29.62        15.75         7.79         3.85        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-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-A5TU TCGA-DU-A5TW TCGA-DU-A5TY 
       14.24        12.59        15.12         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-E1-5302 TCGA-E1-5303 
       26.76         7.13        21.30       124.50        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-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 
       14.33        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        11.87        15.52        24.46 
TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K 
        0.59         5.26         3.72         9.67         7.04         6.64 
TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Z TCGA-FG-A710 
        7.04         4.21         4.08        10.59        10.78        22.95 
TCGA-FG-A713 TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 
        5.23         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-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 
       63.55        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-HW-7486 TCGA-HW-7487 TCGA-HW-7489 
        1.81        16.14         5.33        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         8.61         8.94 
TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM 
       19.59        17.82        10.55         7.89         9.67         6.61 
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-A5F6 
        1.64         2.37         2.30         4.11         5.88         1.28 
TCGA-QH-A65R TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CY 
        5.75         4.83         7.79         4.11         4.18         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-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
        0.23         5.03        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        28.27        28.14        22.49        21.63 
TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       16.37        11.31        15.62        20.05         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       103.76        62.37        72.59        70.55 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO 
       22.92        70.65        10.88         9.30         9.04         7.59 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY 
        6.15         3.39        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-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 
        4.04        18.21        13.02        10.39        87.09        17.42 
TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89Z TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA 
       83.80        31.59         5.00        35.93        25.32        22.59 
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-A8CA TCGA-VM-A8CB 
        9.44         4.57        12.00        33.07        13.51         0.10 
TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH 
        7.89        26.79        10.95 

  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             14.96 
[1] "2.5 - 62.2 (27.2)"  "0.0 - 211.2 (15.0)"
[1] "hr=" "1.4"
D9V2, continuous
D9V3, binary
                   cls
clus                  0   1
  5P GAIN MUTATED     4   4
  5P GAIN WILD-TYPE 172 220
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      4    4
  5P GAIN WILD-TYPE  172  220
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE               4               172
  MALE                 4               220
[1] 2 2
[1] FALSE
D9V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  5P GAIN MUTATED             5                2                 1
  5P GAIN WILD-TYPE         138              102               152
D9V5, multiclass
                   clus
vv                  5P GAIN MUTATED 5P GAIN WILD-TYPE
  ASTROCYTOMA                     5               138
  OLIGOASTROCYTOMA                2               102
  OLIGODENDROGLIOMA               1               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"
D9V6, binary
                   cls
clus                  0   1
  5P GAIN MUTATED     1   7
  5P GAIN WILD-TYPE  88 304
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      1    7
  5P GAIN WILD-TYPE   88  304
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  NO                1                88
  YES               7               304
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5P GAIN MUTATED                                  0     1
  5P GAIN WILD-TYPE                                1     1
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5P GAIN MUTATED                           0     6
  5P GAIN WILD-TYPE                        14   370
D9V7, multiclass
                                  clus
vv                                 5P GAIN MUTATED 5P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 1
  BLACK OR AFRICAN AMERICAN                      0                14
  WHITE                                          6               370
[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  15 352
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      0    7
  5P GAIN WILD-TYPE   15  352
                        clus
vv                       5P GAIN MUTATED 5P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                15
  NOT HISPANIC OR LATINO               7               352
[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 319  71
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                5               390 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                0                71 
$`5Q GAIN MUTATED`
TCGA-DU-A5TT TCGA-QH-A65S TCGA-QH-A6CV TCGA-TM-A7C3 TCGA-VM-A8C9 
        4.96         2.53         2.96        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-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 
       10.92        19.96        31.82        30.31        14.40         8.02 
TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DU-5847 
       30.21        29.62        15.75         7.79         3.85        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-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-A5TU TCGA-DU-A5TW TCGA-DU-A5TY 
       14.24        12.59        15.12         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-E1-5302 TCGA-E1-5303 
       26.76         7.13        21.30       124.50        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-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 
      130.78        14.33        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        11.87        15.52 
TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J 
       24.46         0.59         5.26         3.72         9.67         7.04 
TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Z 
        6.64         7.04         4.21         4.08        10.59        10.78 
TCGA-FG-A710 TCGA-FG-A713 TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 
       22.95         5.23         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-8018 TCGA-HT-8019 TCGA-HT-8104 
       16.24         9.40        63.55        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-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-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 
        8.61         8.94        19.59        17.82        10.55         7.89 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 
        9.67         6.61        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-A5F6 TCGA-QH-A65R TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z 
        5.88         1.28         5.75         4.83         7.79         4.11 
TCGA-QH-A6CS TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 
        4.18         2.20         3.16         0.59         6.31         3.91 
TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-R8-A6MK TCGA-R8-A6ML 
        4.73         1.91         0.23         5.03        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        28.27 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 
       28.14        22.49        21.63        16.37        11.31        15.62 
TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB 
       20.05         9.86        94.62        83.70         5.85       103.76 
TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL 
       62.37        72.59        70.55        22.92        70.65        10.88 
TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ 
        9.30         9.04         7.59         6.15         3.39        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        18.21        13.02 
TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89Z 
       10.39        87.09        17.42        83.80        31.59         5.00 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
       35.93        25.32        22.59        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-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH 
       33.07        13.51         0.10         7.89        26.79        10.95 

  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 
            4.960            14.975 
[1] "2.5 - 49.5 (5.0)"   "0.0 - 211.2 (15.0)"
[1] "hr="     "3300000"
D10V2, continuous
D10V3, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     3   2
  5Q GAIN WILD-TYPE 173 222
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      3    2
  5Q GAIN WILD-TYPE  173  222
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE               3               173
  MALE                 2               222
[1] 2 2
[1] FALSE
D10V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  5Q GAIN MUTATED             2                2                 1
  5Q GAIN WILD-TYPE         141              102               152
D10V5, multiclass
                   clus
vv                  5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  ASTROCYTOMA                     2               141
  OLIGOASTROCYTOMA                2               102
  OLIGODENDROGLIOMA               1               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"
D10V6, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     0   5
  5Q GAIN WILD-TYPE  89 306
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      0    5
  5Q GAIN WILD-TYPE   89  306
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  NO                0                89
  YES               5               306
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5Q GAIN MUTATED                                  0     1
  5Q GAIN WILD-TYPE                                1     1
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5Q GAIN MUTATED                           0     3
  5Q GAIN WILD-TYPE                        14   373
D10V7, multiclass
                                  clus
vv                                 5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 1
  BLACK OR AFRICAN AMERICAN                      0                14
  WHITE                                          3               373
[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  15 355
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      0    4
  5Q GAIN WILD-TYPE   15  355
                        clus
vv                       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                15
  NOT HISPANIC OR LATINO               4               355
[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 318  70
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                7               388 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                1                70 
$`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-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-DU-5847 TCGA-DU-5849 
       29.62        15.75         7.79         3.85        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-6399 TCGA-DU-6400 TCGA-DU-6401 
       49.02        75.16        46.06        65.75         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-6410 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 
        7.96        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-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 
       21.30       124.50        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-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        11.87        15.52        24.46         0.59 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
        5.26         3.72         9.67         7.04         6.64         7.04 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A713 TCGA-FN-7833 
        4.21         4.08        10.78        22.95         5.23         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-7607 
        5.03        29.85        23.18       107.93         4.57         3.16 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 
       22.06        45.99        56.09        57.60         0.23        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 
        0.16        16.24         0.76        44.68         6.05        42.74 
TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 
        0.10        31.69        14.96         0.10         0.10         2.96 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 
       17.52         6.90        14.53        39.48        19.23        39.09 
TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 
        0.23        50.63         0.49        23.61        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 
        0.13         3.68         5.33         2.93         1.71        11.28 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8018 
       31.43         1.64        16.24         9.40        63.55        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-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB 
        0.23        10.49         0.13         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-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         8.61         8.94        19.59        17.82        10.55 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X 
        7.89         9.67         6.61        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-A5F6 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X 
        5.88         1.28         5.75         2.53         4.83         7.79 
TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CV TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
        4.11         4.18         2.96         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-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        28.27        28.14        22.49        21.63        16.37 
TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
       11.31        15.62        20.05         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       103.76        62.37        72.59        70.55        22.92 
TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP 
       70.65        10.88         9.30         9.04         7.59         6.15 
TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ 
        3.39        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-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 
       18.21        13.02        10.39        87.09        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        35.93        25.32        22.59 
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 
        0.10         7.89        26.79        10.95 

  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 
           12.430            14.975 
[1] "2.3 - 114.1 (12.4)" "0.0 - 211.2 (15.0)"
[1] "hr=" "1.3"
D11V2, continuous
D11V3, binary
                   cls
clus                  0   1
  6P GAIN MUTATED     5   2
  6P GAIN WILD-TYPE 171 222
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      5    2
  6P GAIN WILD-TYPE  171  222
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE               5               171
  MALE                 2               222
[1] 2 2
[1] FALSE
D11V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  6P GAIN MUTATED             5                1                 1
  6P GAIN WILD-TYPE         138              103               152
D11V5, multiclass
                   clus
vv                  6P GAIN MUTATED 6P GAIN WILD-TYPE
  ASTROCYTOMA                     5               138
  OLIGOASTROCYTOMA                1               103
  OLIGODENDROGLIOMA               1               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"
D11V6, binary
                   cls
clus                  0   1
  6P GAIN MUTATED     2   5
  6P GAIN WILD-TYPE  87 306
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      2    5
  6P GAIN WILD-TYPE   87  306
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  NO                2                87
  YES               5               306
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6P GAIN MUTATED                                  0     0
  6P GAIN WILD-TYPE                                1     2
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6P GAIN MUTATED                           0     7
  6P GAIN WILD-TYPE                        14   369
D11V7, multiclass
                                  clus
vv                                 6P GAIN MUTATED 6P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 2
  BLACK OR AFRICAN AMERICAN                      0                14
  WHITE                                          7               369
[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  15 352
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      0    7
  6P GAIN WILD-TYPE   15  352
                        clus
vv                       6P GAIN MUTATED 6P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                15
  NOT HISPANIC OR LATINO               7               352
[1] 2 2
[1] FALSE

Clustering(12) Variable = 7P GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                 0   1
  7P GAIN MUTATED    61  31
  7P GAIN WILD-TYPE 263  40
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               92               303 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               31                40 
$`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-DH-A669 TCGA-DH-A66G TCGA-DU-5854 TCGA-DU-6392 
       18.84        18.84        30.21         3.85         8.45       211.17 
TCGA-DU-6395 TCGA-DU-6400 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 
       49.02         1.22         7.04        11.64       133.74        19.89 
TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6410 TCGA-DU-7006 TCGA-DU-7011 TCGA-DU-7012 
       16.83        94.52         7.96        11.47       105.21         6.54 
TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-8161 TCGA-DU-8163 TCGA-DU-8165 
        8.84       117.40        90.77        23.74        20.68        19.13 
TCGA-DU-8166 TCGA-DU-A5TR TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY 
       16.96        12.59         4.96         3.65         5.65        12.20 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76R TCGA-E1-5304 TCGA-E1-5322 TCGA-FG-5962 
       11.41        26.76        21.30        41.13       130.78        47.77 
TCGA-FG-6688 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7643 TCGA-FG-8182 
       18.77        23.97        13.58        15.35        20.09        13.68 
TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A70Z TCGA-HT-7473 TCGA-HT-7477 TCGA-HT-7860 
        0.59         5.26        10.78        16.54        24.26         0.49 
TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-8011 TCGA-HT-8013 TCGA-HT-8104 TCGA-HT-8110 
        1.71        11.28        16.24        63.55        12.23         4.70 
TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A5R5 TCGA-HT-A5R9 TCGA-HT-A5RC TCGA-HT-A617 
       15.72         0.23         0.13         0.07         5.33        16.14 
TCGA-KT-A7W1 TCGA-P5-A5F0 TCGA-QH-A6CS TCGA-QH-A6CV TCGA-QH-A6X9 TCGA-QH-A6XC 
        4.73         4.11         4.18         2.96         1.91         5.03 
TCGA-S9-A6TY TCGA-S9-A6U0 TCGA-S9-A6WM TCGA-S9-A7IQ TCGA-S9-A7IX TCGA-S9-A7IZ 
       22.49        16.37         9.30        14.27        19.63         4.21 
TCGA-S9-A7J0 TCGA-S9-A7QW TCGA-S9-A7R2 TCGA-TM-A7C3 TCGA-TM-A7CA TCGA-TM-A84B 
        9.37         3.58        10.39        49.45        22.59        12.00 
TCGA-TM-A84H TCGA-TM-A84M 
       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-DH-5140 
       15.42        27.81        14.73        13.64        10.92        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        29.62        15.75 
TCGA-DH-A66F TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 
        7.79        18.02        14.56        17.46         6.74        13.38 
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-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6401 TCGA-DU-6408 
       22.42        75.16        46.06        65.75        87.45       114.08 
TCGA-DU-6542 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7018 
        7.73        62.96       156.23       138.28        14.99        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-8162 TCGA-DU-8164 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP 
        5.10         3.98        21.40        15.48        14.17        14.24 
TCGA-DU-A5TS TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 
       15.12         8.65         2.70        77.98         7.23         5.98 
TCGA-DU-A76O TCGA-DU-A7T8 TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5307 
        7.13       124.50        50.14        67.46        79.99        57.93 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-EZ-7264 TCGA-FG-5963 TCGA-FG-5964 
      134.27        78.21        95.57        14.33        17.98        34.36 
TCGA-FG-5965 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 
       32.19        14.93        24.99        17.88        22.55        20.61 
TCGA-FG-8181 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 
       12.95        14.24        16.01        20.09        14.96        11.87 
TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K 
       15.52        24.46         3.72         9.67         7.04         6.64 
TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A710 TCGA-FG-A713 
        7.04         4.21         4.08        10.59        22.95         5.23 
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-7475 TCGA-HT-7476 TCGA-HT-7478 TCGA-HT-7479 
        0.03         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-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
        0.23        50.63        23.61        37.15         0.33         0.13 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8012 
        3.68         5.33         2.93        31.43         1.64         9.40 
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-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-A4DV 
        3.95         0.23        29.59         3.88        16.04        10.49 
TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A618 
       14.70         0.10         2.70        13.02         1.81         5.33 
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         8.61         8.94        19.59        17.82        10.55 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X 
        7.89         9.67         6.61        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-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-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-A6XA TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TS 
        0.23        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        28.27        28.14        21.63        11.31 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA 
       15.62        20.05         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 
      103.76        62.37        72.59        70.55        22.92        70.65 
TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IS 
       10.88         9.04         7.59         6.15         3.39         7.92 
TCGA-S9-A7IY TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QX TCGA-S9-A7QY 
       12.59         8.19         2.04         8.12         4.04        18.21 
TCGA-S9-A7QZ TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89Z 
       13.02        87.09        17.42        83.80        31.59         5.00 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CF TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G 
       35.93        25.32        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 
        7.89        26.79        10.95 

  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 
           13.975            14.990 
[1] "0.1 - 211.2 (14.0)" "0.0 - 182.3 (15.0)"
[1] "hr=" "2.7"
D12V2, continuous
D12V3, binary
                   cls
clus                  0   1
  7P GAIN MUTATED    47  45
  7P GAIN WILD-TYPE 129 179
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     47   45
  7P GAIN WILD-TYPE  129  179
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE              47               129
  MALE                45               179
[1] 2 2
[1] FALSE
D12V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  7P GAIN MUTATED            40               23                29
  7P GAIN WILD-TYPE         103               81               124
D12V5, multiclass
                   clus
vv                  7P GAIN MUTATED 7P GAIN WILD-TYPE
  ASTROCYTOMA                    40               103
  OLIGOASTROCYTOMA               23                81
  OLIGODENDROGLIOMA              29               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"
D12V6, binary
                   cls
clus                  0   1
  7P GAIN MUTATED    22  70
  7P GAIN WILD-TYPE  67 241
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     22   70
  7P GAIN WILD-TYPE   67  241
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  NO               22                67
  YES              70               241
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7P GAIN MUTATED                                  1     1
  7P GAIN WILD-TYPE                                0     1
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7P GAIN MUTATED                           6    84
  7P GAIN WILD-TYPE                         8   292
D12V7, multiclass
                                  clus
vv                                 7P GAIN MUTATED 7P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          1                 1
  BLACK OR AFRICAN AMERICAN                      6                 8
  WHITE                                         84               292
[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  84
  7P GAIN WILD-TYPE  11 275
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      4   84
  7P GAIN WILD-TYPE   11  275
                        clus
vv                       7P GAIN MUTATED 7P GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                11
  NOT HISPANIC OR LATINO              84               275
[1] 2 2
[1] FALSE

Clustering(13) Variable = 7Q GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                 0   1
  7Q GAIN MUTATED    83  36
  7Q GAIN WILD-TYPE 241  35
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              119               276 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               36                35 
$`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-DH-A669 TCGA-DH-A66G 
       12.72        18.84        18.84        10.92        30.21         3.85 
TCGA-DU-5849 TCGA-DU-5854 TCGA-DU-6392 TCGA-DU-6395 TCGA-DU-6399 TCGA-DU-6400 
       14.56         8.45       211.17        49.02        65.75         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-7006 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 
        7.96        11.47       105.21         6.54         8.84       117.40 
TCGA-DU-7292 TCGA-DU-7301 TCGA-DU-7306 TCGA-DU-8161 TCGA-DU-8163 TCGA-DU-8165 
        7.96        25.91        41.98        23.74        20.68        19.13 
TCGA-DU-8166 TCGA-DU-A5TR TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY 
       16.96        12.59         4.96         3.65         5.65        12.20 
TCGA-DU-A6S6 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76R TCGA-DU-A7T8 TCGA-E1-5302 
       77.98        11.41        26.76        21.30       124.50        50.14 
TCGA-E1-5304 TCGA-E1-5322 TCGA-FG-5962 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6690 
       41.13       130.78        47.77        32.19        18.77        24.99 
TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7643 TCGA-FG-8182 TCGA-FG-8186 
       23.97        13.58        15.35        20.09        13.68        16.01 
TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A70Z TCGA-HT-7473 TCGA-HT-7475 TCGA-HT-7477 
        0.59         5.26        10.78        16.54        17.42        24.26 
TCGA-HT-7604 TCGA-HT-7610 TCGA-HT-7693 TCGA-HT-7860 TCGA-HT-7882 TCGA-HT-7884 
      107.93        56.09        17.52         0.49         1.71        11.28 
TCGA-HT-8011 TCGA-HT-8013 TCGA-HT-8104 TCGA-HT-8108 TCGA-HT-8110 TCGA-HT-8564 
       16.24        63.55        12.23         2.50         4.70        15.72 
TCGA-HT-A4DS TCGA-HT-A5R5 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RC TCGA-HT-A616 
        0.23         0.13         0.07        14.70         5.33         1.81 
TCGA-HT-A617 TCGA-HW-7495 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-KT-A7W1 TCGA-P5-A5EV 
       16.14         4.31        17.82        10.55         4.73         0.23 
TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-QH-A6CS TCGA-QH-A6CV TCGA-QH-A6XA TCGA-QH-A6XC 
        2.30         4.11         4.18         2.96         0.23         5.03 
TCGA-S9-A6TY TCGA-S9-A6U0 TCGA-S9-A6WM TCGA-S9-A6WO TCGA-S9-A7IQ TCGA-S9-A7IX 
       22.49        16.37         9.30         7.59        14.27        19.63 
TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7QW TCGA-S9-A7QY TCGA-S9-A7R2 TCGA-TM-A7C3 
        4.21         9.37         3.58        18.21        10.39        49.45 
TCGA-TM-A7C4 TCGA-TM-A7CA TCGA-TM-A84B TCGA-TM-A84H TCGA-TM-A84M 
       35.93        22.59        12.00        24.26        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-DH-5140 TCGA-DH-5141 TCGA-DH-5142 
       27.81        14.73        13.64        19.96        31.82        30.31 
TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DU-5847 
       14.40         8.02        29.62        15.75         7.79        18.02 
TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
       17.46         6.74        13.38         6.81       182.33        18.94 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6396 TCGA-DU-6397 
       17.49        15.16        52.11        22.42        75.16        46.06 
TCGA-DU-6401 TCGA-DU-6408 TCGA-DU-6542 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 
       87.45       114.08         7.73        62.96       156.23       138.28 
TCGA-DU-7010 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7294 
       14.99        90.77        30.67        26.30        10.36        94.32 
TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7309 
       18.94        44.02        62.01        60.30        23.31         2.76 
TCGA-DU-8158 TCGA-DU-8162 TCGA-DU-8164 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP 
        5.10         3.98        21.40        15.48        14.17        14.24 
TCGA-DU-A5TS TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76O 
       15.12         8.65         2.70         7.23         5.98         7.13 
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-FG-5963 TCGA-FG-5964 TCGA-FG-6689 TCGA-FG-7636 TCGA-FG-7638 
       14.33        17.98        34.36        14.93        17.88        22.55 
TCGA-FG-7641 TCGA-FG-8181 TCGA-FG-8185 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 
       20.61        12.95        14.24        20.09        14.96        11.87 
TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K 
       15.52        24.46         3.72         9.67         7.04         6.64 
TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A710 TCGA-FG-A713 
        7.04         4.21         4.08        10.59        22.95         5.23 
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-8018 TCGA-HT-8019 TCGA-HT-8105 TCGA-HT-8106 
        1.64         9.40        21.50        33.01         6.25         0.10 
TCGA-HT-8107 TCGA-HT-8109 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 
        0.46         3.95         0.23        29.59         3.88        16.04 
TCGA-HT-A4DV TCGA-HT-A5RB TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A618 TCGA-HW-7486 
       10.49         0.10         2.70        13.02         5.33        29.92 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-8319 
       13.45         8.32        19.23        40.18        35.90         8.61 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 
        8.94        19.59         7.89         9.67         6.61        19.00 
TCGA-IK-8125 TCGA-KT-A74X TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5F1 
       42.77         5.23         6.71         1.64         2.37         5.88 
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-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-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TS 
        1.91        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        28.27        28.14        21.63        11.31 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA 
       15.62        20.05         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 
      103.76        62.37        72.59        70.55        22.92        70.65 
TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IS TCGA-S9-A7IY 
       10.88         9.04         6.15         3.39         7.92        12.59 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QX TCGA-S9-A7QZ TCGA-S9-A7R3 
        8.19         2.04         8.12         4.04        13.02        87.09 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89Z TCGA-TM-A7C5 TCGA-TM-A7CF 
       17.42        83.80        31.59         5.00        25.32        48.39 
TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L 
       15.09        50.76        34.36        19.36        17.49        40.83 
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 

  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             14.96 
[1] "0.1 - 211.2 (15.3)" "0.0 - 182.3 (15.0)"
[1] "hr=" "2.4"
D13V2, continuous
D13V3, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED    59  62
  7Q GAIN WILD-TYPE 117 162
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     59   62
  7Q GAIN WILD-TYPE  117  162
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE              59               117
  MALE                62               162
[1] 2 2
[1] FALSE
D13V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  7Q GAIN MUTATED            52               32                37
  7Q GAIN WILD-TYPE          91               72               116
D13V5, multiclass
                   clus
vv                  7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  ASTROCYTOMA                    52                91
  OLIGOASTROCYTOMA               32                72
  OLIGODENDROGLIOMA              37               116
[1] 3 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  93
  7Q GAIN WILD-TYPE  61 218
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     28   93
  7Q GAIN WILD-TYPE   61  218
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  NO               28                61
  YES              93               218
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7Q GAIN MUTATED                                  1     1
  7Q GAIN WILD-TYPE                                0     1
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7Q GAIN MUTATED                           7   112
  7Q GAIN WILD-TYPE                         7   264
D13V7, multiclass
                                  clus
vv                                 7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          1                 1
  BLACK OR AFRICAN AMERICAN                      7                 7
  WHITE                                        112               264
[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     5 112
  7Q GAIN WILD-TYPE  10 247
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      5  112
  7Q GAIN WILD-TYPE   10  247
                        clus
vv                       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   5                10
  NOT HISPANIC OR LATINO             112               247
[1] 2 2
[1] FALSE

Clustering(14) Variable = 8P GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                 0   1
  8P GAIN MUTATED    29   8
  8P GAIN WILD-TYPE 295  63
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               37               358 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                8                63 
$`8P GAIN MUTATED`
TCGA-CS-6665 TCGA-CS-6666 TCGA-DB-5281 TCGA-DB-A64X TCGA-DH-A669 TCGA-DU-5871 
       12.43         8.48        78.28        10.92        30.21        18.94 
TCGA-DU-6407 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7304 TCGA-DU-8158 TCGA-DU-8163 
       94.52         8.84       117.40        23.31         5.10        20.68 
TCGA-DU-A5TS TCGA-DU-A6S7 TCGA-E1-5303 TCGA-FG-5962 TCGA-FG-7634 TCGA-FG-A4MT 
       15.12         7.23        67.46        47.77        15.35        24.46 
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-S9-A6TY TCGA-S9-A6WH TCGA-S9-A6WO 
       63.55         0.10         0.23        22.49        22.92         7.59 
TCGA-S9-A7QX TCGA-S9-A89Z TCGA-TM-A7CF TCGA-TM-A84H TCGA-TM-A84Q TCGA-VM-A8C8 
        4.04         5.00        48.39        24.26        18.90        33.07 
TCGA-VM-A8CA 
       13.51 

$`8P GAIN WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
       40.18         0.10        21.01         9.96         6.38        17.69 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 
       23.84        17.95         7.56         8.02         7.40         6.61 
TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 
      122.73        81.96        75.25        47.93        72.92        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-DH-5140 TCGA-DH-5141 TCGA-DH-5142 
       27.81        14.73        13.64        19.96        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        29.62        15.75         7.79         3.85 
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-A5TW TCGA-DU-A5TY 
       14.24        12.59         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-E1-5302 TCGA-E1-5304 TCGA-E1-5305 
        7.13        21.30       124.50        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-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 
       11.87        15.52         0.59         5.26         3.72         9.67 
TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 
        7.04         6.64         7.04         4.21         4.08        10.59 
TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A713 TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 
       10.78        22.95         5.23         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-7480 TCGA-HT-7481 TCGA-HT-7483 TCGA-HT-7485 
       17.42         6.38        75.19        59.18       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-7856 
        2.96        17.52         6.90        14.53        39.48        39.09 
TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 
        0.23        50.63         0.49        23.61        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 
        0.13         3.68         5.33         2.93         1.71        11.28 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8012 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 
       31.43         1.64         9.40        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-HW-7486 TCGA-HW-7487 TCGA-HW-7489 
        1.81        16.14         5.33        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         8.61         8.94 
TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM 
       19.59        17.82        10.55         7.89         9.67         6.61 
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-A5F6 
        1.64         2.37         2.30         4.11         5.88         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-A6CV TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 
        2.96         2.20         3.16         0.59         6.31         3.91 
TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-R8-A6MK TCGA-R8-A6ML 
        4.73         1.91         0.23         5.03        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        28.27 
TCGA-S9-A6TX TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       28.14        21.63        16.37        11.31        15.62        20.05 
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       103.76        62.37 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN 
       72.59        70.55        70.65        10.88         9.30         9.04 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY 
        6.15         3.39        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-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 
       18.21        13.02        10.39        87.09        17.42        83.80 
TCGA-S9-A7R8 TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A84B 
       31.59        49.45        35.93        25.32        22.59        12.00 
TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L 
       15.09        50.76        34.36        19.36        17.49        40.83 
TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-VM-A8C9 
       16.50        29.92         9.44         4.57        12.00        30.08 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH 
        0.10         7.89        26.79        10.95 

  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 
            18.94             14.63 
[1] "0.1 - 117.4 (18.9)" "0.0 - 211.2 (14.6)"
[1] "hr=" "1.1"
D14V2, continuous
D14V3, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    14  23
  8P GAIN WILD-TYPE 162 201
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     14   23
  8P GAIN WILD-TYPE  162  201
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE              14               162
  MALE                23               201
[1] 2 2
[1] FALSE
D14V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  8P GAIN MUTATED            18                9                10
  8P GAIN WILD-TYPE         125               95               143
D14V5, multiclass
                   clus
vv                  8P GAIN MUTATED 8P GAIN WILD-TYPE
  ASTROCYTOMA                    18               125
  OLIGOASTROCYTOMA                9                95
  OLIGODENDROGLIOMA              10               143
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V6, binary
                   cls
clus                  0   1
  8P GAIN MUTATED     7  30
  8P GAIN WILD-TYPE  82 281
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      7   30
  8P GAIN WILD-TYPE   82  281
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  NO                7                82
  YES              30               281
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8P GAIN MUTATED                                  0     0
  8P GAIN WILD-TYPE                                1     2
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8P GAIN MUTATED                           1    35
  8P GAIN WILD-TYPE                        13   341
D14V7, multiclass
                                  clus
vv                                 8P GAIN MUTATED 8P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 2
  BLACK OR AFRICAN AMERICAN                      1                13
  WHITE                                         35               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"
D14V8, binary
                   cls
clus                  0   1
  8P GAIN MUTATED     1  34
  8P GAIN WILD-TYPE  14 325
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      1   34
  8P GAIN WILD-TYPE   14  325
                        clus
vv                       8P GAIN MUTATED 8P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                14
  NOT HISPANIC OR LATINO              34               325
[1] 2 2
[1] FALSE

Clustering(15) Variable = 8Q GAIN MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                 0   1
  8Q GAIN MUTATED    35   9
  8Q GAIN WILD-TYPE 289  62
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               44               351 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                9                62 
$`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-DU-5871 TCGA-DU-6407 TCGA-DU-7013 TCGA-DU-7014 
       14.40        30.21        18.94        94.52         8.84       117.40 
TCGA-DU-7304 TCGA-DU-8158 TCGA-DU-8163 TCGA-DU-A5TS TCGA-DU-A5TW TCGA-DU-A6S7 
       23.31         5.10        20.68        15.12         5.65         7.23 
TCGA-E1-5303 TCGA-FG-5962 TCGA-FG-6691 TCGA-FG-7634 TCGA-FG-A4MT TCGA-HT-7476 
       67.46        47.77        23.97        15.35        24.46         6.54 
TCGA-HT-7477 TCGA-HT-7479 TCGA-HT-7482 TCGA-HT-7855 TCGA-HT-8011 TCGA-HT-8013 
       24.26         7.10        60.03        19.23        16.24        63.55 
TCGA-HT-8106 TCGA-HT-8111 TCGA-P5-A5F1 TCGA-S9-A6TY TCGA-S9-A6WH TCGA-S9-A6WO 
        0.10         0.23         5.88        22.49        22.92         7.59 
TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A89Z TCGA-TM-A7CF TCGA-TM-A84H TCGA-TM-A84Q 
        3.58         4.04         5.00        48.39        24.26        18.90 
TCGA-VM-A8C8 TCGA-VM-A8CA 
       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-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5144 TCGA-DH-A66B 
       13.64        19.96        31.82        30.31         8.02        29.62 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       15.75         7.79         3.85        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-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S8 
        3.65        12.20         8.65         2.70        77.98         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-E1-5304 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-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 
      130.78        14.33        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        11.87        15.52         0.59         5.26         3.72 
TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 
        9.67         7.04         6.64         7.04         4.21         4.08 
TCGA-FG-A6J3 TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A713 TCGA-FN-7833 TCGA-HT-7467 
       10.59        10.78        22.95         5.23         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-7478 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7483 
        3.75        17.42         6.38        75.19        59.18       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-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-8012 TCGA-HT-8018 TCGA-HT-8019 
       11.28        31.43         1.64         9.40        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-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-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-7493 TCGA-HW-7495 TCGA-HW-8319 
        8.32        19.23        40.18        35.90         4.31         8.61 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
        8.94        19.59        17.82        10.55         7.89         9.67 
TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV 
        6.61        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-A5F6 
        6.71         1.64         2.37         2.30         4.11         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-A6CV TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 
        2.96         2.20         3.16         0.59         6.31         3.91 
TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-R8-A6MK TCGA-R8-A6ML 
        4.73         1.91         0.23         5.03        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        28.27 
TCGA-S9-A6TX TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       28.14        21.63        16.37        11.31        15.62        20.05 
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       103.76        62.37 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN 
       72.59        70.55        70.65        10.88         9.30         9.04 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY 
        6.15         3.39        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        18.21 
TCGA-S9-A7QZ TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 
       13.02        10.39        87.09        17.42        83.80        31.59 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A84B TCGA-TM-A84C 
       49.45        35.93        25.32        22.59        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-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-VM-A8C9 TCGA-VM-A8CB 
       29.92         9.44         4.57        12.00        30.08         0.10 
TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH 
        7.89        26.79        10.95 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             0.10              0.03 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           117.40            211.17 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           18.425            14.700 
[1] "0.1 - 117.4 (18.4)" "0.0 - 211.2 (14.7)"
[1] "hr=" "1.2"
D15V2, continuous
D15V3, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED    17  27
  8Q GAIN WILD-TYPE 159 197
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     17   27
  8Q GAIN WILD-TYPE  159  197
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE              17               159
  MALE                27               197
[1] 2 2
[1] FALSE
D15V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  8Q GAIN MUTATED            24               10                10
  8Q GAIN WILD-TYPE         119               94               143
D15V5, multiclass
                   clus
vv                  8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  ASTROCYTOMA                    24               119
  OLIGOASTROCYTOMA               10                94
  OLIGODENDROGLIOMA              10               143
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V6, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED    10  34
  8Q GAIN WILD-TYPE  79 277
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     10   34
  8Q GAIN WILD-TYPE   79  277
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  NO               10                79
  YES              34               277
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8Q GAIN MUTATED                                  0     0
  8Q GAIN WILD-TYPE                                1     2
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8Q GAIN MUTATED                           2    40
  8Q GAIN WILD-TYPE                        12   336
D15V7, multiclass
                                  clus
vv                                 8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 2
  BLACK OR AFRICAN AMERICAN                      2                12
  WHITE                                         40               336
[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  40
  8Q GAIN WILD-TYPE  14 319
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      1   40
  8Q GAIN WILD-TYPE   14  319
                        clus
vv                       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                14
  NOT HISPANIC OR LATINO              40               319
[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 314  67
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               14               381 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                4                67 
$`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        22.92 
TCGA-S9-A6WM TCGA-TM-A7C4 
        9.30        35.93 

$`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-DH-5140 TCGA-DH-5141 
       27.81        14.73        13.64        10.92        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        29.62        15.75 
TCGA-DH-A66F TCGA-DH-A66G TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
        7.79         3.85        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-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-8162 
       25.91        60.30        23.31        41.98         2.76         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-A76R TCGA-DU-A7T8 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 
       21.30       124.50        67.46        41.13        79.99        57.93 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 TCGA-FG-5962 
      134.27        78.21        95.57       130.78        14.33        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        11.87        15.52        24.46         0.59         5.26 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ 
        3.72         9.67         7.04         6.64         7.04         4.21 
TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A713 TCGA-FN-7833 
        4.08        10.59        10.78        22.95         5.23         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-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 
       16.54        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-8018 
       31.43         1.64        16.24         9.40        63.55        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-A5R9 TCGA-HT-A5RA 
       15.72         0.23        10.49         0.13         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-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-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 
       35.90         4.31         8.61         8.94        19.59        17.82 
TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 
       10.55         7.89         9.67         6.61        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-A5F6 TCGA-QH-A65R TCGA-QH-A65S 
        2.30         4.11         5.88         1.28         5.75         2.53 
TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CV TCGA-QH-A6CY 
        4.83         7.79         4.11         4.18         2.96         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-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
        0.23         5.03        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        28.27        28.14        22.49 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       21.63        16.37        11.31        15.62        20.05         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       103.76        62.37        72.59 
TCGA-S9-A6WG TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP 
       70.55        70.65        10.88         9.04         7.59         6.15 
TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ 
        3.39        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-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 
       18.21        13.02        10.39        87.09        17.42        83.80 
TCGA-S9-A7R8 TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF 
       31.59         5.00        49.45        25.32        22.59        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 
        7.89        26.79        10.95 

  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 
            13.71             14.96 
[1] "3.8 - 50.1 (13.7)"  "0.0 - 211.2 (15.0)"
[1] "hr=" "2.8"
D16V2, continuous
D16V3, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    10   4
  9P GAIN WILD-TYPE 166 220
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     10    4
  9P GAIN WILD-TYPE  166  220
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE              10               166
  MALE                 4               220
[1] 2 2
[1] FALSE
D16V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  9P GAIN MUTATED             7                4                 3
  9P GAIN WILD-TYPE         136              100               150
D16V5, multiclass
                   clus
vv                  9P GAIN MUTATED 9P GAIN WILD-TYPE
  ASTROCYTOMA                     7               136
  OLIGOASTROCYTOMA                4               100
  OLIGODENDROGLIOMA               3               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"
D16V6, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     3  11
  9P GAIN WILD-TYPE  86 300
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      3   11
  9P GAIN WILD-TYPE   86  300
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  NO                3                86
  YES              11               300
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9P GAIN MUTATED                                  0     0
  9P GAIN WILD-TYPE                                1     2
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9P GAIN MUTATED                           0    14
  9P GAIN WILD-TYPE                        14   362
D16V7, multiclass
                                  clus
vv                                 9P GAIN MUTATED 9P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 2
  BLACK OR AFRICAN AMERICAN                      0                14
  WHITE                                         14               362
[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  15 345
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      0   14
  9P GAIN WILD-TYPE   15  345
                        clus
vv                       9P GAIN MUTATED 9P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                15
  NOT HISPANIC OR LATINO              14               345
[1] 2 2
[1] FALSE

Clustering(17) Variable = 9Q GAIN MUTATION ANALYSIS
D17V1, survival
                   sevent
clus2                 0   1
  9Q GAIN MUTATED    14   5
  9Q GAIN WILD-TYPE 310  66
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               19               376 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                5                66 
$`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         9.67 
TCGA-FG-A6J3 TCGA-HT-7477 TCGA-HW-8319 TCGA-S9-A6TW TCGA-S9-A6WH TCGA-S9-A6WM 
       10.59        24.26         8.61        28.27        22.92         9.30 
TCGA-S9-A7QW 
        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-DH-5140 TCGA-DH-5141 
       27.81        14.73        13.64        10.92        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        29.62        15.75 
TCGA-DH-A66F TCGA-DH-A66G TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
        7.79         3.85        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-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-7299 TCGA-DU-7300 TCGA-DU-7301 
       10.36         7.96        94.32        44.02        62.01        25.91 
TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8162 TCGA-DU-8163 
       60.30        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-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-A76R 
       77.98         7.23         5.98        11.41        26.76        21.30 
TCGA-DU-A7T8 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 
      124.50        67.46        41.13        79.99        57.93       134.27 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 TCGA-FG-5962 TCGA-FG-5963 
       78.21        95.57       130.78        14.33        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 
       11.87        15.52        24.46         0.59         5.26         3.72 
TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A70Z 
        7.04         6.64         7.04         4.21         4.08        10.78 
TCGA-FG-A710 TCGA-FG-A713 TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 
       22.95         5.23         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-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-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 
        9.40        63.55        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-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-7493 TCGA-HW-7495 TCGA-HW-8320 
        8.32        19.23        40.18        35.90         4.31         8.94 
TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM 
       19.59        17.82        10.55         7.89         9.67         6.61 
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-A5F6 
        1.64         2.37         2.30         4.11         5.88         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-A6CV TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 
        2.96         2.20         3.16         0.59         6.31         3.91 
TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-R8-A6MK TCGA-R8-A6ML 
        4.73         1.91         0.23         5.03        88.83        94.03 
TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TX 
       32.65        59.38        62.17        69.07        18.77        28.14 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       22.49        21.63        16.37        11.31        15.62        20.05 
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       103.76        62.37 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WO 
       72.59        70.55        70.65        10.88         9.04         7.59 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY 
        6.15         3.39        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-A7QX 
        4.21         9.37         8.19         2.04         8.12         4.04 
TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 
       18.21        13.02        10.39        87.09        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        35.93        25.32        22.59 
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 
        0.10         7.89        26.79        10.95 

  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 
           12.430            15.025 
[1] "3.6 - 50.1 (12.4)"  "0.0 - 211.2 (15.0)"
[1] "hr=" "2.8"
D17V2, continuous
D17V3, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    14   5
  9Q GAIN WILD-TYPE 162 219
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     14    5
  9Q GAIN WILD-TYPE  162  219
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE              14               162
  MALE                 5               219
[1] 2 2
[1] FALSE
D17V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  9Q GAIN MUTATED            11                4                 4
  9Q GAIN WILD-TYPE         132              100               149
D17V5, multiclass
                   clus
vv                  9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  ASTROCYTOMA                    11               132
  OLIGOASTROCYTOMA                4               100
  OLIGODENDROGLIOMA               4               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"
D17V6, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     3  16
  9Q GAIN WILD-TYPE  86 295
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      3   16
  9Q GAIN WILD-TYPE   86  295
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  NO                3                86
  YES              16               295
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9Q GAIN MUTATED                                  0     0
  9Q GAIN WILD-TYPE                                1     2
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9Q GAIN MUTATED                           1    18
  9Q GAIN WILD-TYPE                        13   358
D17V7, multiclass
                                  clus
vv                                 9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 2
  BLACK OR AFRICAN AMERICAN                      1                13
  WHITE                                         18               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"
D17V8, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     1  18
  9Q GAIN WILD-TYPE  14 341
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      1   18
  9Q GAIN WILD-TYPE   14  341
                        clus
vv                       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                14
  NOT HISPANIC OR LATINO              18               341
[1] 2 2
[1] FALSE

Clustering(18) Variable = 10P GAIN MUTATION ANALYSIS
D18V1, survival
                    sevent
clus2                  0   1
  10P GAIN MUTATED    29   9
  10P GAIN WILD-TYPE 295  62
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                38                357 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 9                 62 
$`10P GAIN MUTATED`
TCGA-CS-5393 TCGA-CS-6665 TCGA-CS-6667 TCGA-DB-5277 TCGA-DH-A66B TCGA-DU-6396 
       40.18        12.43         7.56        46.65        29.62        75.16 
TCGA-DU-7014 TCGA-DU-7019 TCGA-DU-7299 TCGA-DU-7304 TCGA-DU-A5TR TCGA-DU-A5TS 
      117.40        26.30        44.02        23.31        12.59        15.12 
TCGA-E1-5304 TCGA-E1-5322 TCGA-FG-A4MY TCGA-FG-A60L TCGA-HT-7470 TCGA-HT-7473 
       41.13       130.78         9.67         7.04         8.81        16.54 
TCGA-HT-7476 TCGA-HT-7479 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7688 TCGA-HT-7879 
        6.54         7.10        60.03       154.19        31.69         3.68 
TCGA-HT-8106 TCGA-HT-8111 TCGA-HT-8114 TCGA-HW-7493 TCGA-IK-7675 TCGA-P5-A5EZ 
        0.10         0.23         3.88        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        22.59 
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-DH-5140 TCGA-DH-5141 TCGA-DH-5142 
       14.73        13.64        10.92        19.96        31.82        30.31 
TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G 
       14.40         8.02        30.21        15.75         7.79         3.85 
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-7015 TCGA-DU-7018 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 
       90.77        30.67        10.36         7.96        94.32        18.94 
TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 
       62.01        25.91        60.30        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-A5TT TCGA-DU-A5TU TCGA-DU-A5TW 
       15.48        14.17        14.24         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-E1-5305 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-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 
       14.33        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        11.87        15.52        24.46 
TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A6IZ 
        0.59         5.26         3.72         7.04         6.64         4.21 
TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A713 TCGA-FN-7833 
        4.08        10.59        10.78        22.95         5.23         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-8018 TCGA-HT-8019 
        1.64        16.24         9.40        63.55        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-8113 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 
       29.59        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-HW-7486 TCGA-HW-7487 TCGA-HW-7489 
        1.81        16.14         5.33        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         8.61         8.94        19.59 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-8125 
       17.82        10.55         7.89         9.67         6.61        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-A5F0 TCGA-P5-A5F6 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X 
        4.11         1.28         5.75         2.53         4.83         7.79 
TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CV TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
        4.11         4.18         2.96         2.20         3.16         0.59 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XC TCGA-R8-A6MK 
        6.31         3.91         4.73         1.91         5.03        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 
       28.27        28.14        22.49        21.63        16.37        11.31 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA 
       15.62        20.05         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 
      103.76        62.37        72.59        70.55        22.92        70.65 
TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ 
       10.88         9.30         9.04         7.59         6.15         3.39 
TCGA-S9-A7IQ TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J1 TCGA-S9-A7J2 
       14.27        19.63        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-A7R2 
        8.12         3.58         4.04        18.21        13.02        10.39 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-TM-A7C3 TCGA-TM-A7C4 
       87.09        17.42        83.80        31.59        49.45        35.93 
TCGA-TM-A7C5 TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G 
       25.32        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-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB 
        9.44         4.57        12.00        30.08        13.51         0.10 
TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH 
        7.89        26.79        10.95 

  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 
             15.83              14.96 
[1] "0.1 - 154.2 (15.8)" "0.0 - 211.2 (15.0)"
[1] "hr=" "1.1"
D18V2, continuous
D18V3, binary
                    cls
clus                   0   1
  10P GAIN MUTATED    13  25
  10P GAIN WILD-TYPE 163 199
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     13   25
  10P GAIN WILD-TYPE  163  199
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE               13                163
  MALE                 25                199
[1] 2 2
[1] FALSE
D18V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  10P GAIN MUTATED            17               14                 7
  10P GAIN WILD-TYPE         126               90               146
D18V5, multiclass
                   clus
vv                  10P GAIN MUTATED 10P GAIN WILD-TYPE
  ASTROCYTOMA                     17                126
  OLIGOASTROCYTOMA                14                 90
  OLIGODENDROGLIOMA                7                146
[1] 3 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  21
  10P GAIN WILD-TYPE  72 290
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     17   21
  10P GAIN WILD-TYPE   72  290
     clus
vv    10P GAIN MUTATED 10P GAIN WILD-TYPE
  NO                17                 72
  YES               21                290
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10P GAIN MUTATED                                  0     0
  10P GAIN WILD-TYPE                                1     2
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10P GAIN MUTATED                           1    37
  10P GAIN WILD-TYPE                        13   339
D18V7, multiclass
                                  clus
vv                                 10P GAIN MUTATED 10P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  2
  BLACK OR AFRICAN AMERICAN                       1                 13
  WHITE                                          37                339
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V8, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     4  32
  10P GAIN WILD-TYPE  11 327
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      4   32
  10P GAIN WILD-TYPE   11  327
                        clus
vv                       10P GAIN MUTATED 10P GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                 11
  NOT HISPANIC OR LATINO               32                327
[1] 2 2
[1] FALSE

Clustering(19) Variable = 10Q GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                  0   1
  10Q GAIN MUTATED     6   1
  10Q GAIN WILD-TYPE 318  70
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 7                388 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 1                 70 
$`10Q GAIN MUTATED`
TCGA-CS-5393 TCGA-DB-5277 TCGA-DU-A5TS TCGA-HT-7476 TCGA-HT-8106 TCGA-S9-A7J0 
       40.18        46.65        15.12         6.54         0.10         9.37 
TCGA-S9-A89Z 
        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-DH-5140 
       15.42        27.81        14.73        13.64        10.92        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        29.62 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       15.75         7.79         3.85        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-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-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 
       21.30       124.50        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-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        11.87        15.52        24.46         0.59 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
        5.26         3.72         9.67         7.04         6.64         7.04 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A713 
        4.21         4.08        10.59        10.78        22.95         5.23 
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-7477 TCGA-HT-7478 
        0.03        16.54         3.75        17.42        24.26         6.38 
TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 
        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-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-8564 TCGA-HT-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R9 TCGA-HT-A5RA 
       15.72         0.23        10.49         0.13         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-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-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 
       35.90         4.31         8.61         8.94        19.59        17.82 
TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 
       10.55         7.89         9.67         6.61        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-A5F6 TCGA-QH-A65R TCGA-QH-A65S 
        2.30         4.11         5.88         1.28         5.75         2.53 
TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CV TCGA-QH-A6CY 
        4.83         7.79         4.11         4.18         2.96         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-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
        0.23         5.03        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        28.27        28.14        22.49 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       21.63        16.37        11.31        15.62        20.05         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       103.76        62.37        72.59 
TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN 
       70.55        22.92        70.65        10.88         9.30         9.04 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX 
        7.59         6.15         3.39        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-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 
        4.04        18.21        13.02        10.39        87.09        17.42 
TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA 
       83.80        31.59        49.45        35.93        25.32        22.59 
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 
        0.10         7.89        26.79        10.95 

  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 
             9.370             14.975 
[1] "0.1 - 46.6 (9.4)"   "0.0 - 211.2 (15.0)"
[1] "hr=" "1.3"
D19V2, continuous
D19V3, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     1   6
  10Q GAIN WILD-TYPE 175 218
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      1    6
  10Q GAIN WILD-TYPE  175  218
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  FEMALE                1                175
  MALE                  6                218
[1] 2 2
[1] FALSE
D19V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  10Q GAIN MUTATED             5                0                 2
  10Q GAIN WILD-TYPE         138              104               151
D19V5, multiclass
                   clus
vv                  10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  ASTROCYTOMA                      5                138
  OLIGOASTROCYTOMA                 0                104
  OLIGODENDROGLIOMA                2                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"
D19V6, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     3   4
  10Q GAIN WILD-TYPE  86 307
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      3    4
  10Q GAIN WILD-TYPE   86  307
     clus
vv    10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  NO                 3                 86
  YES                4                307
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10Q GAIN MUTATED                                  0     0
  10Q GAIN WILD-TYPE                                1     2
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10Q GAIN MUTATED                           1     6
  10Q GAIN WILD-TYPE                        13   370
D19V7, multiclass
                                  clus
vv                                 10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  2
  BLACK OR AFRICAN AMERICAN                       1                 13
  WHITE                                           6                370
[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   5
  10Q GAIN WILD-TYPE  14 354
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      1    5
  10Q GAIN WILD-TYPE   14  354
                        clus
vv                       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 14
  NOT HISPANIC OR LATINO                5                354
[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 300  68
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                27                368 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 3                 68 
$`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        15.75 
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        28.27        22.49 
TCGA-S9-A6WH TCGA-S9-A7QY TCGA-VM-A8CA 
       22.92        18.21        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-DH-5140 TCGA-DH-5141 TCGA-DH-5142 
       14.73        13.64        10.92        19.96        31.82        30.31 
TCGA-DH-5143 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66F TCGA-DH-A66G TCGA-DU-5847 
       14.40        30.21        29.62         7.79         3.85        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-5872 TCGA-DU-5874 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
      182.33        17.49        15.16        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-7019 TCGA-DU-7290 
        6.54         8.84       117.40        90.77        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-A5TP 
       20.68        21.40        19.13        16.96        15.48        14.24 
TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TY TCGA-DU-A6S2 
       12.59        15.12         4.96         3.65        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-A76R TCGA-DU-A7T8 TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 
       21.30       124.50        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-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-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX 
       11.87        15.52        24.46         0.59         5.26         3.72 
TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 
        9.67         7.04         6.64         7.04         4.21         4.08 
TCGA-FG-A6J3 TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A713 TCGA-FN-7833 TCGA-HT-7467 
       10.59        10.78        22.95         5.23         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-7686 TCGA-HT-7687 TCGA-HT-7688 
       16.24         0.76        44.68        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-8018 TCGA-HT-8019 TCGA-HT-8104 
       16.24         9.40        63.55        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-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-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-7493 TCGA-HW-7495 TCGA-HW-8319 
        8.32        19.23        40.18        35.90         4.31         8.61 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
        8.94        19.59        17.82        10.55         7.89         9.67 
TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV 
        6.61        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-A5F6 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65Z TCGA-QH-A6CS 
        1.28         5.75         2.53         4.83         4.11         4.18 
TCGA-QH-A6CV TCGA-QH-A6CY TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 
        2.96         2.20         0.59         6.31         3.91         4.73 
TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO 
        1.91         0.23         5.03        88.83        94.03        32.65 
TCGA-R8-A73M TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TX TCGA-S9-A6TZ 
       59.38        62.17        69.07        18.77        28.14        21.63 
TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       16.37        11.31        15.62        20.05         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       103.76        62.37        72.59        70.55 
TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP 
       70.65        10.88         9.30         9.04         7.59         6.15 
TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ 
        3.39        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-A7QZ TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 
       13.02        10.39        87.09        17.42        83.80        31.59 
TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF 
        5.00        49.45        35.93        25.32        22.59        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 
       26.79        10.95 

  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             14.975 
[1] "1.2 - 211.2 (14.2)" "0.0 - 182.3 (15.0)"
[1] "hr=" "1.5"
D20V2, continuous
D20V3, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    15  12
  11P GAIN WILD-TYPE 161 212
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     15   12
  11P GAIN WILD-TYPE  161  212
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE               15                161
  MALE                 12                212
[1] 2 2
[1] FALSE
D20V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  11P GAIN MUTATED             4                9                14
  11P GAIN WILD-TYPE         139               95               139
D20V5, multiclass
                   clus
vv                  11P GAIN MUTATED 11P GAIN WILD-TYPE
  ASTROCYTOMA                      4                139
  OLIGOASTROCYTOMA                 9                 95
  OLIGODENDROGLIOMA               14                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"
D20V6, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     6  21
  11P GAIN WILD-TYPE  83 290
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      6   21
  11P GAIN WILD-TYPE   83  290
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  NO                 6                 83
  YES               21                290
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11P GAIN MUTATED                                  0     0
  11P GAIN WILD-TYPE                                1     2
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11P GAIN MUTATED                           1    25
  11P GAIN WILD-TYPE                        13   351
D20V7, multiclass
                                  clus
vv                                 11P GAIN MUTATED 11P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  2
  BLACK OR AFRICAN AMERICAN                       1                 13
  WHITE                                          25                351
[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  14 334
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      1   25
  11P GAIN WILD-TYPE   14  334
                        clus
vv                       11P GAIN MUTATED 11P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 14
  NOT HISPANIC OR LATINO               25                334
[1] 2 2
[1] FALSE

Clustering(21) Variable = 11Q GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                  0   1
  11Q GAIN MUTATED    40   7
  11Q GAIN WILD-TYPE 284  64
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                47                348 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 7                 64 
$`11Q GAIN MUTATED`
TCGA-CS-5396 TCGA-DB-5277 TCGA-DB-A4X9 TCGA-DB-A64L TCGA-DB-A64Q TCGA-DH-5144 
        9.96        46.65        30.08        11.01         5.98         8.02 
TCGA-DH-A66D TCGA-DH-A66G TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-6392 TCGA-DU-6393 
       15.75         3.85       182.33        18.94       211.17        52.11 
TCGA-DU-6397 TCGA-DU-6400 TCGA-DU-7018 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 
       46.06         1.22        30.67        23.31        41.98         2.76 
TCGA-DU-A5TT TCGA-DU-A5TW TCGA-DU-A6S8 TCGA-FG-5962 TCGA-FG-7634 TCGA-FG-A60L 
        4.96         5.65         5.98        47.77        15.35         7.04 
TCGA-HT-7474 TCGA-HT-7601 TCGA-HT-7604 TCGA-HT-7607 TCGA-HT-7684 TCGA-HT-7688 
        3.75         5.03       107.93         3.16         6.05        31.69 
TCGA-HT-7693 TCGA-HT-8109 TCGA-HW-7490 TCGA-HW-8319 TCGA-QH-A65S TCGA-QH-A65X 
       17.52         3.95        19.23         8.61         2.53         7.79 
TCGA-QH-A6CZ TCGA-S9-A6TW TCGA-S9-A6TY TCGA-S9-A6WD TCGA-S9-A6WH TCGA-S9-A7IZ 
        3.16        28.27        22.49        62.37        22.92         4.21 
TCGA-S9-A7QY TCGA-S9-A89Z TCGA-TM-A84J TCGA-VM-A8C8 TCGA-VM-A8CA 
       18.21         5.00        17.49        33.07        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-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 
       13.64        10.92        19.96        31.82        30.31        14.40 
TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66F TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       30.21        29.62         7.79        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5872 TCGA-DU-5874 
        6.74        13.38         8.45         6.81        17.49        15.16 
TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6399 TCGA-DU-6401 TCGA-DU-6402 
       22.42        49.02        75.16        65.75        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-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-8158 TCGA-DU-8161 TCGA-DU-8162 
       62.01        25.91        60.30         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-A5TU TCGA-DU-A5TY TCGA-DU-A6S2 
       14.24        12.59        15.12         3.65        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-A76R TCGA-DU-A7T8 TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 
       21.30       124.50        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-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-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX 
       11.87        15.52        24.46         0.59         5.26         3.72 
TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 
        9.67         7.04         6.64         4.21         4.08        10.59 
TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A713 TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 
       10.78        22.95         5.23         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-7602 TCGA-HT-7603 TCGA-HT-7605 
       60.03       154.19         4.01        29.85        23.18         4.57 
TCGA-HT-7606 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7616 
       17.29        22.06        45.99        56.09        57.60         0.23 
TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7686 
       14.27         0.16        16.24         0.76        44.68        42.74 
TCGA-HT-7687 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7694 
        0.10        14.96         0.10         0.10         2.96         6.90 
TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 
       14.53        39.48        19.23        39.09         0.23        50.63 
TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 
        0.49        23.61        37.15         0.33         0.13         3.68 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 
        5.33         2.93         1.71        11.28        31.43         1.64 
TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 
       16.24         9.40        63.55        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-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-HW-7486 TCGA-HW-7487 
       13.02         1.81        16.14         5.33        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         8.94        19.59 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 
       17.82        10.55         7.89         9.67         6.61        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-A5F6 TCGA-QH-A65R 
        2.37         2.30         4.11         5.88         1.28         5.75 
TCGA-QH-A65V TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CV TCGA-QH-A6CY TCGA-QH-A6X3 
        4.83         4.11         4.18         2.96         2.20         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-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        28.14        21.63        16.37        11.31        15.62 
TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB 
       20.05         9.86        94.62        83.70         5.85       103.76 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN 
       72.59        70.55        70.65        10.88         9.30         9.04 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX 
        7.59         6.15         3.39        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-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 
        4.04        13.02        10.39        87.09        17.42        83.80 
TCGA-S9-A7R8 TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF 
       31.59        49.45        35.93        25.32        22.59        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-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-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH 
       12.00        30.08         0.10         7.89        26.79        10.95 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              1.22               0.03 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            211.17             156.23 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             15.35              14.96 
[1] "1.2 - 211.2 (15.3)" "0.0 - 156.2 (15.0)"
[1] "hr=" "1.3"
D21V2, continuous
D21V3, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    26  21
  11Q GAIN WILD-TYPE 150 203
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     26   21
  11Q GAIN WILD-TYPE  150  203
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE               26                150
  MALE                 21                203
[1] 2 2
[1] FALSE
D21V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  11Q GAIN MUTATED            12               12                23
  11Q GAIN WILD-TYPE         131               92               130
D21V5, multiclass
                   clus
vv                  11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  ASTROCYTOMA                     12                131
  OLIGOASTROCYTOMA                12                 92
  OLIGODENDROGLIOMA               23                130
[1] 3 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  37
  11Q GAIN WILD-TYPE  79 274
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     10   37
  11Q GAIN WILD-TYPE   79  274
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  NO                10                 79
  YES               37                274
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11Q GAIN MUTATED                                  0     0
  11Q GAIN WILD-TYPE                                1     2
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11Q GAIN MUTATED                           2    43
  11Q GAIN WILD-TYPE                        12   333
D21V7, multiclass
                                  clus
vv                                 11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  2
  BLACK OR AFRICAN AMERICAN                       2                 12
  WHITE                                          43                333
[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  43
  11Q GAIN WILD-TYPE  14 316
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      1   43
  11Q GAIN WILD-TYPE   14  316
                        clus
vv                       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 14
  NOT HISPANIC OR LATINO               43                316
[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 303  65
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                27                368 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 6                 65 
$`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 
        2.96         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-DH-5140 TCGA-DH-5141 TCGA-DH-5142 
       14.73        13.64        10.92        19.96        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        29.62        15.75         7.79         3.85 
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-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6401 
       52.11        22.42        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-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-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-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-E1-5302 TCGA-E1-5303 
       11.41        26.76         7.13        21.30        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-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 
       14.33        47.77        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-8185 TCGA-FG-8186 TCGA-FG-8187 
       20.61        20.09        12.95        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        11.87        24.46         0.59         5.26         3.72 
TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 
        9.67         7.04         6.64         7.04         4.21         4.08 
TCGA-FG-A6J3 TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A713 TCGA-FN-7833 TCGA-HT-7467 
       10.59        10.78        22.95         5.23         0.13         0.10 
TCGA-HT-7468 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7474 TCGA-HT-7475 
        6.67         8.81         0.13         0.03         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-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-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-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-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-A5R9 TCGA-HT-A5RA 
       15.72         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-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         8.61         8.94        19.59        17.82        10.55 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X 
        7.89         9.67         6.61        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-A5F6 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V 
        4.11         5.88         1.28         5.75         2.53         4.83 
TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
        7.79         4.11         4.18         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-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        28.27        28.14        22.49        21.63        16.37 
TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
       11.31        15.62        20.05         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       103.76        62.37        72.59        70.55        22.92 
TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP 
       70.65        10.88         9.30         9.04         7.59         6.15 
TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7J0 
        3.39        14.27         7.92        19.63        12.59         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        18.21 
TCGA-S9-A7QZ TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 
       13.02        10.39        87.09        17.42        83.80        31.59 
TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF 
        5.00        49.45        35.93        25.32        22.59        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 
       26.79        10.95 

  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 
            16.800             14.715 
[1] "1.2 - 124.5 (16.8)" "0.0 - 211.2 (14.7)"
[1] "hr=" "1.1"
D22V2, continuous
D22V3, binary
                    cls
clus                   0   1
  12P GAIN MUTATED     8  19
  12P GAIN WILD-TYPE 168 205
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      8   19
  12P GAIN WILD-TYPE  168  205
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE                8                168
  MALE                 19                205
[1] 2 2
[1] FALSE
D22V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  12P GAIN MUTATED             9                9                 9
  12P GAIN WILD-TYPE         134               95               144
D22V5, multiclass
                   clus
vv                  12P GAIN MUTATED 12P GAIN WILD-TYPE
  ASTROCYTOMA                      9                134
  OLIGOASTROCYTOMA                 9                 95
  OLIGODENDROGLIOMA                9                144
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V6, binary
                    cls
clus                   0   1
  12P GAIN MUTATED     6  21
  12P GAIN WILD-TYPE  83 290
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      6   21
  12P GAIN WILD-TYPE   83  290
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  NO                 6                 83
  YES               21                290
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12P GAIN MUTATED                                  0     1
  12P GAIN WILD-TYPE                                1     1
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12P GAIN MUTATED                           1    25
  12P GAIN WILD-TYPE                        13   351
D22V7, multiclass
                                  clus
vv                                 12P GAIN MUTATED 12P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  1
  BLACK OR AFRICAN AMERICAN                       1                 13
  WHITE                                          25                351
[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  14 333
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      1   26
  12P GAIN WILD-TYPE   14  333
                        clus
vv                       12P GAIN MUTATED 12P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 14
  NOT HISPANIC OR LATINO               26                333
[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 317  65
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                13                382 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 6                 65 
$`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         2.96 
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-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 
       10.92        19.96        31.82        30.31        14.40         8.02 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DU-5847 TCGA-DU-5849 
       29.62        15.75         7.79         3.85        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-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-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-E1-5302 TCGA-E1-5303 
       26.76         7.13        21.30       124.50        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-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 
       14.33        47.77        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-A4MU 
       20.09        14.96        11.87        15.52        24.46         0.59 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
        5.26         3.72         9.67         7.04         6.64         7.04 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A713 
        4.21         4.08        10.59        10.78        22.95         5.23 
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-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-8018 
       31.43         1.64        16.24         9.40        63.55        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-A5R9 TCGA-HT-A5RA 
       15.72         0.23        10.49         0.13         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-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-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 
       35.90         4.31         8.61         8.94        19.59        17.82 
TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 
       10.55         7.89         9.67         6.61        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-A5F6 TCGA-QH-A65R TCGA-QH-A65S 
        2.30         4.11         5.88         1.28         5.75         2.53 
TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CY TCGA-QH-A6CZ 
        4.83         7.79         4.11         4.18         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-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TS 
        5.03        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        28.27        28.14        22.49        21.63 
TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       16.37        11.31        15.62        20.05         9.86        94.62 
TCGA-S9-A6U9 TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH 
       83.70       103.76        62.37        72.59        70.55        22.92 
TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP 
       70.65        10.88         9.30         9.04         7.59         6.15 
TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ 
        3.39        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-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 
       18.21        13.02        10.39        87.09        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        35.93        25.32        22.59 
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 
        0.10         7.89        26.79        10.95 

  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              14.96 
[1] "1.2 - 63.0 (15.3)"  "0.0 - 211.2 (15.0)"
[1] "hr=" "3.6"
D23V2, continuous
D23V3, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED     4   9
  12Q GAIN WILD-TYPE 172 215
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      4    9
  12Q GAIN WILD-TYPE  172  215
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE                4                172
  MALE                  9                215
[1] 2 2
[1] FALSE
D23V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  12Q GAIN MUTATED             5                3                 5
  12Q GAIN WILD-TYPE         138              101               148
D23V5, multiclass
                   clus
vv                  12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  ASTROCYTOMA                      5                138
  OLIGOASTROCYTOMA                 3                101
  OLIGODENDROGLIOMA                5                148
[1] 3 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  87 300
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      2   11
  12Q GAIN WILD-TYPE   87  300
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  NO                 2                 87
  YES               11                300
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12Q GAIN MUTATED                                  0     1
  12Q GAIN WILD-TYPE                                1     1
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12Q GAIN MUTATED                           0    12
  12Q GAIN WILD-TYPE                        14   364
D23V7, multiclass
                                  clus
vv                                 12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  1
  BLACK OR AFRICAN AMERICAN                       0                 14
  WHITE                                          12                364
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V8, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED     0  13
  12Q GAIN WILD-TYPE  15 346
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      0   13
  12Q GAIN WILD-TYPE   15  346
                        clus
vv                       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 15
  NOT HISPANIC OR LATINO               13                346
[1] 2 2
[1] FALSE

Clustering(24) Variable = 13Q GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                  0   1
  13Q GAIN MUTATED     4   0
  13Q GAIN WILD-TYPE 320  71
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 4                391 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 0                 71 
$`13Q GAIN MUTATED`
TCGA-HT-7611 TCGA-QH-A65S TCGA-QH-A6X9 TCGA-VM-A8CA 
       57.60         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-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 
       10.92        19.96        31.82        30.31        14.40         8.02 
TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DU-5847 
       30.21        29.62        15.75         7.79         3.85        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-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-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-E1-5322 TCGA-EZ-7264 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 
       95.57       130.78        14.33        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        11.87 
TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY 
       15.52        24.46         0.59         5.26         3.72         9.67 
TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 
        7.04         6.64         7.04         4.21         4.08        10.59 
TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A713 TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 
       10.78        22.95         5.23         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-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 
       45.99        56.09         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-8018 TCGA-HT-8019 TCGA-HT-8104 
       16.24         9.40        63.55        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-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-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 
        8.61         8.94        19.59        17.82        10.55         7.89 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 
        9.67         6.61        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-A5F6 TCGA-QH-A65R TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z 
        5.88         1.28         5.75         4.83         7.79         4.11 
TCGA-QH-A6CS TCGA-QH-A6CV TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
        4.18         2.96         2.20         3.16         0.59         6.31 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-R8-A6MK TCGA-R8-A6ML 
        3.91         4.73         0.23         5.03        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        28.27 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 
       28.14        22.49        21.63        16.37        11.31        15.62 
TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB 
       20.05         9.86        94.62        83.70         5.85       103.76 
TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL 
       62.37        72.59        70.55        22.92        70.65        10.88 
TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ 
        9.30         9.04         7.59         6.15         3.39        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        18.21        13.02 
TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89Z 
       10.39        87.09        17.42        83.80        31.59         5.00 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B 
       49.45        35.93        25.32        22.59        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-A8CB TCGA-VM-A8CD TCGA-VM-A8CE 
       12.00        33.07        30.08         0.10         7.89        26.79 
TCGA-VM-A8CH 
       10.95 

  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 
              8.02              14.99 
[1] "1.9 - 57.6 (8.0)"   "0.0 - 211.2 (15.0)"
[1] "hr="     "3300000"
D24V2, continuous
D24V3, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     2   3
  13Q GAIN WILD-TYPE 174 221
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      2    3
  13Q GAIN WILD-TYPE  174  221
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE                2                174
  MALE                  3                221
[1] 2 2
[1] FALSE
D24V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  13Q GAIN MUTATED             1                2                 2
  13Q GAIN WILD-TYPE         142              102               151
D24V5, multiclass
                   clus
vv                  13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  ASTROCYTOMA                      1                142
  OLIGOASTROCYTOMA                 2                102
  OLIGODENDROGLIOMA                2                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"
D24V6, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     0   5
  13Q GAIN WILD-TYPE  89 306
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      0    5
  13Q GAIN WILD-TYPE   89  306
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  NO                 0                 89
  YES                5                306
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  13Q GAIN MUTATED                                  0     0
  13Q GAIN WILD-TYPE                                1     2
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  13Q GAIN MUTATED                           0     4
  13Q GAIN WILD-TYPE                        14   372
D24V7, multiclass
                                  clus
vv                                 13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  2
  BLACK OR AFRICAN AMERICAN                       0                 14
  WHITE                                           4                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"
D24V8, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     0   4
  13Q GAIN WILD-TYPE  15 355
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      0    4
  13Q GAIN WILD-TYPE   15  355
                        clus
vv                       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 15
  NOT HISPANIC OR LATINO                4                355
[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 322  70
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 3                392 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 1                 70 
$`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-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        29.62 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       15.75         7.79         3.85        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-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 
       30.67        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-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 
       21.30       124.50        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-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        11.87        15.52        24.46         0.59 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
        5.26         3.72         9.67         7.04         6.64         7.04 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A713 
        4.21         4.08        10.59        10.78        22.95         5.23 
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-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 
       63.55        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-HW-7486 TCGA-HW-7487 TCGA-HW-7489 
        1.81        16.14         5.33        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         8.61         8.94 
TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM 
       19.59        17.82        10.55         7.89         9.67         6.61 
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-A5F6 
        1.64         2.37         2.30         4.11         5.88         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-A6CV TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 
        2.96         2.20         3.16         0.59         6.31         3.91 
TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-R8-A6MK TCGA-R8-A6ML 
        4.73         1.91         0.23         5.03        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        28.27 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 
       28.14        22.49        21.63        16.37        11.31        15.62 
TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB 
       20.05         9.86        94.62        83.70         5.85       103.76 
TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL 
       62.37        72.59        70.55        22.92        70.65        10.88 
TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ 
        9.30         9.04         7.59         6.15         3.39        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        18.21        13.02 
TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89Z 
       10.39        87.09        17.42        83.80        31.59         5.00 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B 
       49.45        35.93        25.32        22.59        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 
       26.79        10.95 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             12.43               0.03 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             30.21             211.17 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             26.30              14.96 
[1] "12.4 - 30.2 (26.3)" "0.0 - 211.2 (15.0)"
[1] "hr=" "2.2"
D25V2, continuous
D25V3, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     1   2
  14Q GAIN WILD-TYPE 175 222
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      1    2
  14Q GAIN WILD-TYPE  175  222
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE                1                175
  MALE                  2                222
[1] 2 2
[1] FALSE
D25V4, continuous
[1] "Remove cluster labels:" "14Q GAIN MUTATED"      
clus
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 2                232 
        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-DH-5140         TCGA-DH-5142         TCGA-DH-5143 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DH-5144         TCGA-DH-A66B         TCGA-DH-A66D 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DH-A66F         TCGA-DH-A66G         TCGA-DU-5851 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-5852         TCGA-DU-5853         TCGA-DU-5854 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-5855         TCGA-DU-5870         TCGA-DU-5871 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-5874         TCGA-DU-6396         TCGA-DU-6403 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-6404         TCGA-DU-6405         TCGA-DU-6407 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-6408         TCGA-DU-6410         TCGA-DU-7011 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-7013         TCGA-DU-7014         TCGA-DU-7015 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-7018         TCGA-DU-7294         TCGA-DU-7298 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-7299         TCGA-DU-7300         TCGA-DU-7301 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-7302         TCGA-DU-7304         TCGA-DU-7306 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-7309         TCGA-DU-8158         TCGA-DU-8161 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-8162         TCGA-DU-8163         TCGA-DU-8165 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-8167         TCGA-DU-8168         TCGA-DU-A5TP 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-A5TR         TCGA-DU-A5TS         TCGA-DU-A5TU 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-A5TW         TCGA-DU-A6S2         TCGA-DU-A6S6 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-A6S7         TCGA-DU-A6S8         TCGA-DU-A76R 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DU-A7T8         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-A713         TCGA-HT-7468 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HT-7470         TCGA-HT-7475         TCGA-HT-7477 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HT-7485         TCGA-HT-7607         TCGA-HT-7609 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HT-7611         TCGA-HT-7689         TCGA-HT-7692 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HT-7693         TCGA-HT-7694         TCGA-HT-7854 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HT-7875         TCGA-HT-7884         TCGA-HT-8564 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HT-A4DV         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-A5F6 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-QH-A65R         TCGA-QH-A65S         TCGA-QH-A65V 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-QH-A65X         TCGA-QH-A65Z         TCGA-QH-A6CS 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-QH-A6CU         TCGA-QH-A6CV         TCGA-QH-A6CW 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-QH-A6CX         TCGA-QH-A6CY         TCGA-QH-A6CZ 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-QH-A6X3         TCGA-QH-A6X4         TCGA-QH-A6X5 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-QH-A6X8         TCGA-QH-A6X9         TCGA-QH-A6XA 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-QH-A6XC         TCGA-S9-A6TS         TCGA-S9-A6TU 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-S9-A6TV         TCGA-S9-A6TW         TCGA-S9-A6TX 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-S9-A6TY         TCGA-S9-A6TZ         TCGA-S9-A6U0 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-S9-A6U1         TCGA-S9-A6U2         TCGA-S9-A6U5 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-S9-A6U6         TCGA-S9-A6U8         TCGA-S9-A6UA 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-S9-A6UB         TCGA-S9-A6WD         TCGA-S9-A6WE 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-S9-A6WG         TCGA-S9-A6WH         TCGA-S9-A6WI 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-S9-A6WL         TCGA-S9-A6WM         TCGA-S9-A6WN 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-S9-A6WO         TCGA-S9-A6WP         TCGA-S9-A6WQ 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-S9-A7IQ         TCGA-S9-A7IS         TCGA-S9-A7IX 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-S9-A7IY         TCGA-S9-A7IZ         TCGA-S9-A7J0 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-S9-A7J1         TCGA-S9-A7J2         TCGA-S9-A7J3 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-S9-A7QW         TCGA-S9-A7QX         TCGA-S9-A7QY 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-S9-A7QZ         TCGA-S9-A7R2         TCGA-S9-A7R3 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-S9-A7R4         TCGA-S9-A7R7         TCGA-S9-A7R8 
"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         142              103               152
D25V5, multiclass
                   clus
vv                  14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  ASTROCYTOMA                      1                142
  OLIGOASTROCYTOMA                 1                103
  OLIGODENDROGLIOMA                1                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"
D25V6, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     2   1
  14Q GAIN WILD-TYPE  87 310
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      2    1
  14Q GAIN WILD-TYPE   87  310
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  NO                 2                 87
  YES                1                310
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  14Q GAIN MUTATED                                  0     0
  14Q GAIN WILD-TYPE                                1     2
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  14Q GAIN MUTATED                           0     3
  14Q GAIN WILD-TYPE                        14   373
D25V7, multiclass
                                  clus
vv                                 14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  2
  BLACK OR AFRICAN AMERICAN                       0                 14
  WHITE                                           3                373
[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  15 356
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      0    3
  14Q GAIN WILD-TYPE   15  356
                        clus
vv                       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 15
  NOT HISPANIC OR LATINO                3                356
[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 320  67
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 8                387 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 4                 67 
$`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-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-DU-5847 TCGA-DU-5849 
       29.62        15.75         7.79         3.85        18.02        14.56 
TCGA-DU-5851 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
       17.46        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-7015 TCGA-DU-7018 
       14.99       105.21         6.54         8.84        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-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-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-E1-5302 TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 
      124.50        50.14        67.46        79.99        57.93       134.27 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 TCGA-FG-5962 TCGA-FG-5963 
       78.21        95.57       130.78        14.33        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 
       11.87        15.52        24.46         0.59         5.26         3.72 
TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 
        9.67         7.04         6.64         7.04         4.21         4.08 
TCGA-FG-A6J3 TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A713 TCGA-FN-7833 TCGA-HT-7467 
       10.59        10.78        22.95         5.23         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-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-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-8018 TCGA-HT-8019 
        1.64        16.24         9.40        63.55        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-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB 
        0.23        10.49         0.13         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-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         8.61         8.94        19.59        17.82        10.55 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X 
        7.89         9.67         6.61        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-A5F6 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V 
        4.11         5.88         1.28         5.75         2.53         4.83 
TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CV TCGA-QH-A6CY TCGA-QH-A6CZ 
        7.79         4.11         4.18         2.96         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-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TS 
        5.03        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        28.27        28.14        22.49        21.63 
TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       16.37        11.31        15.62        20.05         9.86        94.62 
TCGA-S9-A6U9 TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH 
       83.70       103.76        62.37        72.59        70.55        22.92 
TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP 
       70.65        10.88         9.30         9.04         7.59         6.15 
TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7J0 
        3.39        14.27         7.92        19.63        12.59         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        18.21 
TCGA-S9-A7QZ TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 
       13.02        10.39        87.09        17.42        83.80        31.59 
TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF 
        5.00        49.45        35.93        25.32        22.59        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 
        7.89        26.79        10.95 

  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             14.960 
[1] "4.2 - 117.4 (21.2)" "0.0 - 211.2 (15.0)"
[1] "hr=" "2.2"
D26V2, continuous
D26V3, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     2   6
  15Q GAIN WILD-TYPE 174 218
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      2    6
  15Q GAIN WILD-TYPE  174  218
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE                2                174
  MALE                  6                218
[1] 2 2
[1] FALSE
D26V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  15Q GAIN MUTATED             5                2                 1
  15Q GAIN WILD-TYPE         138              102               152
D26V5, multiclass
                   clus
vv                  15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  ASTROCYTOMA                      5                138
  OLIGOASTROCYTOMA                 2                102
  OLIGODENDROGLIOMA                1                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"
D26V6, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     2   6
  15Q GAIN WILD-TYPE  87 305
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      2    6
  15Q GAIN WILD-TYPE   87  305
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  NO                 2                 87
  YES                6                305
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  15Q GAIN MUTATED                                  0     0
  15Q GAIN WILD-TYPE                                1     2
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  15Q GAIN MUTATED                           0     8
  15Q GAIN WILD-TYPE                        14   368
D26V7, multiclass
                                  clus
vv                                 15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  2
  BLACK OR AFRICAN AMERICAN                       0                 14
  WHITE                                           8                368
[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  15 352
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      0    7
  15Q GAIN WILD-TYPE   15  352
                        clus
vv                       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 15
  NOT HISPANIC OR LATINO                7                352
[1] 2 2
[1] FALSE

Clustering(27) Variable = 16P GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                  0   1
  16P GAIN MUTATED     9   5
  16P GAIN WILD-TYPE 315  66
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                14                381 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 5                 66 
$`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        29.62       211.17         1.22        62.96 
TCGA-DU-7010 TCGA-DU-A5TS TCGA-E1-5304 TCGA-FG-5962 TCGA-HT-A618 TCGA-S9-A6WH 
       14.99        15.12        41.13        47.77         5.33        22.92 
TCGA-S9-A7QW TCGA-VM-A8CA 
        3.58        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-DH-5140 
       15.42        27.81        14.73        13.64        10.92        19.96 
TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66D 
       31.82        30.31        14.40         8.02        30.21        15.75 
TCGA-DH-A66F TCGA-DH-A66G TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
        7.79         3.85        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-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 
       15.16        52.11        22.42        49.02        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-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 
      156.23       138.28       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-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 
       12.59         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-E1-5302 TCGA-E1-5303 TCGA-E1-5305 
        7.13        21.30       124.50        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-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        11.87        15.52        24.46         0.59         5.26 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ 
        3.72         9.67         7.04         6.64         7.04         4.21 
TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A713 TCGA-FN-7833 
        4.08        10.59        10.78        22.95         5.23         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-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-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 
       16.14        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         8.61         8.94        19.59        17.82 
TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 
       10.55         7.89         9.67         6.61        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-A5F6 TCGA-QH-A65R TCGA-QH-A65S 
        2.30         4.11         5.88         1.28         5.75         2.53 
TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CV TCGA-QH-A6CY 
        4.83         7.79         4.11         4.18         2.96         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-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
        0.23         5.03        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        28.27        28.14        22.49 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       21.63        16.37        11.31        15.62        20.05         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       103.76        62.37        72.59 
TCGA-S9-A6WG TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO 
       70.55        70.65        10.88         9.30         9.04         7.59 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY 
        6.15         3.39        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-A7QX 
        4.21         9.37         8.19         2.04         8.12         4.04 
TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 
       18.21        13.02        10.39        87.09        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        35.93        25.32        22.59 
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-A8CB 
        9.44         4.57        12.00        33.07        30.08         0.10 
TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH 
        7.89        26.79        10.95 

  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             14.960 
[1] "1.2 - 211.2 (15.1)" "0.0 - 182.3 (15.0)"
[1] "hr=" "1.6"
D27V2, continuous
D27V3, binary
                    cls
clus                   0   1
  16P GAIN MUTATED     8   6
  16P GAIN WILD-TYPE 168 218
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      8    6
  16P GAIN WILD-TYPE  168  218
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE                8                168
  MALE                  6                218
[1] 2 2
[1] FALSE
D27V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  16P GAIN MUTATED             8                2                 4
  16P GAIN WILD-TYPE         135              102               149
D27V5, multiclass
                   clus
vv                  16P GAIN MUTATED 16P GAIN WILD-TYPE
  ASTROCYTOMA                      8                135
  OLIGOASTROCYTOMA                 2                102
  OLIGODENDROGLIOMA                4                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"
D27V6, binary
                    cls
clus                   0   1
  16P GAIN MUTATED     4  10
  16P GAIN WILD-TYPE  85 301
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      4   10
  16P GAIN WILD-TYPE   85  301
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  NO                 4                 85
  YES               10                301
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16P GAIN MUTATED                                  0     0
  16P GAIN WILD-TYPE                                1     2
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16P GAIN MUTATED                           1    12
  16P GAIN WILD-TYPE                        13   364
D27V7, multiclass
                                  clus
vv                                 16P GAIN MUTATED 16P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  2
  BLACK OR AFRICAN AMERICAN                       1                 13
  WHITE                                          12                364
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V8, binary
                    cls
clus                   0   1
  16P GAIN MUTATED     0  13
  16P GAIN WILD-TYPE  15 346
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      0   13
  16P GAIN WILD-TYPE   15  346
                        clus
vv                       16P GAIN MUTATED 16P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 15
  NOT HISPANIC OR LATINO               13                346
[1] 2 2
[1] FALSE

Clustering(28) Variable = 16Q GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                  0   1
  16Q GAIN MUTATED    11   6
  16Q GAIN WILD-TYPE 313  65
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                17                378 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 6                 65 
$`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-A616 TCGA-HT-A618 
       15.12        50.14        41.13        47.77         1.81         5.33 
TCGA-S9-A7J0 TCGA-S9-A7QW TCGA-TM-A84I TCGA-TM-A84Q TCGA-VM-A8CA 
        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-DH-5140 
       15.42        27.81        14.73        13.64        10.92        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        29.62 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       15.75         7.79         3.85        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-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 
       17.49        15.16        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-7008 TCGA-DU-7009 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 
       11.47       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-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-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY 
       14.24        12.59         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-E1-5303 TCGA-E1-5305 
       26.76         7.13        21.30       124.50        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-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        11.87        15.52        24.46         0.59         5.26 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ 
        3.72         9.67         7.04         6.64         7.04         4.21 
TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A713 TCGA-FN-7833 
        4.08        10.59        10.78        22.95         5.23         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-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-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         8.61         8.94        19.59        17.82        10.55 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X 
        7.89         9.67         6.61        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-A5F6 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V 
        4.11         5.88         1.28         5.75         2.53         4.83 
TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CV TCGA-QH-A6CY TCGA-QH-A6CZ 
        7.79         4.11         4.18         2.96         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-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TS 
        5.03        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        28.27        28.14        22.49        21.63 
TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       16.37        11.31        15.62        20.05         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       103.76        62.37        72.59        70.55 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO 
       22.92        70.65        10.88         9.30         9.04         7.59 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY 
        6.15         3.39        14.27         7.92        19.63        12.59 
TCGA-S9-A7IZ TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QX TCGA-S9-A7QY 
        4.21         8.19         2.04         8.12         4.04        18.21 
TCGA-S9-A7QZ TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 
       13.02        10.39        87.09        17.42        83.80        31.59 
TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF 
        5.00        49.45        35.93        25.32        22.59        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-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-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH 
       33.07        30.08         0.10         7.89        26.79        10.95 

  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 
             14.99              14.96 
[1] "1.2 - 211.2 (15.0)" "0.0 - 182.3 (15.0)"
[1] "hr=" "1.8"
D28V2, continuous
D28V3, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     9   8
  16Q GAIN WILD-TYPE 167 216
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      9    8
  16Q GAIN WILD-TYPE  167  216
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE                9                167
  MALE                  8                216
[1] 2 2
[1] FALSE
D28V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  16Q GAIN MUTATED            11                1                 5
  16Q GAIN WILD-TYPE         132              103               148
D28V5, multiclass
                   clus
vv                  16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  ASTROCYTOMA                     11                132
  OLIGOASTROCYTOMA                 1                103
  OLIGODENDROGLIOMA                5                148
[1] 3 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  12
  16Q GAIN WILD-TYPE  84 299
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      5   12
  16Q GAIN WILD-TYPE   84  299
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  NO                 5                 84
  YES               12                299
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16Q GAIN MUTATED                                  0     0
  16Q GAIN WILD-TYPE                                1     2
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16Q GAIN MUTATED                           1    15
  16Q GAIN WILD-TYPE                        13   361
D28V7, multiclass
                                  clus
vv                                 16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  2
  BLACK OR AFRICAN AMERICAN                       1                 13
  WHITE                                          15                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"
D28V8, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     0  16
  16Q GAIN WILD-TYPE  15 343
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      0   16
  16Q GAIN WILD-TYPE   15  343
                        clus
vv                       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 15
  NOT HISPANIC OR LATINO               16                343
[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 312  66
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                17                378 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 5                 66 
$`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         7.79         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         2.96 
TCGA-S9-A6TS TCGA-S9-A6U1 TCGA-S9-A6WL TCGA-TM-A84M TCGA-VM-A8CA 
       62.17        11.31        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-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        29.62 
TCGA-DH-A66D TCGA-DH-A66G TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
       15.75         3.85        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-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-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-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-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-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-FG-5963 TCGA-FG-5964 TCGA-FG-5965 
       95.57       130.78        14.33        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        11.87        15.52        24.46 
TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K 
        0.59         5.26         3.72         9.67         7.04         6.64 
TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A713 
        7.04         4.21         4.08        10.78        22.95         5.23 
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-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-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 
       16.14         5.33        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         8.61         8.94        19.59 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-8125 
       17.82        10.55         7.89         9.67         6.61        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-A5F6 TCGA-QH-A65R TCGA-QH-A65S 
        2.30         4.11         5.88         1.28         5.75         2.53 
TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CY TCGA-QH-A6CZ 
        4.83         7.79         4.11         4.18         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-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TU 
        5.03        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        28.27        28.14        22.49        21.63        16.37 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA 
       15.62        20.05         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 
      103.76        62.37        72.59        70.55        22.92        70.65 
TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ 
        9.30         9.04         7.59         6.15         3.39        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        18.21        13.02 
TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89Z 
       10.39        87.09        17.42        83.80        31.59         5.00 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B 
       49.45        35.93        25.32        22.59        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-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T 
       40.83        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 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              2.96               0.03 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             62.17             211.17 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
            13.510             14.975 
[1] "3.0 - 62.2 (13.5)"  "0.0 - 211.2 (15.0)"
[1] "hr=" "2.4"
D29V2, continuous
D29V3, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     5  12
  17P GAIN WILD-TYPE 171 212
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      5   12
  17P GAIN WILD-TYPE  171  212
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE                5                171
  MALE                 12                212
[1] 2 2
[1] FALSE
D29V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  17P GAIN MUTATED             9                1                 7
  17P GAIN WILD-TYPE         134              103               146
D29V5, multiclass
                   clus
vv                  17P GAIN MUTATED 17P GAIN WILD-TYPE
  ASTROCYTOMA                      9                134
  OLIGOASTROCYTOMA                 1                103
  OLIGODENDROGLIOMA                7                146
[1] 3 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  85 298
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      4   13
  17P GAIN WILD-TYPE   85  298
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  NO                 4                 85
  YES               13                298
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17P GAIN MUTATED                                  0     1
  17P GAIN WILD-TYPE                                1     1
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17P GAIN MUTATED                           0    15
  17P GAIN WILD-TYPE                        14   361
D29V7, multiclass
                                  clus
vv                                 17P GAIN MUTATED 17P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  1
  BLACK OR AFRICAN AMERICAN                       0                 14
  WHITE                                          15                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"
D29V8, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     1  15
  17P GAIN WILD-TYPE  14 344
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      1   15
  17P GAIN WILD-TYPE   14  344
                        clus
vv                       17P GAIN MUTATED 17P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 14
  NOT HISPANIC OR LATINO               15                344
[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 311  65
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                19                376 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 6                 65 
$`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         7.79         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         2.96 
TCGA-S9-A6TS TCGA-S9-A6U1 TCGA-S9-A6UA TCGA-S9-A6WL TCGA-TM-A84M TCGA-VM-A8CA 
       62.17        11.31         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-DH-5140 
       15.42        27.81        14.73        13.64        10.92        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        29.62        15.75 
TCGA-DH-A66G TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 
        3.85        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-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-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-A6S8 
        5.65        12.20         8.65         2.70        77.98         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-E1-5305 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-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 
      130.78        14.33        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-A4MU 
       20.09        14.96        11.87        15.52        24.46         0.59 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
        5.26         3.72         9.67         7.04         6.64         7.04 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A713 
        4.21         4.08        10.59        10.78        22.95         5.23 
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-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-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 
       16.14         5.33        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         8.61         8.94        19.59 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-8125 
       17.82        10.55         7.89         9.67         6.61        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-A5F6 TCGA-QH-A65R TCGA-QH-A65S 
        2.30         4.11         5.88         1.28         5.75         2.53 
TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CY TCGA-QH-A6CZ 
        4.83         7.79         4.11         4.18         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-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TU 
        5.03        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        28.27        28.14        22.49        21.63        16.37 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UB 
       15.62        20.05         9.86        94.62        83.70       103.76 
TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WM 
       62.37        72.59        70.55        22.92        70.65         9.30 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
        9.04         7.59         6.15         3.39        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-A7R2 
        8.12         3.58         4.04        18.21        13.02        10.39 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89Z TCGA-TM-A7C3 
       87.09        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 
       35.93        25.32        22.59        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-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 
       30.08         0.10         7.89        26.79 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              2.96               0.03 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             62.17             211.17 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             12.43              15.04 
[1] "3.0 - 62.2 (12.4)"  "0.0 - 211.2 (15.0)"
[1] "hr=" "2.9"
D30V2, continuous
D30V3, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED     6  13
  17Q GAIN WILD-TYPE 170 211
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      6   13
  17Q GAIN WILD-TYPE  170  211
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE                6                170
  MALE                 13                211
[1] 2 2
[1] FALSE
D30V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  17Q GAIN MUTATED            10                2                 7
  17Q GAIN WILD-TYPE         133              102               146
D30V5, multiclass
                   clus
vv                  17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  ASTROCYTOMA                     10                133
  OLIGOASTROCYTOMA                 2                102
  OLIGODENDROGLIOMA                7                146
[1] 3 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  85 296
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      4   15
  17Q GAIN WILD-TYPE   85  296
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  NO                 4                 85
  YES               15                296
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17Q GAIN MUTATED                                  0     1
  17Q GAIN WILD-TYPE                                1     1
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17Q GAIN MUTATED                           0    16
  17Q GAIN WILD-TYPE                        14   360
D30V7, multiclass
                                  clus
vv                                 17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  1
  BLACK OR AFRICAN AMERICAN                       0                 14
  WHITE                                          16                360
[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  14 344
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      1   15
  17Q GAIN WILD-TYPE   14  344
                        clus
vv                       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 14
  NOT HISPANIC OR LATINO               15                344
[1] 2 2
[1] FALSE

Clustering(31) Variable = 18P GAIN MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                  0   1
  18P GAIN MUTATED     9   3
  18P GAIN WILD-TYPE 315  68
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                12                383 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 3                 68 
$`18P GAIN MUTATED`
TCGA-CS-4938 TCGA-DB-5277 TCGA-DU-7010 TCGA-DU-8165 TCGA-DU-A5TS TCGA-DU-A5TY 
        4.70        46.65        14.99        19.13        15.12        12.20 
TCGA-E1-5304 TCGA-HT-8111 TCGA-HW-7489 TCGA-QH-A6CS TCGA-QH-A6X9 TCGA-S9-A89Z 
       41.13         0.23         8.32         4.18         1.91         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-DH-5140 
       15.42        27.81        14.73        13.64        10.92        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        29.62 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       15.75         7.79         3.85        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-E1-5302 
       11.41        26.76         7.13        21.30       124.50        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-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 
      130.78        14.33        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        11.87        15.52 
TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J 
       24.46         0.59         5.26         3.72         9.67         7.04 
TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Z 
        6.64         7.04         4.21         4.08        10.59        10.78 
TCGA-FG-A710 TCGA-FG-A713 TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 
       22.95         5.23         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-8018 TCGA-HT-8019 TCGA-HT-8104 
       16.24         9.40        63.55        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-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-HW-7486 TCGA-HW-7487 
       13.02         1.81        16.14         5.33        29.92        13.45 
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         8.61         8.94 
TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM 
       19.59        17.82        10.55         7.89         9.67         6.61 
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-A5F6 
        1.64         2.37         2.30         4.11         5.88         1.28 
TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CV 
        5.75         2.53         4.83         7.79         4.11         2.96 
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-A6XA TCGA-QH-A6XC TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
        0.23         5.03        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        28.27        28.14        22.49 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       21.63        16.37        11.31        15.62        20.05         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       103.76        62.37        72.59 
TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN 
       70.55        22.92        70.65        10.88         9.30         9.04 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX 
        7.59         6.15         3.39        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-A7R2 TCGA-S9-A7R3 
        3.58         4.04        18.21        13.02        10.39        87.09 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 
       17.42        83.80        31.59        49.45        35.93        25.32 
TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G 
       22.59        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 
       13.51         0.10         7.89        26.79        10.95 

  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 
             10.26              15.09 
[1] "0.2 - 46.6 (10.3)"  "0.0 - 211.2 (15.1)"
[1] "hr=" "2.9"
D31V2, continuous
D31V3, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     5   7
  18P GAIN WILD-TYPE 171 217
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      5    7
  18P GAIN WILD-TYPE  171  217
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE                5                171
  MALE                  7                217
[1] 2 2
[1] FALSE
D31V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  18P GAIN MUTATED             7                2                 3
  18P GAIN WILD-TYPE         136              102               150
D31V5, multiclass
                   clus
vv                  18P GAIN MUTATED 18P GAIN WILD-TYPE
  ASTROCYTOMA                      7                136
  OLIGOASTROCYTOMA                 2                102
  OLIGODENDROGLIOMA                3                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"
D31V6, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     2  10
  18P GAIN WILD-TYPE  87 301
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      2   10
  18P GAIN WILD-TYPE   87  301
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  NO                 2                 87
  YES               10                301
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18P GAIN MUTATED                                  0     0
  18P GAIN WILD-TYPE                                1     2
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18P GAIN MUTATED                           1    11
  18P GAIN WILD-TYPE                        13   365
D31V7, multiclass
                                  clus
vv                                 18P GAIN MUTATED 18P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  2
  BLACK OR AFRICAN AMERICAN                       1                 13
  WHITE                                          11                365
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V8, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     0  12
  18P GAIN WILD-TYPE  15 347
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      0   12
  18P GAIN WILD-TYPE   15  347
                        clus
vv                       18P GAIN MUTATED 18P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 15
  NOT HISPANIC OR LATINO               12                347
[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 317  69
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 9                386 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 2                 69 
$`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-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 
       10.92        19.96        31.82        30.31        14.40         8.02 
TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DU-5847 
       30.21        29.62        15.75         7.79         3.85        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-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 
      156.23       138.28       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-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-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
        4.96         3.65         5.65         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-E1-5302 TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 
      124.50        50.14        67.46        79.99        57.93       134.27 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 TCGA-FG-5962 TCGA-FG-5963 
       78.21        95.57       130.78        14.33        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 
       11.87        15.52        24.46         0.59         5.26         3.72 
TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 
        9.67         7.04         6.64         7.04         4.21         4.08 
TCGA-FG-A6J3 TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A713 TCGA-FN-7833 TCGA-HT-7467 
       10.59        10.78        22.95         5.23         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-8018 
       31.43         1.64        16.24         9.40        63.55        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-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB 
        0.23        10.49         0.13         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-HW-7486 TCGA-HW-7487 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 
       29.92        13.45        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 
        8.61         8.94        19.59        17.82        10.55         7.89 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 
        9.67         6.61        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-A5F6 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X 
        5.88         1.28         5.75         2.53         4.83         7.79 
TCGA-QH-A65Z TCGA-QH-A6CV TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
        4.11         2.96         2.20         3.16         0.59         6.31 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-R8-A6MK 
        3.91         4.73         1.91         0.23         5.03        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 
       28.27        28.14        22.49        21.63        16.37        11.31 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA 
       15.62        20.05         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 
      103.76        62.37        72.59        70.55        22.92        70.65 
TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ 
       10.88         9.30         9.04         7.59         6.15         3.39 
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        18.21 
TCGA-S9-A7QZ TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 
       13.02        10.39        87.09        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        35.93        25.32        22.59        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 
       26.79        10.95 

  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 
            12.200             15.025 
[1] "0.2 - 41.1 (12.2)"  "0.0 - 211.2 (15.0)"
[1] "hr=" "2.8"
D32V2, continuous
D32V3, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     3   6
  18Q GAIN WILD-TYPE 173 218
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      3    6
  18Q GAIN WILD-TYPE  173  218
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE                3                173
  MALE                  6                218
[1] 2 2
[1] FALSE
D32V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  18Q GAIN MUTATED             5                2                 2
  18Q GAIN WILD-TYPE         138              102               151
D32V5, multiclass
                   clus
vv                  18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  ASTROCYTOMA                      5                138
  OLIGOASTROCYTOMA                 2                102
  OLIGODENDROGLIOMA                2                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"
D32V6, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     1   8
  18Q GAIN WILD-TYPE  88 303
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      1    8
  18Q GAIN WILD-TYPE   88  303
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  NO                 1                 88
  YES                8                303
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18Q GAIN MUTATED                                  0     0
  18Q GAIN WILD-TYPE                                1     2
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18Q GAIN MUTATED                           1     8
  18Q GAIN WILD-TYPE                        13   368
D32V7, multiclass
                                  clus
vv                                 18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  2
  BLACK OR AFRICAN AMERICAN                       1                 13
  WHITE                                           8                368
[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  15 350
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      0    9
  18Q GAIN WILD-TYPE   15  350
                        clus
vv                       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 15
  NOT HISPANIC OR LATINO                9                350
[1] 2 2
[1] FALSE

Clustering(33) Variable = 19P GAIN MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                  0   1
  19P GAIN MUTATED    63  15
  19P GAIN WILD-TYPE 261  56
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                78                317 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                15                 56 
$`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-DH-A669 TCGA-DH-A66F TCGA-DU-5854 TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 
       30.21         7.79         8.45        15.16        52.11        22.42 
TCGA-DU-6397 TCGA-DU-6400 TCGA-DU-6406 TCGA-DU-7009 TCGA-DU-7015 TCGA-DU-7019 
       46.06         1.22        16.83       138.28        90.77        26.30 
TCGA-DU-7298 TCGA-DU-7306 TCGA-DU-8164 TCGA-DU-A5TT TCGA-DU-A6S2 TCGA-DU-A76K 
       18.94        41.98        21.40         4.96         8.65        11.41 
TCGA-E1-5304 TCGA-FG-5962 TCGA-FG-6692 TCGA-FG-7643 TCGA-FG-8186 TCGA-FG-8188 
       41.13        47.77        13.58        20.09        16.01        14.96 
TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A60K TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7480 
        0.59         5.26         6.64         6.67         7.82        75.19 
TCGA-HT-7687 TCGA-HT-7695 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7875 TCGA-HT-7882 
        0.10        14.53         0.49        23.61         0.33         1.71 
TCGA-HT-8012 TCGA-HT-8104 TCGA-HT-A5RA TCGA-HT-A5RC TCGA-HT-A615 TCGA-HW-7495 
        9.40        12.23        14.70         5.33        13.02         4.31 
TCGA-KT-A7W1 TCGA-P5-A5F0 TCGA-QH-A65X TCGA-QH-A6CV TCGA-QH-A6CZ TCGA-QH-A6XC 
        4.73         4.11         7.79         2.96         3.16         5.03 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A73M TCGA-S9-A6TV TCGA-S9-A6TX TCGA-S9-A6TY 
       88.83        94.03        59.38        18.77        28.14        22.49 
TCGA-S9-A6U2 TCGA-S9-A6WE TCGA-S9-A6WM TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7QZ 
       15.62        72.59         9.30         8.19         2.04        13.02 
TCGA-TM-A7C3 TCGA-TM-A84B TCGA-TM-A84G TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CE 
       49.45        12.00        34.36        13.51         0.10        26.79 

$`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-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 
       10.92        19.96        31.82        30.31        14.40         8.02 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66G TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       29.62        15.75         3.85        18.02        14.56        17.46 
TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 
        6.74        13.38         6.81       182.33        18.94        17.49 
TCGA-DU-6392 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6399 TCGA-DU-6401 TCGA-DU-6402 
      211.17        49.02        75.16        65.75        87.45         7.04 
TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 
       11.64       133.74        19.89        94.52       114.08         7.96 
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-7014 TCGA-DU-7018 TCGA-DU-7290 TCGA-DU-7292 
        6.54         8.84       117.40        30.67        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-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8165 
        2.76         5.10        23.74         3.98        20.68        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-A5TY TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 
        3.65         5.65        12.20         2.70        77.98         7.23 
TCGA-DU-A6S8 TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 TCGA-E1-5302 
        5.98        26.76         7.13        21.30       124.50        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-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 
      130.78        14.33        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        11.87 
TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60L 
       15.52        24.46         3.72         9.67         7.04         7.04 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A713 
        4.21         4.08        10.59        10.78        22.95         5.23 
TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 
        0.13         0.10         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-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-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-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7874 
       39.48        19.23        39.09         0.23        50.63        37.15 
TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7884 TCGA-HT-7902 
        0.13         3.68         5.33         2.93        11.28        31.43 
TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8013 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8105 
        1.64        16.24        63.55        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-A5R9 TCGA-HT-A5RB TCGA-HT-A614 TCGA-HT-A616 TCGA-HT-A617 
        0.13         0.07         0.10         2.70         1.81        16.14 
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-8322 TCGA-HW-A5KJ 
       35.90         8.61         8.94        19.59        17.82        10.55 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X 
        7.89         9.67         6.61        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-A5F6 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65Z TCGA-QH-A6CS 
        1.28         5.75         2.53         4.83         4.11         4.18 
TCGA-QH-A6CY TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 
        2.20         0.59         6.31         3.91         4.73         1.91 
TCGA-QH-A6XA TCGA-R8-A6MO TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TW TCGA-S9-A6TZ 
        0.23        32.65        62.17        69.07        28.27        21.63 
TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
       16.37        11.31        20.05         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       103.76        62.37        70.55        22.92        70.65 
TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ 
       10.88         9.04         7.59         6.15         3.39        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        18.21        10.39        87.09        17.42 
TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89Z TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA 
       83.80        31.59         5.00        35.93        25.32        22.59 
TCGA-TM-A7CF TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84J 
       48.39        15.09        50.76        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-A8CD TCGA-VM-A8CH 
       12.00        33.07        30.08         7.89        10.95 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              0.10               0.03 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            138.28             211.17 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             14.83              14.99 
[1] "0.1 - 138.3 (14.8)" "0.0 - 211.2 (15.0)"
[1] "hr=" "1.2"
D33V2, continuous
D33V3, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    31  48
  19P GAIN WILD-TYPE 145 176
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     31   48
  19P GAIN WILD-TYPE  145  176
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE               31                145
  MALE                 48                176
[1] 2 2
[1] FALSE
D33V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  19P GAIN MUTATED            14               16                49
  19P GAIN WILD-TYPE         129               88               104
D33V5, multiclass
                   clus
vv                  19P GAIN MUTATED 19P GAIN WILD-TYPE
  ASTROCYTOMA                     14                129
  OLIGOASTROCYTOMA                16                 88
  OLIGODENDROGLIOMA               49                104
[1] 3 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  63
  19P GAIN WILD-TYPE  73 248
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     16   63
  19P GAIN WILD-TYPE   73  248
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  NO                16                 73
  YES               63                248
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19P GAIN MUTATED                                  0     1
  19P GAIN WILD-TYPE                                1     1
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19P GAIN MUTATED                           3    72
  19P GAIN WILD-TYPE                        11   304
D33V7, multiclass
                                  clus
vv                                 19P GAIN MUTATED 19P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  1
  BLACK OR AFRICAN AMERICAN                       3                 11
  WHITE                                          72                304
[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  70
  19P GAIN WILD-TYPE  11 289
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      4   70
  19P GAIN WILD-TYPE   11  289
                        clus
vv                       19P GAIN MUTATED 19P GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                 11
  NOT HISPANIC OR LATINO               70                289
[1] 2 2
[1] FALSE

Clustering(34) Variable = 19Q GAIN MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                  0   1
  19Q GAIN MUTATED    13   7
  19Q GAIN WILD-TYPE 311  64
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                20                375 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 7                 64 
$`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         0.59         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         2.96         5.03 
TCGA-S9-A6WM TCGA-TM-A7C3 
        9.30        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-DH-5140 
       15.42        27.81        14.73        13.64        10.92        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        29.62 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       15.75         7.79         3.85        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-6403 
       75.16        46.06        65.75         1.22        87.45        11.64 
TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 
      133.74        19.89        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-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 TCGA-E1-5302 
        5.98        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-E1-5322 TCGA-EZ-7264 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 
       95.57       130.78        14.33        47.77        17.98        34.36 
TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-7634 
       32.19        18.77        14.93        24.99        23.97        15.35 
TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 
       17.88        22.55        20.61        12.95        13.68        14.24 
TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT 
       16.01        20.09        14.96        11.87        15.52        24.46 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ 
        3.72         9.67         7.04         6.64         7.04         4.21 
TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A713 TCGA-FN-7833 
        4.08        10.59        10.78        22.95         5.23         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-7874 TCGA-HT-7875 TCGA-HT-7877 
       39.09         0.23        50.63        37.15         0.33         0.13 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 
        3.68         5.33         2.93        11.28        31.43         1.64 
TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8105 
       16.24         9.40        63.55        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-A5R9 TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 
        0.13         0.07         0.10         5.33         2.70        13.02 
TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 
        1.81        16.14         5.33        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         8.61         8.94 
TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM 
       19.59        17.82        10.55         7.89         9.67         6.61 
TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX 
       19.00        42.77         5.23         0.23         6.71         1.64 
TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F6 TCGA-QH-A65R 
        2.37         2.30         4.11         5.88         1.28         5.75 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CY 
        2.53         4.83         7.79         4.11         4.18         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-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TS 
        0.23        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        28.27        28.14        22.49        21.63 
TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       16.37        11.31        15.62        20.05         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       103.76        62.37        72.59        70.55 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP 
       22.92        70.65        10.88         9.04         7.59         6.15 
TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ 
        3.39        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-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 
       18.21        13.02        10.39        87.09        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        35.93        25.32        22.59        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 
        7.89        26.79        10.95 

  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 
             11.82              15.12 
[1] "0.5 - 49.5 (11.8)"  "0.0 - 211.2 (15.1)"
[1] "hr=" "4.9"
D34V2, continuous
D34V3, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     8  12
  19Q GAIN WILD-TYPE 168 212
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      8   12
  19Q GAIN WILD-TYPE  168  212
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE                8                168
  MALE                 12                212
[1] 2 2
[1] FALSE
D34V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  19Q GAIN MUTATED             8                8                 4
  19Q GAIN WILD-TYPE         135               96               149
D34V5, multiclass
                   clus
vv                  19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  ASTROCYTOMA                      8                135
  OLIGOASTROCYTOMA                 8                 96
  OLIGODENDROGLIOMA                4                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"
D34V6, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     5  15
  19Q GAIN WILD-TYPE  84 296
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      5   15
  19Q GAIN WILD-TYPE   84  296
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  NO                 5                 84
  YES               15                296
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19Q GAIN MUTATED                                  0     1
  19Q GAIN WILD-TYPE                                1     1
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19Q GAIN MUTATED                           1    18
  19Q GAIN WILD-TYPE                        13   358
D34V7, multiclass
                                  clus
vv                                 19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  1
  BLACK OR AFRICAN AMERICAN                       1                 13
  WHITE                                          18                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"
D34V8, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     1  18
  19Q GAIN WILD-TYPE  14 341
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      1   18
  19Q GAIN WILD-TYPE   14  341
                        clus
vv                       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 14
  NOT HISPANIC OR LATINO               18                341
[1] 2 2
[1] FALSE

Clustering(35) Variable = 20P GAIN MUTATION ANALYSIS
D35V1, survival
                    sevent
clus2                  0   1
  20P GAIN MUTATED    23  13
  20P GAIN WILD-TYPE 301  58
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                36                359 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                13                 58 
$`20P GAIN MUTATED`
TCGA-CS-5395 TCGA-CS-5397 TCGA-CS-6188 TCGA-CS-6665 TCGA-DH-A669 TCGA-DH-A66B 
       21.01         6.38        23.84        12.43        30.21        29.62 
TCGA-DU-5852 TCGA-DU-5854 TCGA-DU-5871 TCGA-DU-6400 TCGA-DU-6406 TCGA-DU-7298 
        6.74         8.45        18.94         1.22        16.83        18.94 
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-7474 
       26.76        41.13        47.77        15.35         0.59         3.75 
TCGA-HT-7477 TCGA-HT-7860 TCGA-HT-7882 TCGA-HT-8104 TCGA-HT-A5RC TCGA-HW-A5KK 
       24.26         0.49         1.71        12.23         5.33         7.89 
TCGA-QH-A6CV TCGA-QH-A6XC TCGA-S9-A6WH TCGA-S9-A6WM TCGA-TM-A7C3 TCGA-VM-A8CA 
        2.96         5.03        22.92         9.30        49.45        13.51 

$`20P GAIN WILD-TYPE`
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
        4.70         7.69        43.89        18.15        10.62        64.64 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5396 TCGA-CS-6186 TCGA-CS-6290 TCGA-CS-6666 
       40.18         0.10         9.96        17.69        17.95         8.48 
TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 
        7.56         8.02         7.40         6.61       122.73        81.96 
TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 
       75.25        47.93        72.92        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-DH-5140 TCGA-DH-5141 TCGA-DH-5142 
       14.73        13.64        10.92        19.96        31.82        30.31 
TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DU-5847 
       14.40         8.02        15.75         7.79         3.85        18.02 
TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5853 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5872 
       14.56        17.46        13.38         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-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-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 
       19.89        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-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 
        7.96        94.32        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-8163 
       23.31        41.98         2.76         5.10        23.74        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-A5TU TCGA-DU-A5TW TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
       15.12         3.65         5.65         8.65         2.70        77.98 
TCGA-DU-A6S8 TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 TCGA-E1-5302 TCGA-E1-5303 
        5.98         7.13        21.30       124.50        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-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 
       14.33        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        11.87        15.52        24.46         5.26         3.72 
TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 
        9.67         7.04         6.64         7.04         4.21         4.08 
TCGA-FG-A6J3 TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A713 TCGA-FN-7833 TCGA-HT-7467 
       10.59        10.78        22.95         5.23         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-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-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-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 
        2.93        11.28        31.43         1.64        16.24         9.40 
TCGA-HT-8013 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 
       63.55        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-A5R9 
       16.04        15.72         0.23        10.49         0.13         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-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-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 
       35.90         4.31         8.61         8.94        19.59        17.82 
TCGA-HW-A5KJ TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X 
       10.55         9.67         6.61        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-A5F6 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V 
        4.11         5.88         1.28         5.75         2.53         4.83 
TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
        7.79         4.11         4.18         2.20         3.16         0.59 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-R8-A6MK 
        6.31         3.91         4.73         1.91         0.23        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 
       28.27        28.14        22.49        21.63        16.37        11.31 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA 
       15.62        20.05         9.86        94.62        83.70         5.85 
TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WI TCGA-S9-A6WL 
      103.76        62.37        72.59        70.55        70.65        10.88 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
        9.04         7.59         6.15         3.39        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-A7R2 
        8.12         3.58         4.04        18.21        13.02        10.39 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89Z TCGA-TM-A7C4 
       87.09        17.42        83.80        31.59         5.00        35.93 
TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F 
       25.32        22.59        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-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH 
       30.08         0.10         7.89        26.79        10.95 

  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 
            12.215             15.120 
[1] "0.5 - 49.5 (12.2)"  "0.0 - 211.2 (15.1)"
[1] "hr=" "4.9"
D35V2, continuous
D35V3, binary
                    cls
clus                   0   1
  20P GAIN MUTATED    18  18
  20P GAIN WILD-TYPE 158 206
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     18   18
  20P GAIN WILD-TYPE  158  206
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE               18                158
  MALE                 18                206
[1] 2 2
[1] FALSE
D35V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  20P GAIN MUTATED            17                8                11
  20P GAIN WILD-TYPE         126               96               142
D35V5, multiclass
                   clus
vv                  20P GAIN MUTATED 20P GAIN WILD-TYPE
  ASTROCYTOMA                     17                126
  OLIGOASTROCYTOMA                 8                 96
  OLIGODENDROGLIOMA               11                142
[1] 3 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  29
  20P GAIN WILD-TYPE  82 282
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      7   29
  20P GAIN WILD-TYPE   82  282
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  NO                 7                 82
  YES               29                282
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20P GAIN MUTATED                                  0     1
  20P GAIN WILD-TYPE                                1     1
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20P GAIN MUTATED                           2    32
  20P GAIN WILD-TYPE                        12   344
D35V7, multiclass
                                  clus
vv                                 20P GAIN MUTATED 20P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  1
  BLACK OR AFRICAN AMERICAN                       2                 12
  WHITE                                          32                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"
D35V8, binary
                    cls
clus                   0   1
  20P GAIN MUTATED     1  32
  20P GAIN WILD-TYPE  14 327
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      1   32
  20P GAIN WILD-TYPE   14  327
                        clus
vv                       20P GAIN MUTATED 20P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 14
  NOT HISPANIC OR LATINO               32                327
[1] 2 2
[1] FALSE

Clustering(36) Variable = 20Q GAIN MUTATION ANALYSIS
D36V1, survival
                    sevent
clus2                  0   1
  20Q GAIN MUTATED    24  13
  20Q GAIN WILD-TYPE 300  58
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                37                358 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                13                 58 
$`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         0.59        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         2.96         5.03        22.92         9.30        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-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 
       10.92        19.96        31.82        30.31        14.40         8.02 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DU-5847 TCGA-DU-5849 
       29.62        15.75         7.79         3.85        18.02        14.56 
TCGA-DU-5851 TCGA-DU-5853 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5872 TCGA-DU-5874 
       17.46        13.38         6.81       182.33        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-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-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-8163 
       23.31        41.98         2.76         5.10        23.74        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-A5TU TCGA-DU-A5TW TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
       15.12         3.65         5.65         8.65         2.70        77.98 
TCGA-DU-A6S8 TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 TCGA-E1-5302 TCGA-E1-5303 
        5.98         7.13        21.30       124.50        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-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 
       14.33        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        11.87        15.52        24.46         5.26         3.72 
TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 
        9.67         7.04         6.64         7.04         4.21         4.08 
TCGA-FG-A6J3 TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A713 TCGA-FN-7833 TCGA-HT-7467 
       10.59        10.78        22.95         5.23         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-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-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-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-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-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 
        2.93        11.28        31.43         1.64        16.24         9.40 
TCGA-HT-8013 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 
       63.55        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-A5R9 TCGA-HT-A5RA 
       15.72         0.23        10.49         0.13         0.07        14.70 
TCGA-HT-A5RB TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 
        0.10         2.70        13.02         1.81        16.14         5.33 
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         8.61         8.94        19.59        17.82        10.55 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 
        9.67         6.61        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-A5F6 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X 
        5.88         1.28         5.75         2.53         4.83         7.79 
TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
        4.11         4.18         2.20         3.16         0.59         6.31 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-R8-A6MK TCGA-R8-A6ML 
        3.91         4.73         1.91         0.23        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        28.27 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 
       28.14        22.49        21.63        16.37        11.31        15.62 
TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB 
       20.05         9.86        94.62        83.70         5.85       103.76 
TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN 
       62.37        72.59        70.55        70.65        10.88         9.04 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX 
        7.59         6.15         3.39        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-A7R2 TCGA-S9-A7R3 
        3.58         4.04        18.21        13.02        10.39        87.09 
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        35.93        25.32 
TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G 
       22.59        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 
        0.10         7.89        26.79        10.95 

  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 
            12.230             15.105 
[1] "0.5 - 49.5 (12.2)"  "0.0 - 211.2 (15.1)"
[1] "hr=" "4.9"
D36V2, continuous
D36V3, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED    20  17
  20Q GAIN WILD-TYPE 156 207
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     20   17
  20Q GAIN WILD-TYPE  156  207
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE               20                156
  MALE                 17                207
[1] 2 2
[1] FALSE
D36V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  20Q GAIN MUTATED            17                8                12
  20Q GAIN WILD-TYPE         126               96               141
D36V5, multiclass
                   clus
vv                  20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  ASTROCYTOMA                     17                126
  OLIGOASTROCYTOMA                 8                 96
  OLIGODENDROGLIOMA               12                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"
D36V6, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED     7  30
  20Q GAIN WILD-TYPE  82 281
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      7   30
  20Q GAIN WILD-TYPE   82  281
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  NO                 7                 82
  YES               30                281
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20Q GAIN MUTATED                                  0     1
  20Q GAIN WILD-TYPE                                1     1
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20Q GAIN MUTATED                           1    34
  20Q GAIN WILD-TYPE                        13   342
D36V7, multiclass
                                  clus
vv                                 20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  1
  BLACK OR AFRICAN AMERICAN                       1                 13
  WHITE                                          34                342
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V8, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED     1  33
  20Q GAIN WILD-TYPE  14 326
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      1   33
  20Q GAIN WILD-TYPE   14  326
                        clus
vv                       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 14
  NOT HISPANIC OR LATINO               33                326
[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 310  64
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                21                374 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 7                 64 
$`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         2.96         1.91 
TCGA-S9-A6WH TCGA-S9-A6WL TCGA-TM-A84H 
       22.92        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-DH-5140 
       16.08        15.42        27.81        14.73        10.92        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        29.62 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       15.75         7.79         3.85        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-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 
       17.49        15.16        22.42        49.02        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-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-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-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-8168 TCGA-DU-A5TP 
       21.40        19.13        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-A6S8 TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 
       77.98         5.98        26.76         7.13        21.30       124.50 
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-FG-5963 TCGA-FG-5964 TCGA-FG-5965 
       95.57       130.78        14.33        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        11.87        15.52        24.46 
TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K 
        0.59         5.26         3.72         9.67         7.04         6.64 
TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Z TCGA-FG-A710 
        7.04         4.21         4.08        10.59        10.78        22.95 
TCGA-FG-A713 TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 
        5.23         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-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-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 
       63.55        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-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 
        0.07         0.10         5.33         2.70        13.02         1.81 
TCGA-HT-A617 TCGA-HT-A618 TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 
       16.14         5.33        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         8.61         8.94        19.59 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 
       17.82        10.55         7.89         9.67         6.61        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-A5F6 TCGA-QH-A65R 
        2.37         2.30         4.11         5.88         1.28         5.75 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CY 
        2.53         4.83         7.79         4.11         4.18         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-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TS 
        5.03        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        28.27        28.14        22.49        21.63 
TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       16.37        11.31        15.62        20.05         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       103.76        62.37        72.59        70.55 
TCGA-S9-A6WI TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ 
       70.65         9.30         9.04         7.59         6.15         3.39 
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        18.21 
TCGA-S9-A7QZ TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 
       13.02        10.39        87.09        17.42        83.80        31.59 
TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF 
        5.00        49.45        35.93        25.32        22.59        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-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 
       26.79        10.95 

  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 
             13.64              15.04 
[1] "1.2 - 211.2 (13.6)" "0.0 - 182.3 (15.0)"
[1] "hr=" "1.7"
D37V2, continuous
D37V3, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    11  10
  21Q GAIN WILD-TYPE 165 214
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     11   10
  21Q GAIN WILD-TYPE  165  214
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE               11                165
  MALE                 10                214
[1] 2 2
[1] FALSE
D37V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  21Q GAIN MUTATED             8                4                 9
  21Q GAIN WILD-TYPE         135              100               144
D37V5, multiclass
                   clus
vv                  21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  ASTROCYTOMA                      8                135
  OLIGOASTROCYTOMA                 4                100
  OLIGODENDROGLIOMA                9                144
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V6, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     5  16
  21Q GAIN WILD-TYPE  84 295
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      5   16
  21Q GAIN WILD-TYPE   84  295
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  NO                 5                 84
  YES               16                295
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  21Q GAIN MUTATED                                  0     1
  21Q GAIN WILD-TYPE                                1     1
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  21Q GAIN MUTATED                           0    20
  21Q GAIN WILD-TYPE                        14   356
D37V7, multiclass
                                  clus
vv                                 21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  1
  BLACK OR AFRICAN AMERICAN                       0                 14
  WHITE                                          20                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"
D37V8, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     0  21
  21Q GAIN WILD-TYPE  15 338
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      0   21
  21Q GAIN WILD-TYPE   15  338
                        clus
vv                       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 15
  NOT HISPANIC OR LATINO               21                338
[1] 2 2
[1] FALSE

Clustering(38) Variable = 22Q GAIN MUTATION ANALYSIS
D38V1, survival
                    sevent
clus2                  0   1
  22Q GAIN MUTATED    12   2
  22Q GAIN WILD-TYPE 312  69
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                14                381 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 2                 69 
$`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         9.30        17.49 
TCGA-VM-A8CA TCGA-VM-A8CB 
       13.51         0.10 

$`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-DH-5140 
       15.42        27.81        14.73        13.64        10.92        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        29.62 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 
       15.75         7.79         3.85        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-6394 TCGA-DU-6395 TCGA-DU-6396 
       17.49        15.16       211.17        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-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-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-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 
      124.50        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-FG-5963 
      134.27        78.21        95.57       130.78        14.33        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 
       11.87        15.52        24.46         0.59         5.26         3.72 
TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 
        9.67         7.04         6.64         7.04         4.21         4.08 
TCGA-FG-A6J3 TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A713 TCGA-FN-7833 TCGA-HT-7467 
       10.59        10.78        22.95         5.23         0.13         0.10 
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-8013 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 
        1.64        16.24        63.55        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-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-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 
        8.61         8.94        19.59        17.82        10.55         7.89 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 
        9.67         6.61        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-A5F6 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X 
        5.88         1.28         5.75         2.53         4.83         7.79 
TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CV TCGA-QH-A6CY TCGA-QH-A6X3 TCGA-QH-A6X4 
        4.11         4.18         2.96         2.20         0.59         6.31 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-R8-A6MK 
        3.91         4.73         1.91         0.23         5.03        88.83 
TCGA-R8-A6MO TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX 
       32.65        62.17        69.07        18.77        28.27        28.14 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       22.49        21.63        16.37        11.31        15.62        20.05 
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       103.76        62.37 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN 
       72.59        70.55        22.92        70.65        10.88         9.04 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX 
        7.59         6.15         3.39        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-A7R2 TCGA-S9-A7R3 
        3.58         4.04        18.21        13.02        10.39        87.09 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 
       17.42        83.80        31.59         5.00        49.45        35.93 
TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F 
       25.32        22.59        48.39        12.00        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-A8C8 TCGA-VM-A8C9 
       18.90         9.44         4.57        12.00        33.07        30.08 
TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH 
        7.89        26.79        10.95 

  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 
            10.915             15.090 
[1] "0.1 - 94.0 (10.9)"  "0.0 - 211.2 (15.1)"
[1] "hr=" "1.1"
D38V2, continuous
D38V3, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED     6   8
  22Q GAIN WILD-TYPE 170 216
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      6    8
  22Q GAIN WILD-TYPE  170  216
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE                6                170
  MALE                  8                216
[1] 2 2
[1] FALSE
D38V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  22Q GAIN MUTATED             2                1                11
  22Q GAIN WILD-TYPE         141              103               142
D38V5, multiclass
                   clus
vv                  22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  ASTROCYTOMA                      2                141
  OLIGOASTROCYTOMA                 1                103
  OLIGODENDROGLIOMA               11                142
[1] 3 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  11
  22Q GAIN WILD-TYPE  86 300
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      3   11
  22Q GAIN WILD-TYPE   86  300
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  NO                 3                 86
  YES               11                300
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  22Q GAIN MUTATED                                  0     0
  22Q GAIN WILD-TYPE                                1     2
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  22Q GAIN MUTATED                           0    12
  22Q GAIN WILD-TYPE                        14   364
D38V7, multiclass
                                  clus
vv                                 22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  2
  BLACK OR AFRICAN AMERICAN                       0                 14
  WHITE                                          12                364
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V8, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED     1  10
  22Q GAIN WILD-TYPE  14 349
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      1   10
  22Q GAIN WILD-TYPE   14  349
                        clus
vv                       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 14
  NOT HISPANIC OR LATINO               10                349
[1] 2 2
[1] FALSE

Clustering(39) Variable = XQ GAIN MUTATION ANALYSIS
D39V1, survival
                   sevent
clus2                 0   1
  XQ GAIN MUTATED    22   6
  XQ GAIN WILD-TYPE 302  65
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               28               367 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                6                65 
$`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         9.67 
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-HW-7493 TCGA-QH-A65S TCGA-QH-A6CV 
       31.43        63.55        16.04        35.90         2.53         2.96 
TCGA-S9-A6TS TCGA-S9-A7IZ TCGA-S9-A7QX TCGA-TM-A84H 
       62.17         4.21         4.04        24.26 

$`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-DH-5140 TCGA-DH-5141 
       27.81        14.73        13.64        10.92        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        29.62        15.75 
TCGA-DH-A66F TCGA-DH-A66G TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
        7.79         3.85        18.02        14.56        17.46         6.74 
TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5872 TCGA-DU-5874 
       13.38         8.45         6.81       182.33        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-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 
       65.75         1.22         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-7008 
       16.83       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-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-A5TU TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
       12.59         3.65        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-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 
      124.50        50.14        67.46        41.13        79.99        57.93 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-EZ-7264 TCGA-FG-5962 TCGA-FG-5963 
      134.27        78.21        95.57        14.33        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 
       11.87        15.52        24.46         0.59         5.26         3.72 
TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 
        7.04         6.64         7.04         4.21         4.08        10.59 
TCGA-FG-A70Z TCGA-FG-A710 TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 
       10.78        22.95         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-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-7610 TCGA-HT-7611 
        4.57        17.29         3.16        22.06        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-7692 
        6.05        42.74         0.10         0.10         0.10         2.96 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 
       17.52         6.90        14.53        39.48        19.23        39.09 
TCGA-HT-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-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 
       16.24         9.40        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-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-HW-7486 TCGA-HW-7487 TCGA-HW-7489 
        1.81        16.14         5.33        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         8.61         8.94        19.59 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 
       17.82        10.55         7.89         9.67         6.61        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-A5F6 TCGA-QH-A65R 
        2.37         2.30         4.11         5.88         1.28         5.75 
TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CY TCGA-QH-A6CZ 
        4.83         7.79         4.11         4.18         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-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TU 
        5.03        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        28.27        28.14        22.49        21.63        16.37 
TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
       11.31        15.62        20.05         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       103.76        62.37        72.59        70.55        22.92 
TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP 
       70.65        10.88         9.30         9.04         7.59         6.15 
TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7J0 
        3.39        14.27         7.92        19.63        12.59         9.37 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QY TCGA-S9-A7QZ 
        8.19         2.04         8.12         3.58        18.21        13.02 
TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89Z 
       10.39        87.09        17.42        83.80        31.59         5.00 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B 
       49.45        35.93        25.32        22.59        48.39        12.00 
TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84I TCGA-TM-A84J TCGA-TM-A84L 
       15.09        50.76        34.36        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 
       10.95 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             0.23              0.03 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
           130.78            211.17 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            15.58             14.93 
[1] "0.2 - 130.8 (15.6)" "0.0 - 211.2 (14.9)"
[1] "hr=" "1"  
D39V2, continuous
D39V3, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    20   8
  XQ GAIN WILD-TYPE 156 216
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     20    8
  XQ GAIN WILD-TYPE  156  216
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE              20               156
  MALE                 8               216
[1] 2 2
[1] FALSE
D39V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  XQ GAIN MUTATED            11               11                 6
  XQ GAIN WILD-TYPE         132               93               147
D39V5, multiclass
                   clus
vv                  XQ GAIN MUTATED XQ GAIN WILD-TYPE
  ASTROCYTOMA                    11               132
  OLIGOASTROCYTOMA               11                93
  OLIGODENDROGLIOMA               6               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"
D39V6, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     8  20
  XQ GAIN WILD-TYPE  81 291
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      8   20
  XQ GAIN WILD-TYPE   81  291
     clus
vv    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  NO                8                81
  YES              20               291
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XQ GAIN MUTATED                                  0     1
  XQ GAIN WILD-TYPE                                1     1
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XQ GAIN MUTATED                           2    25
  XQ GAIN WILD-TYPE                        12   351
D39V7, multiclass
                                  clus
vv                                 XQ GAIN MUTATED XQ GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 1
  BLACK OR AFRICAN AMERICAN                      2                12
  WHITE                                         25               351
[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     2  26
  XQ GAIN WILD-TYPE  13 333
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      2   26
  XQ GAIN WILD-TYPE   13  333
                        clus
vv                       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                13
  NOT HISPANIC OR LATINO              26               333
[1] 2 2
[1] FALSE

Clustering(40) Variable = 1P LOSS MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                 0   1
  1P LOSS MUTATED   129  16
  1P LOSS WILD-TYPE 195  55
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
              145               250 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               16                55 
$`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-DH-5141 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66F TCGA-DU-5849 TCGA-DU-5870 
       31.82         8.02        30.21         7.79        14.56       182.33 
TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6397 TCGA-DU-6400 TCGA-DU-6410 
       15.16        52.11        22.42        46.06         1.22         7.96 
TCGA-DU-7009 TCGA-DU-7014 TCGA-DU-7018 TCGA-DU-7294 TCGA-DU-7300 TCGA-DU-7302 
      138.28       117.40        30.67        94.32        62.01        60.30 
TCGA-DU-8158 TCGA-DU-8164 TCGA-DU-8168 TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
        5.10        21.40        14.17         8.65         2.70        77.98 
TCGA-DU-A6S8 TCGA-DU-A76R TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 
        5.98        21.30       134.27        78.21        95.57       130.78 
TCGA-EZ-7264 TCGA-FG-5962 TCGA-FG-5964 TCGA-FG-7634 TCGA-FG-7638 TCGA-FG-7641 
       14.33        47.77        34.36        15.35        22.55        20.61 
TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8189 TCGA-FG-A60K TCGA-FG-A6IZ 
       14.24        16.01        20.09        11.87         6.64         4.21 
TCGA-FG-A6J1 TCGA-FG-A710 TCGA-FG-A713 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7471 
        4.08        22.95         5.23         0.10         6.67         0.13 
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        10.55        42.77         5.23         1.64 
TCGA-P5-A5F0 TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CV TCGA-QH-A6CY 
        4.11         4.83         7.79         4.11         2.96         2.20 
TCGA-QH-A6CZ TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-R8-A6MK TCGA-R8-A6ML 
        3.16         6.31         3.91         4.73        88.83        94.03 
TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6U2 
       32.65        59.38        28.27        28.14        22.49        15.62 
TCGA-S9-A6U5 TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WH TCGA-S9-A6WI 
       20.05       103.76        62.37        72.59        22.92        70.65 
TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WP TCGA-S9-A7IQ TCGA-S9-A7IY TCGA-S9-A7J1 
       10.88         9.04         6.15        14.27        12.59         8.19 
TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-TM-A7C5 TCGA-TM-A84G 
        2.04         8.12        18.21        13.02        25.32        34.36 
TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84R TCGA-TM-A84S TCGA-VM-A8CA TCGA-VM-A8CB 
       16.50        29.92         9.44         4.57        13.51         0.10 
TCGA-VM-A8CE 
       26.79 

$`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-DH-5140 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-A66B TCGA-DH-A66D 
       10.92        19.96        30.31        14.40        29.62        15.75 
TCGA-DH-A66G TCGA-DU-5847 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 
        3.85        18.02        17.46         6.74        13.38         8.45 
TCGA-DU-5855 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-6392 TCGA-DU-6395 TCGA-DU-6396 
        6.81        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-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 
       16.83        94.52       114.08         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-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7301 
       26.30        10.36         7.96        18.94        44.02        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-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS 
       19.13        16.96        15.48        14.24        12.59        15.12 
TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S7 TCGA-DU-A76K 
        4.96         3.65         5.65        12.20         7.23        11.41 
TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A7T8 TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 
       26.76         7.13       124.50        50.14        67.46        41.13 
TCGA-E1-5305 TCGA-E1-5307 TCGA-FG-5963 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 
       79.99        57.93        17.98        32.19        18.77        14.93 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7636 TCGA-FG-7643 TCGA-FG-8181 
       24.99        23.97        13.58        17.88        20.09        12.95 
TCGA-FG-8182 TCGA-FG-8188 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW 
       13.68        14.96        15.52        24.46         0.59         5.26 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60L TCGA-FG-A6J3 TCGA-FG-A70Z 
        3.72         9.67         7.04         7.04        10.59        10.78 
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-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7482 
       17.42         6.54        24.26         6.38         7.10        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-7606 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7676 TCGA-HT-7680 
       17.29        45.99        56.09        57.60         0.16         0.76 
TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 
        6.05        42.74        31.69        14.96         0.10         0.10 
TCGA-HT-7693 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 
       17.52        39.48        19.23        50.63         0.49        23.61 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8011 
        3.68         5.33         1.71        11.28        31.43        16.24 
TCGA-HT-8013 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8106 TCGA-HT-8107 
       63.55        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-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 
        0.23         0.13        14.70         0.10         5.33         2.70 
TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7493 
        1.81        16.14         5.33         8.32        19.23        35.90 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM 
        8.61         8.94        19.59         7.89         9.67         6.61 
TCGA-IK-7675 TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EY TCGA-P5-A5EZ 
       19.00         4.73         0.23         6.71         2.37         2.30 
TCGA-P5-A5F1 TCGA-P5-A5F6 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A6CS TCGA-QH-A6X3 
        5.88         1.28         5.75         2.53         4.18         0.59 
TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV 
        1.91         0.23         5.03        62.17        69.07        18.77 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
       21.63        16.37        11.31         9.86        94.62        83.70 
TCGA-S9-A6UA TCGA-S9-A6WG TCGA-S9-A6WM TCGA-S9-A6WO TCGA-S9-A6WQ TCGA-S9-A7IS 
        5.85        70.55         9.30         7.59         3.39         7.92 
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-A89Z TCGA-TM-A7C3 
       87.09        17.42        83.80        31.59         5.00        49.45 
TCGA-TM-A7C4 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F 
       35.93        22.59        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 
       33.07        30.08         7.89        10.95 

  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 
            14.27             15.45 
[1] "0.1 - 182.3 (14.3)" "0.0 - 211.2 (15.4)"
[1] "hr=" "2.2"
D40V2, continuous
D40V3, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    66  81
  1P LOSS WILD-TYPE 110 143
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     66   81
  1P LOSS WILD-TYPE  110  143
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE              66               110
  MALE                81               143
[1] 2 2
[1] FALSE
D40V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  1P LOSS MUTATED             8               30               109
  1P LOSS WILD-TYPE         135               74                44
D40V5, multiclass
                   clus
vv                  1P LOSS MUTATED 1P LOSS WILD-TYPE
  ASTROCYTOMA                     8               135
  OLIGOASTROCYTOMA               30                74
  OLIGODENDROGLIOMA             109                44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V6, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    23 124
  1P LOSS WILD-TYPE  66 187
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     23  124
  1P LOSS WILD-TYPE   66  187
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  NO               23                66
  YES             124               187
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1P LOSS MUTATED                                  0     2
  1P LOSS WILD-TYPE                                1     0
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1P LOSS MUTATED                           4   136
  1P LOSS WILD-TYPE                        10   240
D40V7, multiclass
                                  clus
vv                                 1P LOSS MUTATED 1P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 0
  BLACK OR AFRICAN AMERICAN                      4                10
  WHITE                                        136               240
[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     6 130
  1P LOSS WILD-TYPE   9 229
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      6  130
  1P LOSS WILD-TYPE    9  229
                        clus
vv                       1P LOSS MUTATED 1P LOSS WILD-TYPE
  HISPANIC OR LATINO                   6                 9
  NOT HISPANIC OR LATINO             130               229
[1] 2 2
[1] FALSE

Clustering(41) Variable = 1Q LOSS MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                 0   1
  1Q LOSS MUTATED    14   4
  1Q LOSS WILD-TYPE 310  67
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               18               377 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                4                67 
$`1Q LOSS MUTATED`
TCGA-CS-5396 TCGA-DB-5279 TCGA-DH-5141 TCGA-DH-5144 TCGA-DH-A669 TCGA-DU-6400 
        9.96        44.52        31.82         8.02        30.21         1.22 
TCGA-DU-7294 TCGA-DU-8158 TCGA-DU-A5TS TCGA-E1-5322 TCGA-FG-5962 TCGA-FG-8185 
       94.32         5.10        15.12       130.78        47.77        14.24 
TCGA-HT-7857 TCGA-HT-8113 TCGA-QH-A65S TCGA-QH-A65Z TCGA-QH-A6CV TCGA-S9-A6WI 
        0.23        29.59         2.53         4.11         2.96        70.65 

$`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-DH-5140 
       15.42        27.81        14.73        13.64        10.92        19.96 
TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G 
       30.31        14.40        29.62        15.75         7.79         3.85 
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-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-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-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-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 
       21.30       124.50        50.14        67.46        41.13        79.99 
TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-EZ-7264 TCGA-FG-5963 
       57.93       134.27        78.21        95.57        14.33        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-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 
       12.95        13.68        16.01        20.09        14.96        11.87 
TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY 
       15.52        24.46         0.59         5.26         3.72         9.67 
TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 
        7.04         6.64         7.04         4.21         4.08        10.59 
TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A713 TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 
       10.78        22.95         5.23         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-7858 
        6.90        14.53        39.48        19.23        39.09        50.63 
TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 
        0.49        23.61        37.15         0.33         0.13         3.68 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 
        5.33         2.93         1.71        11.28        31.43         1.64 
TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 
       16.24         9.40        63.55        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-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A4DV 
        0.23         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-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-7493 TCGA-HW-7495 TCGA-HW-8319 
        8.32        19.23        40.18        35.90         4.31         8.61 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
        8.94        19.59        17.82        10.55         7.89         9.67 
TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV 
        6.61        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-A5F6 TCGA-QH-A65R TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A6CS TCGA-QH-A6CY 
        1.28         5.75         4.83         7.79         4.18         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-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
        0.23         5.03        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        28.27        28.14        22.49 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       21.63        16.37        11.31        15.62        20.05         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       103.76        62.37        72.59 
TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO 
       70.55        22.92        10.88         9.30         9.04         7.59 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY 
        6.15         3.39        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-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 
        4.04        18.21        13.02        10.39        87.09        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        35.93        25.32 
TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G 
       22.59        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 
       13.51         0.10         7.89        26.79        10.95 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
             0.23              0.03 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
           130.78            211.17 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            14.68             14.96 
[1] "0.2 - 130.8 (14.7)" "0.0 - 211.2 (15.0)"
[1] "hr=" "1"  
D41V2, continuous
D41V3, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED    10   8
  1Q LOSS WILD-TYPE 166 216
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     10    8
  1Q LOSS WILD-TYPE  166  216
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE              10               166
  MALE                 8               216
[1] 2 2
[1] FALSE
D41V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  1Q LOSS MUTATED             3                4                11
  1Q LOSS WILD-TYPE         140              100               142
D41V5, multiclass
                   clus
vv                  1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  ASTROCYTOMA                     3               140
  OLIGOASTROCYTOMA                4               100
  OLIGODENDROGLIOMA              11               142
[1] 3 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  12
  1Q LOSS WILD-TYPE  83 299
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      6   12
  1Q LOSS WILD-TYPE   83  299
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  NO                6                83
  YES              12               299
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1Q LOSS MUTATED                                  0     1
  1Q LOSS WILD-TYPE                                1     1
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1Q LOSS MUTATED                           2    14
  1Q LOSS WILD-TYPE                        12   362
D41V7, multiclass
                                  clus
vv                                 1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 1
  BLACK OR AFRICAN AMERICAN                      2                12
  WHITE                                         14               362
[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  16
  1Q LOSS WILD-TYPE  14 343
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      1   16
  1Q LOSS WILD-TYPE   14  343
                        clus
vv                       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                14
  NOT HISPANIC OR LATINO              16               343
[1] 2 2
[1] FALSE

Clustering(42) Variable = 2P LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                 0   1
  2P LOSS MUTATED     9   4
  2P LOSS WILD-TYPE 315  67
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               13               382 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                4                67 
$`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-HW-7493 TCGA-P5-A5F6 
        7.82        24.26         0.10         2.96        35.90         1.28 
TCGA-VM-A8C8 
       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-DH-5140 
       15.42        27.81        14.73        13.64        10.92        19.96 
TCGA-DH-5141 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D 
       31.82        14.40         8.02        30.21        29.62        15.75 
TCGA-DH-A66F TCGA-DH-A66G TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
        7.79         3.85        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-7011 
        7.73        11.47        62.96       156.23       138.28       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-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-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-FG-5962 TCGA-FG-5963 
       78.21        95.57       130.78        14.33        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 
       11.87        15.52        24.46         0.59         5.26         3.72 
TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 
        9.67         7.04         6.64         7.04         4.21         4.08 
TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A713 TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 
       10.78        22.95         5.23         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-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-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-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 
       16.14         5.33        29.92        13.45         8.32        19.23 
TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 
       40.18         4.31         8.61         8.94        19.59        17.82 
TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 
       10.55         7.89         9.67         6.61        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-QH-A65R TCGA-QH-A65S TCGA-QH-A65V 
        2.30         4.11         5.88         5.75         2.53         4.83 
TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CV TCGA-QH-A6CY TCGA-QH-A6CZ 
        7.79         4.11         4.18         2.96         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-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TS 
        5.03        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        28.27        28.14        22.49        21.63 
TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       16.37        11.31        15.62        20.05         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       103.76        62.37        72.59        70.55 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO 
       22.92        70.65        10.88         9.30         9.04         7.59 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY 
        6.15         3.39        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-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 
        4.04        18.21        13.02        10.39        87.09        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        35.93        25.32 
TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G 
       22.59        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-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 
        0.10         7.89        26.79        10.95 

  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             14.96 
[1] "0.1 - 117.4 (15.0)" "0.0 - 211.2 (15.0)"
[1] "hr=" "1.8"
D42V2, continuous
D42V3, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     4  10
  2P LOSS WILD-TYPE 172 214
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      4   10
  2P LOSS WILD-TYPE  172  214
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE               4               172
  MALE                10               214
[1] 2 2
[1] FALSE
D42V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  2P LOSS MUTATED             6                4                 4
  2P LOSS WILD-TYPE         137              100               149
D42V5, multiclass
                   clus
vv                  2P LOSS MUTATED 2P LOSS WILD-TYPE
  ASTROCYTOMA                     6               137
  OLIGOASTROCYTOMA                4               100
  OLIGODENDROGLIOMA               4               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"
D42V6, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     3  11
  2P LOSS WILD-TYPE  86 300
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      3   11
  2P LOSS WILD-TYPE   86  300
     clus
vv    2P LOSS MUTATED 2P LOSS WILD-TYPE
  NO                3                86
  YES              11               300
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2P LOSS MUTATED                                  0     0
  2P LOSS WILD-TYPE                                1     2
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2P LOSS MUTATED                           0    14
  2P LOSS WILD-TYPE                        14   362
D42V7, multiclass
                                  clus
vv                                 2P LOSS MUTATED 2P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 2
  BLACK OR AFRICAN AMERICAN                      0                14
  WHITE                                         14               362
[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  13
  2P LOSS WILD-TYPE  15 346
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      0   13
  2P LOSS WILD-TYPE   15  346
                        clus
vv                       2P LOSS MUTATED 2P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                15
  NOT HISPANIC OR LATINO              13               346
[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 314  69
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               12               383 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                2                69 
$`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        29.62       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-DH-5140 
       15.42        27.81        14.73        13.64        10.92        19.96 
TCGA-DH-5141 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66D TCGA-DH-A66F 
       31.82        14.40         8.02        30.21        15.75         7.79 
TCGA-DH-A66G TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 
        3.85        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-6410 TCGA-DU-6542 TCGA-DU-7006 
       19.89        16.83        94.52         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-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-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-FG-5962 TCGA-FG-5963 
       78.21        95.57       130.78        14.33        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 
       11.87        15.52        24.46         0.59         5.26         3.72 
TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 
        9.67         7.04         6.64         7.04         4.21         4.08 
TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A713 TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 
       10.78        22.95         5.23         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-7691 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 
       14.96         0.10        17.52         6.90        14.53        39.48 
TCGA-HT-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-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 
       63.55        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-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 
        1.81        16.14        29.92        13.45         8.32        19.23 
TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 
       40.18         4.31         8.61         8.94        19.59        17.82 
TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 
       10.55         7.89         9.67         6.61        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-QH-A65R TCGA-QH-A65S TCGA-QH-A65V 
        2.30         4.11         5.88         5.75         2.53         4.83 
TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CV TCGA-QH-A6CY TCGA-QH-A6CZ 
        7.79         4.11         4.18         2.96         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-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TS 
        5.03        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        28.27        28.14        22.49        21.63 
TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       16.37        11.31        15.62        20.05         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       103.76        62.37        72.59        70.55 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO 
       22.92        70.65        10.88         9.30         9.04         7.59 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY 
        6.15         3.39        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-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 
        4.04        18.21        13.02        10.39        87.09        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        35.93        25.32 
TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G 
       22.59        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 
       13.51         0.10         7.89        26.79        10.95 

  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            14.960 
[1] "0.1 - 114.1 (17.4)" "0.0 - 211.2 (15.0)"
[1] "hr=" "1.1"
D43V2, continuous
D43V3, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     4   9
  2Q LOSS WILD-TYPE 172 215
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      4    9
  2Q LOSS WILD-TYPE  172  215
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE               4               172
  MALE                 9               215
[1] 2 2
[1] FALSE
D43V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  2Q LOSS MUTATED             8                3                 2
  2Q LOSS WILD-TYPE         135              101               151
D43V5, multiclass
                   clus
vv                  2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  ASTROCYTOMA                     8               135
  OLIGOASTROCYTOMA                3               101
  OLIGODENDROGLIOMA               2               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"
D43V6, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     3  10
  2Q LOSS WILD-TYPE  86 301
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      3   10
  2Q LOSS WILD-TYPE   86  301
     clus
vv    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  NO                3                86
  YES              10               301
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2Q LOSS MUTATED                                  0     0
  2Q LOSS WILD-TYPE                                1     2
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2Q LOSS MUTATED                           0    13
  2Q LOSS WILD-TYPE                        14   363
D43V7, multiclass
                                  clus
vv                                 2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 2
  BLACK OR AFRICAN AMERICAN                      0                14
  WHITE                                         13               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"
D43V8, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     0  13
  2Q LOSS WILD-TYPE  15 346
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      0   13
  2Q LOSS WILD-TYPE   15  346
                        clus
vv                       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                15
  NOT HISPANIC OR LATINO              13               346
[1] 2 2
[1] FALSE

Clustering(44) Variable = 3P LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                 0   1
  3P LOSS MUTATED    12   6
  3P LOSS WILD-TYPE 312  65
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               18               377 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                6                65 
$`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        15.75        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-TM-A84B TCGA-TM-A84J TCGA-VM-A8C8 
       14.70        19.00         1.28        12.00        17.49        33.07 

$`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-DH-5140 
       15.42        27.81        14.73        13.64        10.92        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        29.62 
TCGA-DH-A66F TCGA-DH-A66G TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
        7.79         3.85        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-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-7301 
       10.36         7.96        94.32        18.94        44.02        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-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-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-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-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 
      130.78        14.33        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        11.87        15.52 
TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J 
       24.46         0.59         5.26         3.72         9.67         7.04 
TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Z 
        6.64         7.04         4.21         4.08        10.59        10.78 
TCGA-FG-A710 TCGA-FG-A713 TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7470 
       22.95         5.23         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-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-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-A5R9 TCGA-HT-A5RB TCGA-HT-A5RC 
        0.23        10.49         0.13         0.07         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-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 
        8.61         8.94        19.59        17.82        10.55         7.89 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV 
        9.67         6.61        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-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-A6CV TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 
        2.96         2.20         3.16         0.59         6.31         3.91 
TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-R8-A6MK TCGA-R8-A6ML 
        4.73         1.91         0.23         5.03        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        28.27 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 
       28.14        22.49        21.63        16.37        11.31        15.62 
TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB 
       20.05         9.86        94.62        83.70         5.85       103.76 
TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL 
       62.37        72.59        70.55        22.92        70.65        10.88 
TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ 
        9.30         9.04         7.59         6.15         3.39        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        18.21        13.02 
TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89Z 
       10.39        87.09        17.42        83.80        31.59         5.00 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84C 
       49.45        35.93        25.32        22.59        48.39        15.09 
TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84L TCGA-TM-A84M 
       50.76        34.36        24.26        19.36        40.83        16.50 
TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T TCGA-VM-A8C9 
       29.92        18.90         9.44         4.57        12.00        30.08 
TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH 
       13.51         0.10         7.89        26.79        10.95 

  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 
           15.735            14.960 
[1] "0.1 - 75.2 (15.7)"  "0.0 - 211.2 (15.0)"
[1] "hr=" "2.5"
D44V2, continuous
D44V3, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     6  13
  3P LOSS WILD-TYPE 170 211
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      6   13
  3P LOSS WILD-TYPE  170  211
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE               6               170
  MALE                13               211
[1] 2 2
[1] FALSE
D44V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  3P LOSS MUTATED             9                3                 7
  3P LOSS WILD-TYPE         134              101               146
D44V5, multiclass
                   clus
vv                  3P LOSS MUTATED 3P LOSS WILD-TYPE
  ASTROCYTOMA                     9               134
  OLIGOASTROCYTOMA                3               101
  OLIGODENDROGLIOMA               7               146
[1] 3 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  15
  3P LOSS WILD-TYPE  85 296
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      4   15
  3P LOSS WILD-TYPE   85  296
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  NO                4                85
  YES              15               296
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3P LOSS MUTATED                                  0     0
  3P LOSS WILD-TYPE                                1     2
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3P LOSS MUTATED                           0    19
  3P LOSS WILD-TYPE                        14   357
D44V7, multiclass
                                  clus
vv                                 3P LOSS MUTATED 3P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 2
  BLACK OR AFRICAN AMERICAN                      0                14
  WHITE                                         19               357
[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  16
  3P LOSS WILD-TYPE  13 343
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      2   16
  3P LOSS WILD-TYPE   13  343
                        clus
vv                       3P LOSS MUTATED 3P LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                13
  NOT HISPANIC OR LATINO              16               343
[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 311  61
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               23               372 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               10                61 
$`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-DH-5140 TCGA-DH-5141 
       27.81        14.73        13.64        10.92        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        29.62        15.75 
TCGA-DH-A66F TCGA-DH-A66G TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
        7.79         3.85        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-6408 TCGA-DU-6410 TCGA-DU-6542 
       19.89        16.83        94.52       114.08         7.96         7.73 
TCGA-DU-7006 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 
       11.47       156.23       138.28        14.99       105.21         6.54 
TCGA-DU-7013 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 
        8.84        90.77        30.67        26.30        10.36         7.96 
TCGA-DU-7294 TCGA-DU-7299 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 
       94.32        44.02        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-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS 
       19.13        16.96        14.17        14.24        12.59        15.12 
TCGA-DU-A5TT TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
        4.96         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-A7T8 
        7.23         5.98        11.41        26.76         7.13       124.50 
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-FG-5962 TCGA-FG-5963 TCGA-FG-5964 
       95.57       130.78        14.33        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        11.87 
TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY 
       15.52        24.46         0.59         5.26         3.72         9.67 
TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 
        7.04         6.64         7.04         4.21         4.08        10.59 
TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A713 TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 
       10.78        22.95         5.23         0.13         0.10         6.67 
TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 
        8.81         0.13        16.54         3.75        17.42         6.54 
TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 
        6.38         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-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 
       63.55        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-A5R9 TCGA-HT-A5RA 
       16.04         0.23        10.49         0.13         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-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-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 
       35.90         4.31         8.61         8.94        19.59        17.82 
TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-8125 TCGA-KT-A74X 
       10.55         7.89         9.67         6.61        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-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X 
        4.11         5.88         5.75         2.53         4.83         7.79 
TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CV TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
        4.11         4.18         2.96         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-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 
       28.27        28.14        22.49        21.63        16.37        11.31 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA 
       15.62        20.05         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 
      103.76        62.37        72.59        70.55        22.92        70.65 
TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ 
       10.88         9.30         9.04         7.59         6.15         3.39 
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        18.21 
TCGA-S9-A7QZ TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 
       13.02        10.39        87.09        17.42        83.80        31.59 
TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF 
        5.00        49.45        35.93        25.32        22.59        48.39 
TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84L 
       15.09        50.76        34.36        24.26        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-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 

  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 
            18.94             14.63 
[1] "0.0 - 117.4 (18.9)" "0.1 - 211.2 (14.6)"
[1] "hr=" "2.1"
D45V2, continuous
D45V3, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     6  17
  3Q LOSS WILD-TYPE 170 207
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      6   17
  3Q LOSS WILD-TYPE  170  207
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE               6               170
  MALE                17               207
[1] 2 2
[1] FALSE
D45V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  3Q LOSS MUTATED             9                5                 9
  3Q LOSS WILD-TYPE         134               99               144
D45V5, multiclass
                   clus
vv                  3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  ASTROCYTOMA                     9               134
  OLIGOASTROCYTOMA                5                99
  OLIGODENDROGLIOMA               9               144
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V6, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     6  17
  3Q LOSS WILD-TYPE  83 294
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      6   17
  3Q LOSS WILD-TYPE   83  294
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  NO                6                83
  YES              17               294
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3Q LOSS MUTATED                                  0     0
  3Q LOSS WILD-TYPE                                1     2
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3Q LOSS MUTATED                           1    22
  3Q LOSS WILD-TYPE                        13   354
D45V7, multiclass
                                  clus
vv                                 3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 2
  BLACK OR AFRICAN AMERICAN                      1                13
  WHITE                                         22               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"
D45V8, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     2  20
  3Q LOSS WILD-TYPE  13 339
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      2   20
  3Q LOSS WILD-TYPE   13  339
                        clus
vv                       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                13
  NOT HISPANIC OR LATINO              20               339
[1] 2 2
[1] FALSE

Clustering(46) Variable = 4P LOSS MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                 0   1
  4P LOSS MUTATED    45  11
  4P LOSS WILD-TYPE 279  60
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               56               339 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               11                60 
$`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-DU-6399 TCGA-DU-6400 
       13.64        10.92        30.21         3.85        65.75         1.22 
TCGA-DU-6410 TCGA-DU-7010 TCGA-DU-7018 TCGA-DU-7294 TCGA-DU-8165 TCGA-DU-8166 
        7.96        14.99        30.67        94.32        19.13        16.96 
TCGA-DU-8168 TCGA-DU-A6S3 TCGA-DU-A6S8 TCGA-DU-A76R TCGA-DU-A7T8 TCGA-E1-5302 
       14.17         2.70         5.98        21.30       124.50        50.14 
TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5311 TCGA-FG-5962 TCGA-FG-5964 TCGA-FG-7636 
       67.46        41.13       134.27        47.77        34.36        17.88 
TCGA-FG-7638 TCGA-FG-A60J TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-HT-7467 TCGA-HT-7468 
       22.55         7.04         4.21         4.08         0.10         6.67 
TCGA-HT-7471 TCGA-HT-7475 TCGA-HT-7480 TCGA-HT-7677 TCGA-HT-7688 TCGA-HT-7692 
        0.13        17.42        75.19        16.24        31.69         2.96 
TCGA-HT-8105 TCGA-HT-A5R9 TCGA-HW-7487 TCGA-HW-7491 TCGA-IK-8125 TCGA-P5-A5EV 
        6.25         0.07        13.45        40.18        42.77         0.23 
TCGA-S9-A6TW TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WL TCGA-S9-A7IY TCGA-S9-A7IZ 
       28.27       103.76        62.37        10.88        12.59         4.21 
TCGA-TM-A7C5 TCGA-TM-A84T 
       25.32        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-DH-5140 
        5.98        16.08        15.42        27.81        14.73        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        29.62        15.75 
TCGA-DH-A66F TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 
        7.79        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-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-7008 
       94.52       114.08         7.73        11.47        62.96       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-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-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-8167 TCGA-DU-A5TP 
       23.74         3.98        20.68        21.40        15.48        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-A6S6 TCGA-DU-A6S7 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O 
        8.65        77.98         7.23        11.41        26.76         7.13 
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-FG-5963 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 
       17.98        32.19        18.77        14.93        24.99        23.97 
TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 
       13.58        15.35        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        11.87        15.52 
TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60K 
       24.46         0.59         5.26         3.72         9.67         6.64 
TCGA-FG-A60L TCGA-FG-A6J3 TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A713 TCGA-FN-7833 
        7.04        10.59        10.78        22.95         5.23         0.13 
TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7476 
        7.82         8.81         0.03        16.54         3.75         6.54 
TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 
       24.26         6.38         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-7680 TCGA-HT-7681 TCGA-HT-7684 
        0.23        14.27         0.16         0.76        44.68         6.05 
TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7693 
       42.74         0.10        14.96         0.10         0.10        17.52 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 
        6.90        14.53        39.48        19.23        39.09         0.23 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
       50.63         0.49        23.61        37.15         0.33         0.13 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 
        3.68         5.33         2.93         1.71        11.28        31.43 
TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8018 TCGA-HT-8019 
        1.64        16.24         9.40        63.55        21.50        33.01 
TCGA-HT-8104 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 
       12.23         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-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 
       10.49         0.13        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-7489 
       13.02         1.81        16.14         5.33        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         8.61         8.94        19.59 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 
       17.82        10.55         7.89         9.67         6.61        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-A5F6 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V 
        4.11         5.88         1.28         5.75         2.53         4.83 
TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CV TCGA-QH-A6CY TCGA-QH-A6CZ 
        7.79         4.11         4.18         2.96         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-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TS 
        5.03        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        28.14        22.49        21.63        16.37 
TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
       11.31        15.62        20.05         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        70.55        22.92        70.65         9.30 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
        9.04         7.59         6.15         3.39        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-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 
        4.04        18.21        13.02        10.39        87.09        17.42 
TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7CA 
       83.80        31.59         5.00        49.45        35.93        22.59 
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-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB 
        9.44         4.57        33.07        30.08        13.51         0.10 
TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH 
        7.89        26.79        10.95 

  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 
            17.19             14.73 
[1] "0.1 - 134.3 (17.2)" "0.0 - 211.2 (14.7)"
[1] "hr=" "1.1"
D46V2, continuous
D46V3, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    19  37
  4P LOSS WILD-TYPE 157 187
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     19   37
  4P LOSS WILD-TYPE  157  187
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE              19               157
  MALE                37               187
[1] 2 2
[1] FALSE
D46V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  4P LOSS MUTATED            10               14                32
  4P LOSS WILD-TYPE         133               90               121
D46V5, multiclass
                   clus
vv                  4P LOSS MUTATED 4P LOSS WILD-TYPE
  ASTROCYTOMA                    10               133
  OLIGOASTROCYTOMA               14                90
  OLIGODENDROGLIOMA              32               121
[1] 3 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  40
  4P LOSS WILD-TYPE  73 271
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     16   40
  4P LOSS WILD-TYPE   73  271
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  NO               16                73
  YES              40               271
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4P LOSS MUTATED                                  0     0
  4P LOSS WILD-TYPE                                1     2
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4P LOSS MUTATED                           0    55
  4P LOSS WILD-TYPE                        14   321
D46V7, multiclass
                                  clus
vv                                 4P LOSS MUTATED 4P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 2
  BLACK OR AFRICAN AMERICAN                      0                14
  WHITE                                         55               321
[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  54
  4P LOSS WILD-TYPE  15 305
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      0   54
  4P LOSS WILD-TYPE   15  305
                        clus
vv                       4P LOSS MUTATED 4P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                15
  NOT HISPANIC OR LATINO              54               305
[1] 2 2
[1] FALSE

Clustering(47) Variable = 4Q LOSS MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                 0   1
  4Q LOSS MUTATED    58  14
  4Q LOSS WILD-TYPE 266  57
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               72               323 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               14                57 
$`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-DH-A669 TCGA-DH-A66B TCGA-DH-A66G 
       18.84        12.59        13.64        30.21        29.62         3.85 
TCGA-DU-5853 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6410 TCGA-DU-7008 TCGA-DU-7010 
       13.38        65.75         1.22         7.96       156.23        14.99 
TCGA-DU-7018 TCGA-DU-7294 TCGA-DU-7299 TCGA-DU-7302 TCGA-DU-7309 TCGA-DU-8165 
       30.67        94.32        44.02        60.30         2.76        19.13 
TCGA-DU-8168 TCGA-DU-A5TS TCGA-DU-A6S3 TCGA-DU-A6S8 TCGA-DU-A76R TCGA-DU-A7T8 
       14.17        15.12         2.70         5.98        21.30       124.50 
TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5311 TCGA-EZ-7264 TCGA-FG-5962 
       50.14        67.46        41.13       134.27        14.33        47.77 
TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-A60J TCGA-FG-A6IZ 
       17.98        34.36        17.88        22.55         7.04         4.21 
TCGA-FG-A6J1 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7471 TCGA-HT-7480 TCGA-HT-7677 
        4.08         0.10         6.67         0.13        75.19        16.24 
TCGA-HT-7688 TCGA-HT-7692 TCGA-HT-7856 TCGA-HT-8105 TCGA-HT-A5R9 TCGA-HW-7487 
       31.69         2.96        39.09         6.25         0.07        13.45 
TCGA-HW-7491 TCGA-HW-7493 TCGA-IK-8125 TCGA-P5-A5EV TCGA-QH-A6X4 TCGA-QH-A6XA 
       40.18        35.90        42.77         0.23         6.31         0.23 
TCGA-S9-A6TW TCGA-S9-A6WD TCGA-S9-A6WL TCGA-S9-A6WP TCGA-S9-A7IS TCGA-S9-A7IY 
       28.27        62.37        10.88         6.15         7.92        12.59 
TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A84R TCGA-TM-A84T 
        4.21         9.37        35.93        25.32         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-DH-5140 TCGA-DH-5141 
       15.42        27.81        14.73        10.92        19.96        31.82 
TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A66D TCGA-DH-A66F TCGA-DU-5847 
       30.31        14.40         8.02        15.75         7.79        18.02 
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-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-7009 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 
       11.47        62.96       138.28       105.21         6.54         8.84 
TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7298 
      117.40        90.77        26.30        10.36         7.96        18.94 
TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-8158 TCGA-DU-8161 
       62.01        25.91        23.31        41.98         5.10        23.74 
TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-A5TP 
        3.98        20.68        21.40        16.96        15.48        14.24 
TCGA-DU-A5TR TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 
       12.59         4.96         3.65         5.65        12.20         8.65 
TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-E1-5305 
       77.98         7.23        11.41        26.76         7.13        79.99 
TCGA-E1-5307 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-FG-5965 TCGA-FG-6688 
       57.93        78.21        95.57       130.78        32.19        18.77 
TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7641 
       14.93        24.99        23.97        13.58        15.35        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        11.87        15.52        24.46         0.59         5.26 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6J3 TCGA-FG-A70Z 
        3.72         9.67         6.64         7.04        10.59        10.78 
TCGA-FG-A710 TCGA-FG-A713 TCGA-FN-7833 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7472 
       22.95         5.23         0.13         7.82         8.81         0.03 
TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 
       16.54         3.75        17.42         6.54        24.26         6.38 
TCGA-HT-7479 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
        7.10        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-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 
        0.16         0.76        44.68         6.05        42.74         0.10 
TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 
       14.96         0.10         0.10        17.52         6.90        14.53 
TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 
       39.48        19.23         0.23        50.63         0.49        23.61 
TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 
       37.15         0.33         0.13         3.68         5.33         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-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8106 TCGA-HT-8107 
       63.55        21.50        33.01        12.23         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-A5RA 
       16.04        15.72         0.23        10.49         0.13        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-HW-7486 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7495 TCGA-HW-8319 
        5.33        29.92         8.32        19.23         4.31         8.61 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
        8.94        19.59        17.82        10.55         7.89         9.67 
TCGA-HW-A5KM TCGA-IK-7675 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EW TCGA-P5-A5EX 
        6.61        19.00         5.23         4.73         6.71         1.64 
TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F6 TCGA-QH-A65R 
        2.37         2.30         4.11         5.88         1.28         5.75 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CV 
        2.53         4.83         7.79         4.11         4.18         2.96 
TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 
        2.20         3.16         0.59         3.91         4.73         1.91 
TCGA-QH-A6XC TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TS 
        5.03        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        28.14        22.49        21.63        16.37 
TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
       11.31        15.62        20.05         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       103.76        72.59        70.55        22.92        70.65 
TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IX 
        9.30         9.04         7.59         3.39        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        18.21 
TCGA-S9-A7QZ TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 
       13.02        10.39        87.09        17.42        83.80        31.59 
TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
        5.00        49.45        22.59        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-A84S TCGA-VM-A8C8 TCGA-VM-A8C9 
       16.50        29.92        18.90         4.57        33.07        30.08 
TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH 
       13.51         0.10         7.89        26.79        10.95 

  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 
            17.06             14.73 
[1] "0.1 - 156.2 (17.1)" "0.0 - 211.2 (14.7)"
[1] "hr=" "1.1"
D47V2, continuous
D47V3, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED    27  45
  4Q LOSS WILD-TYPE 149 179
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     27   45
  4Q LOSS WILD-TYPE  149  179
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE              27               149
  MALE                45               179
[1] 2 2
[1] FALSE
D47V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  4Q LOSS MUTATED            16               17                39
  4Q LOSS WILD-TYPE         127               87               114
D47V5, multiclass
                   clus
vv                  4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  ASTROCYTOMA                    16               127
  OLIGOASTROCYTOMA               17                87
  OLIGODENDROGLIOMA              39               114
[1] 3 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  53
  4Q LOSS WILD-TYPE  70 258
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     19   53
  4Q LOSS WILD-TYPE   70  258
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  NO               19                70
  YES              53               258
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4Q LOSS MUTATED                                  0     0
  4Q LOSS WILD-TYPE                                1     2
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4Q LOSS MUTATED                           1    70
  4Q LOSS WILD-TYPE                        13   306
D47V7, multiclass
                                  clus
vv                                 4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 2
  BLACK OR AFRICAN AMERICAN                      1                13
  WHITE                                         70               306
[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  69
  4Q LOSS WILD-TYPE  15 290
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      0   69
  4Q LOSS WILD-TYPE   15  290
                        clus
vv                       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                15
  NOT HISPANIC OR LATINO              69               290
[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 302  65
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               28               367 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                6                65 
$`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        15.75         3.85        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         9.30        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-DH-5141 
       16.08        15.42        27.81        14.73        13.64        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        29.62         7.79 
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-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-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-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-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 
       21.30       124.50        67.46        41.13        79.99        57.93 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 TCGA-FG-5962 
      134.27        78.21        95.57       130.78        14.33        47.77 
TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-6688 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 
       17.98        34.36        18.77        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        11.87 
TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY 
       15.52        24.46         0.59         5.26         3.72         9.67 
TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A70Z 
        7.04         6.64         7.04         4.21         4.08        10.78 
TCGA-FG-A710 TCGA-FG-A713 TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 
       22.95         5.23         0.13         0.10         6.67         7.82 
TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7476 TCGA-HT-7477 
        8.81         0.13         0.03        16.54         6.54        24.26 
TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 
        6.38         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-7689 TCGA-HT-7690 TCGA-HT-7691 
        6.05        42.74         0.10        14.96         0.10         0.10 
TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 
        2.96        17.52         6.90        14.53        39.48        19.23 
TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 
       39.09         0.23        50.63         0.49        23.61        37.15 
TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 
        0.33         0.13         3.68         5.33         2.93         1.71 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8018 
       31.43         1.64        16.24         9.40        63.55        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-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-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HW-7486 
        5.33        13.02         1.81        16.14         5.33        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 
        8.61         8.94        19.59        17.82        10.55         7.89 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 
        9.67         6.61        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-A5F6 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X 
        5.88         1.28         5.75         2.53         4.83         7.79 
TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CV TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
        4.11         4.18         2.96         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-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        28.27        28.14        22.49        21.63        16.37 
TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
       11.31        15.62        20.05         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       103.76        62.37        72.59        70.55        22.92 
TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ 
       70.65        10.88         9.04         7.59         6.15         3.39 
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        18.21 
TCGA-S9-A7QZ TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R8 TCGA-S9-A89Z 
       13.02        10.39        87.09        17.42        31.59         5.00 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B 
       49.45        35.93        25.32        22.59        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-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 
       10.95 

  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 
           18.985            14.560 
[1] "0.1 - 83.8 (19.0)"  "0.0 - 211.2 (14.6)"
[1] "hr=" "1.1"
D48V2, continuous
D48V3, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    11  17
  5P LOSS WILD-TYPE 165 207
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     11   17
  5P LOSS WILD-TYPE  165  207
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE              11               165
  MALE                17               207
[1] 2 2
[1] FALSE
D48V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  5P LOSS MUTATED            13               11                 4
  5P LOSS WILD-TYPE         130               93               149
D48V5, multiclass
                   clus
vv                  5P LOSS MUTATED 5P LOSS WILD-TYPE
  ASTROCYTOMA                    13               130
  OLIGOASTROCYTOMA               11                93
  OLIGODENDROGLIOMA               4               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"
D48V6, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    12  16
  5P LOSS WILD-TYPE  77 295
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     12   16
  5P LOSS WILD-TYPE   77  295
     clus
vv    5P LOSS MUTATED 5P LOSS WILD-TYPE
  NO               12                77
  YES              16               295
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5P LOSS MUTATED                                  0     0
  5P LOSS WILD-TYPE                                1     2
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5P LOSS MUTATED                           0    28
  5P LOSS WILD-TYPE                        14   348
D48V7, multiclass
                                  clus
vv                                 5P LOSS MUTATED 5P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 2
  BLACK OR AFRICAN AMERICAN                      0                14
  WHITE                                         28               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"
D48V8, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     0  27
  5P LOSS WILD-TYPE  15 332
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      0   27
  5P LOSS WILD-TYPE   15  332
                        clus
vv                       5P LOSS MUTATED 5P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                15
  NOT HISPANIC OR LATINO              27               332
[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 307  60
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               28               367 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               11                60 
$`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        15.75         3.85        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         9.30        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-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       13.64        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66F TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
       29.62         7.79        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-6400 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 
       46.06         1.22         7.04        11.64       133.74        19.89 
TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7008 
       16.83        94.52         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-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-E1-5303 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 
       21.30       124.50        67.46        79.99        57.93       134.27 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 TCGA-FG-5962 TCGA-FG-5963 
       78.21        95.57       130.78        14.33        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 
       11.87        15.52        24.46         0.59         5.26         3.72 
TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 
        9.67         7.04         6.64         7.04         4.21         4.08 
TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A713 TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 
       10.78        22.95         5.23         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-7880 
        0.49        23.61        37.15         0.33         0.13         5.33 
TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 
        2.93         1.71        31.43         1.64        16.24         9.40 
TCGA-HT-8013 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8107 
       63.55        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-A5R9 
       16.04        15.72         0.23        10.49         0.13         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-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         8.61         8.94        19.59        17.82        10.55 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 
        7.89         9.67         6.61        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-A5F6 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X 
        5.88         1.28         5.75         2.53         4.83         7.79 
TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CV TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
        4.11         4.18         2.96         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-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 
       28.27        28.14        22.49        21.63        16.37        11.31 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA 
       15.62        20.05         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 
      103.76        62.37        72.59        70.55        22.92        70.65 
TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ 
       10.88         9.04         7.59         6.15         3.39        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        18.21        13.02 
TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89Z 
       10.39        87.09        17.42        83.80        31.59         5.00 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B 
       49.45        35.93        25.32        22.59        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-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 
       10.95 

  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 
           19.065            14.730 
[1] "0.1 - 114.1 (19.1)" "0.0 - 211.2 (14.7)"
[1] "hr=" "1.9"
D49V2, continuous
D49V3, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    15  13
  5Q LOSS WILD-TYPE 161 211
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     15   13
  5Q LOSS WILD-TYPE  161  211
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE              15               161
  MALE                13               211
[1] 2 2
[1] FALSE
D49V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  5Q LOSS MUTATED            16                6                 6
  5Q LOSS WILD-TYPE         127               98               147
D49V5, multiclass
                   clus
vv                  5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  ASTROCYTOMA                    16               127
  OLIGOASTROCYTOMA                6                98
  OLIGODENDROGLIOMA               6               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"
D49V6, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    11  17
  5Q LOSS WILD-TYPE  78 294
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     11   17
  5Q LOSS WILD-TYPE   78  294
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  NO               11                78
  YES              17               294
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5Q LOSS MUTATED                                  0     0
  5Q LOSS WILD-TYPE                                1     2
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5Q LOSS MUTATED                           0    28
  5Q LOSS WILD-TYPE                        14   348
D49V7, multiclass
                                  clus
vv                                 5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 2
  BLACK OR AFRICAN AMERICAN                      0                14
  WHITE                                         28               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"
D49V8, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED     1  27
  5Q LOSS WILD-TYPE  14 332
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      1   27
  5Q LOSS WILD-TYPE   14  332
                        clus
vv                       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                14
  NOT HISPANIC OR LATINO              27               332
[1] 2 2
[1] FALSE

Clustering(50) Variable = 6P LOSS MUTATION ANALYSIS
D50V1, survival
                   sevent
clus2                 0   1
  6P LOSS MUTATED    15   8
  6P LOSS WILD-TYPE 309  63
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               23               372 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                8                63 
$`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-A5F6 
        2.96        19.23        15.72         0.23        16.14         1.28 
TCGA-QH-A6CS TCGA-S9-A6TZ TCGA-TM-A7CF TCGA-VM-A8C8 TCGA-VM-A8CD 
        4.18        21.63        48.39        33.07         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-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 
       10.92        19.96        31.82        30.31        14.40         8.02 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DU-5847 TCGA-DU-5849 
       29.62        15.75         7.79         3.85        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-6399 TCGA-DU-6401 TCGA-DU-6402 
       49.02        75.16        46.06        65.75        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-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 
        2.76         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-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-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 
      124.50        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-FG-5962 
      134.27        78.21        95.57       130.78        14.33        47.77 
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-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY 
       11.87        24.46         0.59         5.26         3.72         9.67 
TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 
        7.04         6.64         7.04         4.21         4.08        10.59 
TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A713 TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 
       10.78        22.95         5.23         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-7693 TCGA-HT-7694 
       31.69        14.96         0.10         0.10        17.52         6.90 
TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 
       14.53        39.48        39.09         0.23        50.63         0.49 
TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 
       23.61        37.15         0.33         0.13         3.68         5.33 
TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 
        2.93         1.71        11.28        31.43         1.64        16.24 
TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 
        9.40        63.55        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-A5R9 
       29.59         3.88        16.04        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-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-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 
       35.90         4.31         8.61         8.94        19.59        17.82 
TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 
       10.55         7.89         9.67         6.61        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-QH-A65R TCGA-QH-A65S TCGA-QH-A65V 
        2.30         4.11         5.88         5.75         2.53         4.83 
TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CV TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
        7.79         4.11         2.96         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-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        28.27        28.14        22.49        16.37        11.31 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA 
       15.62        20.05         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 
      103.76        62.37        72.59        70.55        22.92        70.65 
TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ 
       10.88         9.30         9.04         7.59         6.15         3.39 
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        18.21 
TCGA-S9-A7QZ TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 
       13.02        10.39        87.09        17.42        83.80        31.59 
TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A84B 
        5.00        49.45        35.93        25.32        22.59        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-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CE TCGA-VM-A8CH 
       12.00        30.08        13.51         0.10        26.79        10.95 

  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 
           15.720            14.945 
[1] "0.2 - 48.4 (15.7)"  "0.0 - 211.2 (14.9)"
[1] "hr=" "3.9"
D50V2, continuous
D50V3, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    10  14
  6P LOSS WILD-TYPE 166 210
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     10   14
  6P LOSS WILD-TYPE  166  210
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE              10               166
  MALE                14               210
[1] 2 2
[1] FALSE
D50V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  6P LOSS MUTATED            14                4                 6
  6P LOSS WILD-TYPE         129              100               147
D50V5, multiclass
                   clus
vv                  6P LOSS MUTATED 6P LOSS WILD-TYPE
  ASTROCYTOMA                    14               129
  OLIGOASTROCYTOMA                4               100
  OLIGODENDROGLIOMA               6               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"
D50V6, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     5  19
  6P LOSS WILD-TYPE  84 292
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      5   19
  6P LOSS WILD-TYPE   84  292
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  NO                5                84
  YES              19               292
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6P LOSS MUTATED                                  1     0
  6P LOSS WILD-TYPE                                0     2
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6P LOSS MUTATED                           0    23
  6P LOSS WILD-TYPE                        14   353
D50V7, multiclass
                                  clus
vv                                 6P LOSS MUTATED 6P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          0                 2
  BLACK OR AFRICAN AMERICAN                      0                14
  WHITE                                         23               353
[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  20
  6P LOSS WILD-TYPE  14 339
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      1   20
  6P LOSS WILD-TYPE   14  339
                        clus
vv                       6P LOSS MUTATED 6P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                14
  NOT HISPANIC OR LATINO              20               339
[1] 2 2
[1] FALSE

Clustering(51) Variable = 6Q LOSS MUTATION ANALYSIS
D51V1, survival
                   sevent
clus2                 0   1
  6Q LOSS MUTATED    33  12
  6Q LOSS WILD-TYPE 291  59
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               45               350 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               12                59 
$`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        29.62        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-A5F6 TCGA-QH-A6CS TCGA-S9-A6TZ TCGA-S9-A7R8 TCGA-TM-A7CF 
        2.30         1.28         4.18        21.63        31.59        48.39 
TCGA-TM-A84Q TCGA-VM-A8C8 TCGA-VM-A8CD 
       18.90        33.07         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-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A66D 
       19.96        31.82        30.31        14.40         8.02        15.75 
TCGA-DH-A66F TCGA-DH-A66G TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 
        7.79         3.85        14.56        17.46         6.74        13.38 
TCGA-DU-5854 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 
        8.45       182.33        18.94        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-6406 TCGA-DU-6407 TCGA-DU-6408 
        7.04        11.64       133.74        16.83        94.52       114.08 
TCGA-DU-6410 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 
        7.96        11.47        62.96       156.23       138.28        14.99 
TCGA-DU-7011 TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 
      105.21         8.84       117.40        90.77        30.67        26.30 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 
       10.36         7.96        94.32        44.02        62.01        25.91 
TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8162 TCGA-DU-8163 
       60.30        23.31        41.98         2.76         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-E1-5302 TCGA-E1-5303 
       26.76         7.13        21.30       124.50        50.14        67.46 
TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 
       41.13        79.99       134.27        78.21        95.57       130.78 
TCGA-EZ-7264 TCGA-FG-5962 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 
       14.33        47.77        34.36        32.19        18.77        14.93 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7638 TCGA-FG-7641 
       24.99        23.97        13.58        15.35        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        11.87        24.46         0.59         5.26         3.72 
TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 
        9.67         7.04         6.64         7.04         4.21         4.08 
TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A713 TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 
       10.78        22.95         5.23         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-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-7690 TCGA-HT-7691 
       44.68         6.05        42.74         0.10         0.10         0.10 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7856 TCGA-HT-7857 
       17.52         6.90        14.53        39.48        39.09         0.23 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
       50.63         0.49        23.61        37.15         0.33         0.13 
TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 
        3.68         5.33         2.93         1.71        11.28        31.43 
TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8018 TCGA-HT-8019 
        1.64        16.24         9.40        63.55        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-A5R9 TCGA-HT-A5RA TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 
        0.13         0.07        14.70         5.33         2.70        13.02 
TCGA-HT-A616 TCGA-HT-A618 TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 
        1.81         5.33        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         8.61         8.94        19.59 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 
       17.82        10.55         9.67         6.61        19.00        42.77 
TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5F0 
        5.23         4.73         6.71         1.64         2.37         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-A6CV TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 
        2.96         2.20         3.16         0.59         6.31         3.91 
TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-R8-A6MK TCGA-R8-A6ML 
        4.73         1.91         0.23         5.03        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        28.27 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       28.14        22.49        16.37        11.31        15.62        20.05 
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       103.76        62.37 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM 
       72.59        70.55        22.92        70.65        10.88         9.30 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
        9.04         7.59         6.15         3.39        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-A7R2 
        8.12         3.58         4.04        18.21        13.02        10.39 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 
       87.09        17.42        83.80         5.00        49.45        35.93 
TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G 
       25.32        22.59        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 
       26.79        10.95 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             0.10              0.03 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            57.93            211.17 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           16.140            14.715 
[1] "0.1 - 57.9 (16.1)"  "0.0 - 211.2 (14.7)"
[1] "hr=" "3.2"
D51V2, continuous
D51V3, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    21  26
  6Q LOSS WILD-TYPE 155 198
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     21   26
  6Q LOSS WILD-TYPE  155  198
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE              21               155
  MALE                26               198
[1] 2 2
[1] FALSE
D51V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  6Q LOSS MUTATED            30                9                 8
  6Q LOSS WILD-TYPE         113               95               145
D51V5, multiclass
                   clus
vv                  6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  ASTROCYTOMA                    30               113
  OLIGOASTROCYTOMA                9                95
  OLIGODENDROGLIOMA               8               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"
D51V6, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    15  32
  6Q LOSS WILD-TYPE  74 279
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     15   32
  6Q LOSS WILD-TYPE   74  279
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  NO               15                74
  YES              32               279
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6Q LOSS MUTATED                                  1     0
  6Q LOSS WILD-TYPE                                0     2
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6Q LOSS MUTATED                           3    43
  6Q LOSS WILD-TYPE                        11   333
D51V7, multiclass
                                  clus
vv                                 6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          0                 2
  BLACK OR AFRICAN AMERICAN                      3                11
  WHITE                                         43               333
[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  40
  6Q LOSS WILD-TYPE  13 319
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      2   40
  6Q LOSS WILD-TYPE   13  319
                        clus
vv                       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                13
  NOT HISPANIC OR LATINO              40               319
[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 322  70
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                3               392 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                1                70 
$`7P LOSS MUTATED`
TCGA-HW-A5KL TCGA-P5-A5F6 TCGA-S9-A6TS 
        9.67         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-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 
       10.92        19.96        31.82        30.31        14.40         8.02 
TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DU-5847 
       30.21        29.62        15.75         7.79         3.85        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-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-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-E1-5322 TCGA-EZ-7264 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 
       95.57       130.78        14.33        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        11.87 
TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY 
       15.52        24.46         0.59         5.26         3.72         9.67 
TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 
        7.04         6.64         7.04         4.21         4.08        10.59 
TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A713 TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 
       10.78        22.95         5.23         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-8018 TCGA-HT-8019 
        1.64        16.24         9.40        63.55        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-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB 
        0.23        10.49         0.13         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-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         8.61         8.94        19.59        17.82        10.55 
TCGA-HW-A5KK TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 
        7.89         6.61        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-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-A6CV TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
        4.18         2.96         2.20         3.16         0.59         6.31 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-R8-A6MK 
        3.91         4.73         1.91         0.23         5.03        88.83 
TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW 
       94.03        32.65        59.38        69.07        18.77        28.27 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 
       28.14        22.49        21.63        16.37        11.31        15.62 
TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB 
       20.05         9.86        94.62        83.70         5.85       103.76 
TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL 
       62.37        72.59        70.55        22.92        70.65        10.88 
TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ 
        9.30         9.04         7.59         6.15         3.39        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        18.21        13.02 
TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89Z 
       10.39        87.09        17.42        83.80        31.59         5.00 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B 
       49.45        35.93        25.32        22.59        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 
       26.79        10.95 

  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 
            9.670            14.975 
[1] "1.3 - 62.2 (9.7)"   "0.0 - 211.2 (15.0)"
[1] "hr=" "2"  
D52V2, continuous
D52V3, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     2   1
  7P LOSS WILD-TYPE 174 223
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      2    1
  7P LOSS WILD-TYPE  174  223
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  FEMALE               2               174
  MALE                 1               223
[1] 2 2
[1] FALSE
D52V4, continuous
[1] "Remove cluster labels:" "7P LOSS MUTATED"       
clus
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                2               232 
       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-DH-5140        TCGA-DH-5142        TCGA-DH-5143        TCGA-DH-5144 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DH-A66B        TCGA-DH-A66D        TCGA-DH-A66F        TCGA-DH-A66G 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-5851        TCGA-DU-5852        TCGA-DU-5853        TCGA-DU-5854 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-5855        TCGA-DU-5870        TCGA-DU-5871        TCGA-DU-5874 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-6396        TCGA-DU-6403        TCGA-DU-6404        TCGA-DU-6405 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-6407        TCGA-DU-6408        TCGA-DU-6410        TCGA-DU-7011 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-7013        TCGA-DU-7014        TCGA-DU-7015        TCGA-DU-7018 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-7019        TCGA-DU-7294        TCGA-DU-7298        TCGA-DU-7299 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-7300        TCGA-DU-7301        TCGA-DU-7302        TCGA-DU-7304 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-7306        TCGA-DU-7309        TCGA-DU-8158        TCGA-DU-8161 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-8162        TCGA-DU-8163        TCGA-DU-8165        TCGA-DU-8167 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-8168        TCGA-DU-A5TP        TCGA-DU-A5TR        TCGA-DU-A5TS 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-A5TU        TCGA-DU-A5TW        TCGA-DU-A6S2        TCGA-DU-A6S6 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DU-A6S7        TCGA-DU-A6S8        TCGA-DU-A76R        TCGA-DU-A7T8 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-E1-5302        TCGA-E1-5303        TCGA-E1-5304        TCGA-E1-5305 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-E1-5307        TCGA-E1-5311        TCGA-E1-5318        TCGA-E1-5319 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-E1-5322        TCGA-FG-5963        TCGA-FG-5965        TCGA-FG-6688 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FG-6689        TCGA-FG-6690        TCGA-FG-6691        TCGA-FG-7636 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FG-7638        TCGA-FG-8181        TCGA-FG-8185        TCGA-FG-8186 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FG-8187        TCGA-FG-8188        TCGA-FG-8189        TCGA-FG-A4MT 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FG-A4MW        TCGA-FG-A4MX        TCGA-FG-A60J        TCGA-FG-A60L 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FG-A6J1        TCGA-FG-A6J3        TCGA-FG-A713        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-A5RA        TCGA-HT-A5RC        TCGA-HT-A615        TCGA-HT-A617 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HT-A618        TCGA-IK-7675        TCGA-KT-A74X        TCGA-KT-A7W1 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-P5-A5EU        TCGA-P5-A5EV        TCGA-P5-A5EW        TCGA-P5-A5EX 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-P5-A5F0        TCGA-QH-A65R        TCGA-QH-A65S        TCGA-QH-A65V 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-QH-A65X        TCGA-QH-A65Z        TCGA-QH-A6CS        TCGA-QH-A6CU 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-QH-A6CV        TCGA-QH-A6CW        TCGA-QH-A6CX        TCGA-QH-A6CY 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-QH-A6CZ        TCGA-QH-A6X3        TCGA-QH-A6X4        TCGA-QH-A6X5 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-QH-A6X8        TCGA-QH-A6X9        TCGA-QH-A6XA        TCGA-QH-A6XC 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-S9-A6TU        TCGA-S9-A6TV        TCGA-S9-A6TW        TCGA-S9-A6TX 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-S9-A6TY        TCGA-S9-A6TZ        TCGA-S9-A6U0        TCGA-S9-A6U1 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-S9-A6U2        TCGA-S9-A6U5        TCGA-S9-A6U6        TCGA-S9-A6U8 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-S9-A6UA        TCGA-S9-A6UB        TCGA-S9-A6WD        TCGA-S9-A6WE 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-S9-A6WG        TCGA-S9-A6WH        TCGA-S9-A6WI        TCGA-S9-A6WL 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-S9-A6WM        TCGA-S9-A6WN        TCGA-S9-A6WO        TCGA-S9-A6WP 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-S9-A6WQ        TCGA-S9-A7IQ        TCGA-S9-A7IS        TCGA-S9-A7IX 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-S9-A7IY        TCGA-S9-A7IZ        TCGA-S9-A7J0        TCGA-S9-A7J1 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-S9-A7J2        TCGA-S9-A7J3        TCGA-S9-A7QW        TCGA-S9-A7QX 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-S9-A7QY        TCGA-S9-A7QZ        TCGA-S9-A7R2        TCGA-S9-A7R3 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-S9-A7R4        TCGA-S9-A7R7        TCGA-S9-A7R8        TCGA-S9-A89Z 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-TM-A7C3        TCGA-TM-A7C4        TCGA-TM-A7C5        TCGA-TM-A7CA 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-TM-A7CF        TCGA-TM-A84B        TCGA-TM-A84C        TCGA-TM-A84F 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-TM-A84G        TCGA-TM-A84H        TCGA-TM-A84I        TCGA-TM-A84J 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-TM-A84L        TCGA-TM-A84M        TCGA-TM-A84O        TCGA-TM-A84Q 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-TM-A84R        TCGA-TM-A84S        TCGA-TM-A84T        TCGA-VM-A8C8 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-VM-A8CA        TCGA-VM-A8CD        TCGA-VM-A8CE        TCGA-VM-A8CH 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  7P LOSS MUTATED             2                0                 1
  7P LOSS WILD-TYPE         141              104               152
D52V5, multiclass
                   clus
vv                  7P LOSS MUTATED 7P LOSS WILD-TYPE
  ASTROCYTOMA                     2               141
  OLIGOASTROCYTOMA                0               104
  OLIGODENDROGLIOMA               1               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"
D52V6, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     0   3
  7P LOSS WILD-TYPE  89 308
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      0    3
  7P LOSS WILD-TYPE   89  308
     clus
vv    7P LOSS MUTATED 7P LOSS WILD-TYPE
  NO                0                89
  YES               3               308
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7P LOSS MUTATED                                  0     0
  7P LOSS WILD-TYPE                                1     2
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7P LOSS MUTATED                           0     3
  7P LOSS WILD-TYPE                        14   373
D52V7, multiclass
                                  clus
vv                                 7P LOSS MUTATED 7P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 2
  BLACK OR AFRICAN AMERICAN                      0                14
  WHITE                                          3               373
[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  15 357
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      0    2
  7P LOSS WILD-TYPE   15  357
                        clus
vv                       7P LOSS MUTATED 7P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                15
  NOT HISPANIC OR LATINO               2               357
[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 322  70
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                3               392 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                1                70 
$`7Q LOSS MUTATED`
TCGA-DH-A66B TCGA-P5-A5F6 TCGA-S9-A6TS 
       29.62         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-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 
       10.92        19.96        31.82        30.31        14.40         8.02 
TCGA-DH-A669 TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DU-5847 TCGA-DU-5849 
       30.21        15.75         7.79         3.85        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-6399 TCGA-DU-6400 TCGA-DU-6401 
       49.02        75.16        46.06        65.75         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-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-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-E1-5302 TCGA-E1-5303 
       26.76         7.13        21.30       124.50        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-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 
      130.78        14.33        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        11.87        15.52 
TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J 
       24.46         0.59         5.26         3.72         9.67         7.04 
TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Z 
        6.64         7.04         4.21         4.08        10.59        10.78 
TCGA-FG-A710 TCGA-FG-A713 TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 
       22.95         5.23         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-8018 TCGA-HT-8019 TCGA-HT-8104 
       16.24         9.40        63.55        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-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-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 
        8.61         8.94        19.59        17.82        10.55         7.89 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 
        9.67         6.61        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-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-A6CV TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
        4.18         2.96         2.20         3.16         0.59         6.31 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-R8-A6MK 
        3.91         4.73         1.91         0.23         5.03        88.83 
TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW 
       94.03        32.65        59.38        69.07        18.77        28.27 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 
       28.14        22.49        21.63        16.37        11.31        15.62 
TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB 
       20.05         9.86        94.62        83.70         5.85       103.76 
TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL 
       62.37        72.59        70.55        22.92        70.65        10.88 
TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ 
        9.30         9.04         7.59         6.15         3.39        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        18.21        13.02 
TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89Z 
       10.39        87.09        17.42        83.80        31.59         5.00 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B 
       49.45        35.93        25.32        22.59        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 
       26.79        10.95 

  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 
            29.62             14.96 
[1] "1.3 - 62.2 (29.6)"  "0.0 - 211.2 (15.0)"
[1] "hr=" "1.6"
D53V2, continuous
D53V3, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     1   2
  7Q LOSS WILD-TYPE 175 222
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      1    2
  7Q LOSS WILD-TYPE  175  222
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  FEMALE               1               175
  MALE                 2               222
[1] 2 2
[1] FALSE
D53V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  7Q LOSS MUTATED             2                0                 1
  7Q LOSS WILD-TYPE         141              104               152
D53V5, multiclass
                   clus
vv                  7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  ASTROCYTOMA                     2               141
  OLIGOASTROCYTOMA                0               104
  OLIGODENDROGLIOMA               1               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"
D53V6, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     0   3
  7Q LOSS WILD-TYPE  89 308
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      0    3
  7Q LOSS WILD-TYPE   89  308
     clus
vv    7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  NO                0                89
  YES               3               308
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7Q LOSS MUTATED                                  0     0
  7Q LOSS WILD-TYPE                                1     2
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7Q LOSS MUTATED                           0     3
  7Q LOSS WILD-TYPE                        14   373
D53V7, multiclass
                                  clus
vv                                 7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 2
  BLACK OR AFRICAN AMERICAN                      0                14
  WHITE                                          3               373
[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  15 356
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      0    3
  7Q LOSS WILD-TYPE   15  356
                        clus
vv                       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                15
  NOT HISPANIC OR LATINO               3               356
[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 316  67
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               12               383 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                4                67 
$`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        29.62        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         2.96         9.30 

$`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-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66D 
       31.82        30.31        14.40         8.02        30.21        15.75 
TCGA-DH-A66F TCGA-DH-A66G TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
        7.79         3.85        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-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-FG-5962 TCGA-FG-5963 TCGA-FG-5964 
       95.57       130.78        14.33        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        11.87 
TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY 
       15.52        24.46         0.59         5.26         3.72         9.67 
TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 
        7.04         6.64         7.04         4.21         4.08        10.59 
TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A713 TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 
       10.78        22.95         5.23         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-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-8018 TCGA-HT-8019 TCGA-HT-8104 
       16.24         9.40        63.55        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-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-HW-7486 TCGA-HW-7487 TCGA-HW-7489 
        1.81        16.14         5.33        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         8.61         8.94 
TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM 
       19.59        17.82        10.55         7.89         9.67         6.61 
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-QH-A65R 
        1.64         2.37         2.30         4.11         5.88         5.75 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CY 
        2.53         4.83         7.79         4.11         4.18         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-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
        0.23         5.03        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        28.27        28.14        22.49 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       21.63        16.37        11.31        15.62        20.05         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       103.76        62.37        72.59 
TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WO 
       70.55        22.92        70.65        10.88         9.04         7.59 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY 
        6.15         3.39        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-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 
        4.04        18.21        13.02        10.39        87.09        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        35.93        25.32 
TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G 
       22.59        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 
       13.51         0.10         7.89        26.79        10.95 

  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 
           17.425            14.960 
[1] "0.2 - 46.6 (17.4)"  "0.0 - 211.2 (15.0)"
[1] "hr=" "2.8"
D54V2, continuous
D54V3, binary
                   cls
clus                  0   1
  8P LOSS MUTATED     5   8
  8P LOSS WILD-TYPE 171 216
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      5    8
  8P LOSS WILD-TYPE  171  216
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE               5               171
  MALE                 8               216
[1] 2 2
[1] FALSE
D54V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  8P LOSS MUTATED             8                2                 3
  8P LOSS WILD-TYPE         135              102               150
D54V5, multiclass
                   clus
vv                  8P LOSS MUTATED 8P LOSS WILD-TYPE
  ASTROCYTOMA                     8               135
  OLIGOASTROCYTOMA                2               102
  OLIGODENDROGLIOMA               3               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"
D54V6, binary
                   cls
clus                  0   1
  8P LOSS MUTATED     4   9
  8P LOSS WILD-TYPE  85 302
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      4    9
  8P LOSS WILD-TYPE   85  302
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  NO                4                85
  YES               9               302
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8P LOSS MUTATED                                  0     1
  8P LOSS WILD-TYPE                                1     1
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8P LOSS MUTATED                           0    12
  8P LOSS WILD-TYPE                        14   364
D54V7, multiclass
                                  clus
vv                                 8P LOSS MUTATED 8P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 1
  BLACK OR AFRICAN AMERICAN                      0                14
  WHITE                                         12               364
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V8, binary
                   cls
clus                  0   1
  8P LOSS MUTATED     1  12
  8P LOSS WILD-TYPE  14 347
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      1   12
  8P LOSS WILD-TYPE   14  347
                        clus
vv                       8P LOSS MUTATED 8P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                14
  NOT HISPANIC OR LATINO              12               347
[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 318  68
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                9               386 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                3                68 
$`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         2.96         9.30 

$`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-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       10.92        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DU-5847 TCGA-DU-5849 
       29.62        15.75         7.79         3.85        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-6399 TCGA-DU-6400 TCGA-DU-6401 
       49.02        75.16        46.06        65.75         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-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-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-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-E1-5302 TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5307 
       21.30       124.50        50.14        67.46        79.99        57.93 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 TCGA-FG-5962 
      134.27        78.21        95.57       130.78        14.33        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        11.87        15.52        24.46         0.59         5.26 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ 
        3.72         9.67         7.04         6.64         7.04         4.21 
TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A713 TCGA-FN-7833 
        4.08        10.59        10.78        22.95         5.23         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-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-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB 
       16.04        10.49         0.13         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-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         8.61         8.94        19.59        17.82        10.55 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X 
        7.89         9.67         6.61        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-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X 
        4.11         5.88         5.75         2.53         4.83         7.79 
TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
        4.11         4.18         2.20         3.16         0.59         6.31 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-R8-A6MK 
        3.91         4.73         1.91         0.23         5.03        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 
       28.27        28.14        22.49        21.63        16.37        11.31 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA 
       15.62        20.05         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 
      103.76        62.37        72.59        70.55        22.92        70.65 
TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ 
       10.88         9.04         7.59         6.15         3.39        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        18.21        13.02 
TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89Z 
       10.39        87.09        17.42        83.80        31.59         5.00 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B 
       49.45        35.93        25.32        22.59        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 
       26.79        10.95 

  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 
           11.470            14.975 
[1] "0.2 - 41.1 (11.5)"  "0.0 - 211.2 (15.0)"
[1] "hr=" "4.2"
D55V2, continuous
D55V3, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     5   4
  8Q LOSS WILD-TYPE 171 220
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      5    4
  8Q LOSS WILD-TYPE  171  220
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE               5               171
  MALE                 4               220
[1] 2 2
[1] FALSE
D55V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  8Q LOSS MUTATED             5                2                 2
  8Q LOSS WILD-TYPE         138              102               151
D55V5, multiclass
                   clus
vv                  8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  ASTROCYTOMA                     5               138
  OLIGOASTROCYTOMA                2               102
  OLIGODENDROGLIOMA               2               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"
D55V6, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     2   7
  8Q LOSS WILD-TYPE  87 304
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      2    7
  8Q LOSS WILD-TYPE   87  304
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  NO                2                87
  YES               7               304
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8Q LOSS MUTATED                                  0     1
  8Q LOSS WILD-TYPE                                1     1
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8Q LOSS MUTATED                           0     8
  8Q LOSS WILD-TYPE                        14   368
D55V7, multiclass
                                  clus
vv                                 8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 1
  BLACK OR AFRICAN AMERICAN                      0                14
  WHITE                                          8               368
[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  14 351
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      1    8
  8Q LOSS WILD-TYPE   14  351
                        clus
vv                       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                14
  NOT HISPANIC OR LATINO               8               351
[1] 2 2
[1] FALSE

Clustering(56) Variable = 9P LOSS MUTATION ANALYSIS
D56V1, survival
                   sevent
clus2                 0   1
  9P LOSS MUTATED    59  26
  9P LOSS WILD-TYPE 265  45
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               85               310 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               26                45 
$`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-DU-5847 TCGA-DU-5851 
       18.38        12.59        11.01        14.73        18.02        17.46 
TCGA-DU-5855 TCGA-DU-6395 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6402 TCGA-DU-6403 
        6.81        49.02        46.06        65.75         7.04        11.64 
TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7019 
        7.73        11.47        62.96       117.40        90.77        26.30 
TCGA-DU-7292 TCGA-DU-7298 TCGA-DU-7301 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-8162 
        7.96        18.94        25.91        23.31        41.98         3.98 
TCGA-DU-8168 TCGA-DU-A5TY TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-E1-5304 TCGA-E1-5307 
       14.17        12.20         7.23         5.98        41.13        57.93 
TCGA-EZ-7264 TCGA-FG-5963 TCGA-FG-5965 TCGA-FG-6690 TCGA-FG-6692 TCGA-FG-7636 
       14.33        17.98        32.19        24.99        13.58        17.88 
TCGA-FG-8185 TCGA-FG-A4MW TCGA-FG-A4MX TCGA-HT-7471 TCGA-HT-7477 TCGA-HT-7606 
       14.24         5.26         3.72         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         8.94        17.82 
TCGA-HW-A5KM TCGA-IK-7675 TCGA-P5-A5EV TCGA-P5-A5F6 TCGA-QH-A6CV TCGA-QH-A6CZ 
        6.61        19.00         0.23         1.28         2.96         3.16 
TCGA-S9-A6TS TCGA-S9-A6TW TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IZ TCGA-S9-A7J0 
       62.17        28.27         7.92        19.63         4.21         9.37 
TCGA-S9-A7R3 TCGA-S9-A7R8 TCGA-TM-A7CF TCGA-TM-A84H TCGA-TM-A84J TCGA-VM-A8CB 
       87.09        31.59        48.39        24.26        17.49         0.10 
TCGA-VM-A8CD 
        7.89 

$`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-DH-5140 TCGA-DH-5141 TCGA-DH-5142 
       27.81        13.64        10.92        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        29.62        15.75         7.79 
TCGA-DH-A66G TCGA-DU-5849 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5870 
        3.85        14.56         6.74        13.38         8.45       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-6400 TCGA-DU-6401 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 
       75.16         1.22        87.45       133.74        19.89        16.83 
TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 
       94.52       114.08         7.96       156.23       138.28        14.99 
TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7018 TCGA-DU-7290 TCGA-DU-7294 
      105.21         6.54         8.84        30.67        10.36        94.32 
TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7302 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 
       44.02        62.01        60.30         2.76         5.10        23.74 
TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-A5TP 
       20.68        21.40        19.13        16.96        15.48        14.24 
TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A6S2 
       12.59        15.12         4.96         3.65         5.65         8.65 
TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R 
        2.70        77.98        11.41        26.76         7.13        21.30 
TCGA-DU-A7T8 TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5311 TCGA-E1-5318 
      124.50        50.14        67.46        79.99       134.27        78.21 
TCGA-E1-5319 TCGA-E1-5322 TCGA-FG-5962 TCGA-FG-5964 TCGA-FG-6688 TCGA-FG-6689 
       95.57       130.78        47.77        34.36        18.77        14.93 
TCGA-FG-6691 TCGA-FG-7634 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 
       23.97        15.35        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        11.87        15.52 
TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
       24.46         0.59         9.67         7.04         6.64         7.04 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A713 
        4.21         4.08        10.59        10.78        22.95         5.23 
TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7472 
        0.13         0.10         6.67         7.82         8.81         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-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-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-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 
        1.71        11.28         1.64        16.24         9.40        63.55 
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-A5R9 TCGA-HT-A5RC TCGA-HT-A615 
        0.23        10.49         0.13         0.07         5.33        13.02 
TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 
        1.81        16.14         5.33        29.92        13.45         8.32 
TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8321 TCGA-HW-A5KJ 
       40.18        35.90         4.31         8.61        19.59        10.55 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EW 
        7.89         9.67        42.77         5.23         4.73         6.71 
TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-QH-A65R 
        1.64         2.37         2.30         4.11         5.88         5.75 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CY 
        2.53         4.83         7.79         4.11         4.18         2.20 
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-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TU 
        5.03        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        28.14        22.49        21.63        16.37        11.31 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA 
       15.62        20.05         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 
      103.76        62.37        72.59        70.55        22.92        70.65 
TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ 
       10.88         9.30         9.04         7.59         6.15         3.39 
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        18.21        13.02        10.39        17.42        83.80 
TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A84B 
        5.00        49.45        35.93        25.32        22.59        12.00 
TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84I TCGA-TM-A84L TCGA-TM-A84M 
       15.09        50.76        34.36        19.36        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-A8CE TCGA-VM-A8CH 
       30.08        13.51        26.79        10.95 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             0.10              0.03 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           117.40            211.17 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           14.960            14.975 
[1] "0.1 - 117.4 (15.0)" "0.0 - 211.2 (15.0)"
[1] "hr=" "2.8"
D56V2, continuous
D56V3, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    34  52
  9P LOSS WILD-TYPE 142 172
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     34   52
  9P LOSS WILD-TYPE  142  172
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE              34               142
  MALE                52               172
[1] 2 2
[1] FALSE
D56V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  9P LOSS MUTATED            40               20                26
  9P LOSS WILD-TYPE         103               84               127
D56V5, multiclass
                   clus
vv                  9P LOSS MUTATED 9P LOSS WILD-TYPE
  ASTROCYTOMA                    40               103
  OLIGOASTROCYTOMA               20                84
  OLIGODENDROGLIOMA              26               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"
D56V6, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    27  59
  9P LOSS WILD-TYPE  62 252
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     27   59
  9P LOSS WILD-TYPE   62  252
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  NO               27                62
  YES              59               252
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9P LOSS MUTATED                                  0     1
  9P LOSS WILD-TYPE                                1     1
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9P LOSS MUTATED                           2    81
  9P LOSS WILD-TYPE                        12   295
D56V7, multiclass
                                  clus
vv                                 9P LOSS MUTATED 9P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 1
  BLACK OR AFRICAN AMERICAN                      2                12
  WHITE                                         81               295
[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  77
  9P LOSS WILD-TYPE  13 282
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      2   77
  9P LOSS WILD-TYPE   13  282
                        clus
vv                       9P LOSS MUTATED 9P LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                13
  NOT HISPANIC OR LATINO              77               282
[1] 2 2
[1] FALSE

Clustering(57) Variable = 9Q LOSS MUTATION ANALYSIS
D57V1, survival
                   sevent
clus2                 0   1
  9Q LOSS MUTATED    23  11
  9Q LOSS WILD-TYPE 301  60
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               34               361 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               11                60 
$`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-DU-6397 TCGA-DU-7007 TCGA-DU-7014 TCGA-DU-7304 TCGA-DU-8162 
       11.01        46.06        62.96       117.40        23.31         3.98 
TCGA-DU-8168 TCGA-DU-A5TY TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-E1-5304 TCGA-E1-5307 
       14.17        12.20         7.23         5.98        41.13        57.93 
TCGA-EZ-7264 TCGA-HT-7471 TCGA-HT-7687 TCGA-HT-7689 TCGA-HT-7692 TCGA-HT-A5RB 
       14.33         0.13         0.10        14.96         2.96         0.10 
TCGA-HT-A614 TCGA-IK-7675 TCGA-P5-A5F6 TCGA-QH-A6CV TCGA-QH-A6CZ TCGA-S9-A6U9 
        2.70        19.00         1.28         2.96         3.16        83.70 
TCGA-S9-A7IS TCGA-TM-A84H TCGA-TM-A84J TCGA-TM-A84T 
        7.92        24.26        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-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-DU-5847 TCGA-DU-5849 
       29.62        15.75         7.79         3.85        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-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 
       49.02        75.16        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-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-7015 TCGA-DU-7018 TCGA-DU-7019 
      105.21         6.54         8.84        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-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 
       25.91        60.30        41.98         2.76         5.10        23.74 
TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-A5TP 
       20.68        21.40        19.13        16.96        15.48        14.24 
TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A6S2 
       12.59        15.12         4.96         3.65         5.65         8.65 
TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A76R 
        2.70        77.98        11.41        26.76         7.13        21.30 
TCGA-DU-A7T8 TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5305 TCGA-E1-5311 TCGA-E1-5318 
      124.50        50.14        67.46        79.99       134.27        78.21 
TCGA-E1-5319 TCGA-E1-5322 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 
       95.57       130.78        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        11.87        15.52 
TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J 
       24.46         0.59         5.26         3.72         9.67         7.04 
TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Z 
        6.64         7.04         4.21         4.08        10.59        10.78 
TCGA-FG-A710 TCGA-FG-A713 TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 
       22.95         5.23         0.13         0.10         6.67         7.82 
TCGA-HT-7470 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 
        8.81         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-7688 TCGA-HT-7690 TCGA-HT-7691 
       44.68         6.05        42.74        31.69         0.10         0.10 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 
       17.52         6.90        14.53        39.48        19.23        39.09 
TCGA-HT-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-8018 
       31.43         1.64        16.24         9.40        63.55        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-A5R9 TCGA-HT-A5RA 
       15.72         0.23        10.49         0.13         0.07        14.70 
TCGA-HT-A5RC TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HW-7486 
        5.33        13.02         1.81        16.14         5.33        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 
        8.61         8.94        19.59        17.82        10.55         7.89 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV 
        9.67         6.61        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-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-A6CY TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 
        2.20         0.59         6.31         3.91         4.73         1.91 
TCGA-QH-A6XA TCGA-QH-A6XC TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
        0.23         5.03        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        28.27        28.14        22.49 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 
       21.63        16.37        11.31        15.62        20.05         9.86 
TCGA-S9-A6U8 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG 
       94.62         5.85       103.76        62.37        72.59        70.55 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO 
       22.92        70.65        10.88         9.30         9.04         7.59 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ 
        6.15         3.39        14.27        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-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 
       18.21        13.02        10.39        87.09        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        35.93        25.32        22.59 
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 
       10.95 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             0.10              0.03 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           117.40            211.17 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           12.395            15.160 
[1] "0.1 - 117.4 (12.4)" "0.0 - 211.2 (15.2)"
[1] "hr=" "2.3"
D57V2, continuous
D57V3, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    14  20
  9Q LOSS WILD-TYPE 162 204
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     14   20
  9Q LOSS WILD-TYPE  162  204
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE              14               162
  MALE                20               204
[1] 2 2
[1] FALSE
D57V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  9Q LOSS MUTATED            12                9                13
  9Q LOSS WILD-TYPE         131               95               140
D57V5, multiclass
                   clus
vv                  9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  ASTROCYTOMA                    12               131
  OLIGOASTROCYTOMA                9                95
  OLIGODENDROGLIOMA              13               140
[1] 3 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  26
  9Q LOSS WILD-TYPE  81 285
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      8   26
  9Q LOSS WILD-TYPE   81  285
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  NO                8                81
  YES              26               285
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9Q LOSS MUTATED                                  0     1
  9Q LOSS WILD-TYPE                                1     1
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9Q LOSS MUTATED                           0    32
  9Q LOSS WILD-TYPE                        14   344
D57V7, multiclass
                                  clus
vv                                 9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 1
  BLACK OR AFRICAN AMERICAN                      0                14
  WHITE                                         32               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"
D57V8, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED     2  31
  9Q LOSS WILD-TYPE  13 328
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      2   31
  9Q LOSS WILD-TYPE   13  328
                        clus
vv                       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                13
  NOT HISPANIC OR LATINO              31               328
[1] 2 2
[1] FALSE

Clustering(58) Variable = 10P LOSS MUTATION ANALYSIS
D58V1, survival
                    sevent
clus2                  0   1
  10P LOSS MUTATED    36  30
  10P LOSS WILD-TYPE 288  41
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                66                329 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                30                 41 
$`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         0.59 
TCGA-FG-A4MW TCGA-FG-A70Z TCGA-HT-7471 TCGA-HT-7857 TCGA-HT-7860 TCGA-HT-7882 
        5.26        10.78         0.13         0.23         0.49         1.71 
TCGA-HT-8011 TCGA-HT-8104 TCGA-HT-8110 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A5RA 
       16.24        12.23         4.70        15.72         0.23        14.70 
TCGA-HT-A5RC TCGA-HT-A617 TCGA-HW-A5KK TCGA-KT-A7W1 TCGA-QH-A6CS TCGA-QH-A6CV 
        5.33        16.14         7.89         4.73         4.18         2.96 
TCGA-QH-A6XC TCGA-S9-A6TS TCGA-S9-A6U0 TCGA-S9-A6UA TCGA-S9-A6WM TCGA-S9-A7IX 
        5.03        62.17        16.37         5.85         9.30        19.63 
TCGA-S9-A7R2 TCGA-TM-A7C3 TCGA-TM-A84B TCGA-TM-A84I TCGA-TM-A84J TCGA-VM-A8CD 
       10.39        49.45        12.00        19.36        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-DH-5141 
       15.42        27.81        14.73        13.64        10.92        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        29.62        15.75         7.79 
TCGA-DH-A66G TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5853 TCGA-DU-5855 TCGA-DU-5870 
        3.85        14.56        17.46        13.38         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-6399 TCGA-DU-6400 TCGA-DU-6401 
       49.02        75.16        46.06        65.75         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-7008 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7014 TCGA-DU-7015 
      156.23       138.28        14.99       105.21       117.40        90.77 
TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7294 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 
       30.67        26.30        94.32        44.02        62.01        25.91 
TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8162 TCGA-DU-8163 
       60.30        23.31        41.98         2.76         3.98        20.68 
TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS 
       21.40        16.96        14.17        14.24        12.59        15.12 
TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
        4.96         3.65         5.65         8.65         2.70        77.98 
TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76O TCGA-DU-A7T8 TCGA-E1-5302 TCGA-E1-5303 
        7.23         5.98         7.13       124.50        50.14        67.46 
TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 
       41.13        79.99        57.93        78.21        95.57       130.78 
TCGA-EZ-7264 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6689 
       14.33        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 
       11.87        15.52        24.46         3.72         9.67         7.04 
TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A710 
        6.64         7.04         4.21         4.08        10.59        22.95 
TCGA-FG-A713 TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 
        5.23         0.13         0.10         6.67         7.82         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-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-7873 TCGA-HT-7874 TCGA-HT-7875 
       19.23        39.09        50.63        23.61        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7884 TCGA-HT-7902 
        0.13         3.68         5.33         2.93        11.28        31.43 
TCGA-HT-8010 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8105 
        1.64         9.40        63.55        21.50        33.01         6.25 
TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8111 TCGA-HT-8113 
        0.10         0.46         2.50         3.95         0.23        29.59 
TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R9 TCGA-HT-A5RB 
        3.88        16.04        10.49         0.13         0.07         0.10 
TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A618 TCGA-HW-7486 TCGA-HW-7487 
        2.70        13.02         1.81         5.33        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         8.61 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KL TCGA-HW-A5KM 
        8.94        19.59        17.82        10.55         9.67         6.61 
TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX 
       19.00        42.77         5.23         0.23         6.71         1.64 
TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F6 TCGA-QH-A65R 
        2.37         2.30         4.11         5.88         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-A6XA 
        0.59         6.31         3.91         4.73         1.91         0.23 
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 
       28.27        28.14        22.49        21.63        11.31        15.62 
TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UB TCGA-S9-A6WD 
       20.05         9.86        94.62        83.70       103.76        62.37 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN 
       72.59        70.55        22.92        70.65        10.88         9.04 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IY 
        7.59         6.15         3.39        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-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 
        4.04        18.21        13.02        87.09        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        35.93        25.32        22.59        48.39 
TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84L TCGA-TM-A84M 
       15.09        50.76        34.36        24.26        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 
       30.08        13.51         0.10        26.79        10.95 

  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 
             11.82              15.35 
[1] "0.1 - 134.3 (11.8)" "0.0 - 211.2 (15.3)"
[1] "hr=" "7.7"
D58V2, continuous
D58V3, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    32  34
  10P LOSS WILD-TYPE 144 190
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     32   34
  10P LOSS WILD-TYPE  144  190
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE               32                144
  MALE                 34                190
[1] 2 2
[1] FALSE
D58V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  10P LOSS MUTATED            39               13                14
  10P LOSS WILD-TYPE         104               91               139
D58V5, multiclass
                   clus
vv                  10P LOSS MUTATED 10P LOSS WILD-TYPE
  ASTROCYTOMA                     39                104
  OLIGOASTROCYTOMA                13                 91
  OLIGODENDROGLIOMA               14                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"
D58V6, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    12  54
  10P LOSS WILD-TYPE  77 257
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     12   54
  10P LOSS WILD-TYPE   77  257
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  NO                12                 77
  YES               54                257
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10P LOSS MUTATED                                  1     1
  10P LOSS WILD-TYPE                                0     1
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10P LOSS MUTATED                           5    58
  10P LOSS WILD-TYPE                         9   318
D58V7, multiclass
                                  clus
vv                                 10P LOSS MUTATED 10P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           1                  1
  BLACK OR AFRICAN AMERICAN                       5                  9
  WHITE                                          58                318
[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  59
  10P LOSS WILD-TYPE  13 300
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      2   59
  10P LOSS WILD-TYPE   13  300
                        clus
vv                       10P LOSS MUTATED 10P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                 13
  NOT HISPANIC OR LATINO               59                300
[1] 2 2
[1] FALSE

Clustering(59) Variable = 10Q LOSS MUTATION ANALYSIS
D59V1, survival
                    sevent
clus2                  0   1
  10Q LOSS MUTATED    42  34
  10Q LOSS WILD-TYPE 282  37
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                76                319 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                34                 37 
$`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-DU-5847 
       44.52        11.01        18.84        19.96        30.21        18.02 
TCGA-DU-5852 TCGA-DU-5854 TCGA-DU-6396 TCGA-DU-6399 TCGA-DU-6402 TCGA-DU-6403 
        6.74         8.45        75.16        65.75         7.04        11.64 
TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-7006 TCGA-DU-7008 TCGA-DU-7010 TCGA-DU-7012 
       19.89        16.83        11.47       156.23        14.99         6.54 
TCGA-DU-7013 TCGA-DU-7014 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7298 TCGA-DU-8158 
        8.84       117.40        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         0.59 
TCGA-FG-A4MW TCGA-FG-A6J3 TCGA-FG-A70Z TCGA-HT-7471 TCGA-HT-7483 TCGA-HT-7857 
        5.26        10.59        10.78         0.13       154.19         0.23 
TCGA-HT-7860 TCGA-HT-7882 TCGA-HT-8011 TCGA-HT-8104 TCGA-HT-8110 TCGA-HT-8564 
        0.49         1.71        16.24        12.23         4.70        15.72 
TCGA-HT-A4DS TCGA-HT-A5RA TCGA-HT-A5RC TCGA-HT-A617 TCGA-HW-8321 TCGA-HW-A5KK 
        0.23        14.70         5.33        16.14        19.59         7.89 
TCGA-KT-A7W1 TCGA-P5-A5EZ TCGA-QH-A6CS TCGA-QH-A6CV TCGA-QH-A6XC TCGA-S9-A6TS 
        4.73         2.30         4.18         2.96         5.03        62.17 
TCGA-S9-A6U0 TCGA-S9-A6UA TCGA-S9-A6WM TCGA-S9-A7IX TCGA-S9-A7R2 TCGA-TM-A7C3 
       16.37         5.85         9.30        19.63        10.39        49.45 
TCGA-TM-A84B TCGA-TM-A84I TCGA-TM-A84J TCGA-VM-A8CD 
       12.00        19.36        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-DH-5141 TCGA-DH-5142 
       27.81        14.73        13.64        10.92        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        29.62        15.75         7.79         3.85 
TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5853 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
       14.56        17.46        13.38         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-6397 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6404 TCGA-DU-6407 TCGA-DU-6408 
       46.06         1.22        87.45       133.74        94.52       114.08 
TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7007 TCGA-DU-7009 TCGA-DU-7011 TCGA-DU-7015 
        7.96         7.73        62.96       138.28       105.21        90.77 
TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7294 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 
       30.67        26.30        94.32        44.02        62.01        25.91 
TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8162 TCGA-DU-8163 
       60.30        23.31        41.98         2.76         3.98        20.68 
TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS 
       21.40        16.96        14.17        14.24        12.59        15.12 
TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
        4.96         3.65         5.65         8.65         2.70        77.98 
TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76O TCGA-DU-A7T8 TCGA-E1-5302 TCGA-E1-5303 
        7.23         5.98         7.13       124.50        50.14        67.46 
TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 
       41.13        79.99        57.93        78.21        95.57       130.78 
TCGA-EZ-7264 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6689 
       14.33        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 
       11.87        15.52        24.46         3.72         9.67         7.04 
TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A710 TCGA-FG-A713 
        6.64         7.04         4.21         4.08        22.95         5.23 
TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7472 
        0.13         0.10         6.67         7.82         8.81         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-7485 TCGA-HT-7601 
        7.10        75.19        59.18        60.03         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-8018 TCGA-HT-8019 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 
       63.55        21.50        33.01         6.25         0.10         0.46 
TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 
        2.50         3.95         0.23        29.59         3.88        16.04 
TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R9 TCGA-HT-A5RB TCGA-HT-A614 TCGA-HT-A615 
       10.49         0.13         0.07         0.10         2.70        13.02 
TCGA-HT-A616 TCGA-HT-A618 TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 
        1.81         5.33        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-8322 
       40.18        35.90         4.31         8.61         8.94        17.82 
TCGA-HW-A5KJ TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X 
       10.55         9.67         6.61        19.00        42.77         5.23 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5F0 TCGA-P5-A5F1 
        0.23         6.71         1.64         2.37         4.11         5.88 
TCGA-P5-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-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-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
        1.91         0.23        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        28.27        28.14        22.49        21.63 
TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
       11.31        15.62        20.05         9.86        94.62        83.70 
TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI 
      103.76        62.37        72.59        70.55        22.92        70.65 
TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ 
       10.88         9.04         7.59         6.15         3.39        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-A7QZ TCGA-S9-A7R3 
        8.12         3.58         4.04        18.21        13.02        87.09 
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        35.93        25.32 
TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H 
       22.59        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 
       10.95 

  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 
             12.33              15.16 
[1] "0.1 - 156.2 (12.3)" "0.0 - 211.2 (15.2)"
[1] "hr=" "4.7"
D59V2, continuous
D59V3, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    37  40
  10Q LOSS WILD-TYPE 139 184
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     37   40
  10Q LOSS WILD-TYPE  139  184
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE               37                139
  MALE                 40                184
[1] 2 2
[1] FALSE
D59V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  10Q LOSS MUTATED            45               15                17
  10Q LOSS WILD-TYPE          98               89               136
D59V5, multiclass
                   clus
vv                  10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  ASTROCYTOMA                     45                 98
  OLIGOASTROCYTOMA                15                 89
  OLIGODENDROGLIOMA               17                136
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V6, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    15  62
  10Q LOSS WILD-TYPE  74 249
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     15   62
  10Q LOSS WILD-TYPE   74  249
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  NO                15                 74
  YES               62                249
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10Q LOSS MUTATED                                  1     1
  10Q LOSS WILD-TYPE                                0     1
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10Q LOSS MUTATED                           5    69
  10Q LOSS WILD-TYPE                         9   307
D59V7, multiclass
                                  clus
vv                                 10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           1                  1
  BLACK OR AFRICAN AMERICAN                       5                  9
  WHITE                                          69                307
[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  70
  10Q LOSS WILD-TYPE  13 289
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      2   70
  10Q LOSS WILD-TYPE   13  289
                        clus
vv                       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                 13
  NOT HISPANIC OR LATINO               70                289
[1] 2 2
[1] FALSE

Clustering(60) Variable = 11P LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                  0   1
  11P LOSS MUTATED    36  13
  11P LOSS WILD-TYPE 288  58
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                49                346 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                13                 58 
$`11P LOSS MUTATED`
TCGA-CS-6665 TCGA-DB-5277 TCGA-DH-5140 TCGA-DH-5142 TCGA-DH-A66G TCGA-DU-6396 
       12.43        46.65        19.96        30.31         3.85        75.16 
TCGA-DU-6408 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7010 TCGA-DU-7014 
      114.08        11.47        62.96       156.23        14.99       117.40 
TCGA-DU-7015 TCGA-DU-8158 TCGA-DU-8165 TCGA-DU-A5TR TCGA-DU-A5TS TCGA-E1-5302 
       90.77         5.10        19.13        12.59        15.12        50.14 
TCGA-E1-5304 TCGA-FG-6689 TCGA-FG-A4MW TCGA-FG-A60L TCGA-HT-7470 TCGA-HT-7477 
       41.13        14.93         5.26         7.04         8.81        24.26 
TCGA-HT-7478 TCGA-HT-7601 TCGA-HT-7686 TCGA-HT-7693 TCGA-HT-7873 TCGA-HT-7902 
        6.38         5.03        42.74        17.52        23.61        31.43 
TCGA-HT-8013 TCGA-HT-8018 TCGA-HT-8111 TCGA-HT-8564 TCGA-HT-A614 TCGA-HT-A616 
       63.55        21.50         0.23        15.72         2.70         1.81 
TCGA-HT-A618 TCGA-HW-8319 TCGA-IK-7675 TCGA-P5-A5F6 TCGA-QH-A65S TCGA-S9-A6TV 
        5.33         8.61        19.00         1.28         2.53        18.77 
TCGA-S9-A6WM TCGA-S9-A7R7 TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A84I 
        9.30        83.80         5.00        49.45        35.93        19.36 
TCGA-TM-A84J 
       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-DH-5141 
       15.42        27.81        14.73        13.64        10.92        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        29.62        15.75         7.79 
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-6410 TCGA-DU-6542 TCGA-DU-7009 TCGA-DU-7011 TCGA-DU-7012 
       94.52         7.96         7.73       138.28       105.21         6.54 
TCGA-DU-7013 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 
        8.84        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-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-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-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 
      130.78        14.33        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        11.87        15.52        24.46 
TCGA-FG-A4MU TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A6IZ 
        0.59         3.72         9.67         7.04         6.64         4.21 
TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A713 TCGA-FN-7833 
        4.08        10.59        10.78        22.95         5.23         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-7479 TCGA-HT-7480 TCGA-HT-7481 
        3.75        17.42         6.54         7.10        75.19        59.18 
TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 
       60.03       154.19         4.01        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-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 
        0.10         2.96         6.90        14.53        39.48        19.23 
TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7874 TCGA-HT-7875 
       39.09         0.23        50.63         0.49        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 
        0.13         3.68         5.33         2.93         1.71        11.28 
TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 
        1.64        16.24         9.40        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-A4DS TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R9 
        3.88        16.04         0.23        10.49         0.13         0.07 
TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A615 TCGA-HT-A617 TCGA-HW-7486 
       14.70         0.10         5.33        13.02        16.14        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 
        8.94        19.59        17.82        10.55         7.89         9.67 
TCGA-HW-A5KM TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW 
        6.61        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-QH-A65R 
        1.64         2.37         2.30         4.11         5.88         5.75 
TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CV TCGA-QH-A6CY 
        4.83         7.79         4.11         4.18         2.96         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-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
        0.23         5.03        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        28.27        28.14        22.49        21.63 
TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       16.37        11.31        15.62        20.05         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       103.76        62.37        72.59        70.55 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP 
       22.92        70.65        10.88         9.04         7.59         6.15 
TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ 
        3.39        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-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R8 
       18.21        13.02        10.39        87.09        17.42        31.59 
TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F 
       25.32        22.59        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 
        0.10         7.89        26.79        10.95 

  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 
            17.520             14.545 
[1] "0.2 - 156.2 (17.5)" "0.0 - 211.2 (14.5)"
[1] "hr=" "1.3"
D60V2, continuous
D60V3, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    25  24
  11P LOSS WILD-TYPE 151 200
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     25   24
  11P LOSS WILD-TYPE  151  200
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE               25                151
  MALE                 24                200
[1] 2 2
[1] FALSE
D60V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  11P LOSS MUTATED            25               12                12
  11P LOSS WILD-TYPE         118               92               141
D60V5, multiclass
                   clus
vv                  11P LOSS MUTATED 11P LOSS WILD-TYPE
  ASTROCYTOMA                     25                118
  OLIGOASTROCYTOMA                12                 92
  OLIGODENDROGLIOMA               12                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"
D60V6, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    13  36
  11P LOSS WILD-TYPE  76 275
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     13   36
  11P LOSS WILD-TYPE   76  275
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  NO                13                 76
  YES               36                275
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11P LOSS MUTATED                                  0     0
  11P LOSS WILD-TYPE                                1     2
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11P LOSS MUTATED                           1    48
  11P LOSS WILD-TYPE                        13   328
D60V7, multiclass
                                  clus
vv                                 11P LOSS MUTATED 11P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  2
  BLACK OR AFRICAN AMERICAN                       1                 13
  WHITE                                          48                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"
D60V8, binary
                    cls
clus                   0   1
  11P LOSS MUTATED     2  47
  11P LOSS WILD-TYPE  13 312
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      2   47
  11P LOSS WILD-TYPE   13  312
                        clus
vv                       11P LOSS MUTATED 11P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                 13
  NOT HISPANIC OR LATINO               47                312
[1] 2 2
[1] FALSE

Clustering(61) Variable = 11Q LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                  0   1
  11Q LOSS MUTATED    12   5
  11Q LOSS WILD-TYPE 312  66
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                17                378 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 5                 66 
$`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-A614 
        5.26        24.26        21.50         0.23        15.72         2.70 
TCGA-P5-A5F6 TCGA-S9-A6TV TCGA-S9-A6WM TCGA-TM-A7C3 TCGA-TM-A84I 
        1.28        18.77         9.30        49.45        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-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       10.92        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DU-5847 TCGA-DU-5849 
       29.62        15.75         7.79         3.85        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-6399 TCGA-DU-6400 TCGA-DU-6401 
       49.02        75.16        46.06        65.75         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-7007 TCGA-DU-7008 TCGA-DU-7009 
      114.08         7.96         7.73        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-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-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-FG-5962 TCGA-FG-5963 TCGA-FG-5964 
       95.57       130.78        14.33        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        11.87 
TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J 
       15.52        24.46         0.59         3.72         9.67         7.04 
TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Z 
        6.64         7.04         4.21         4.08        10.59        10.78 
TCGA-FG-A710 TCGA-FG-A713 TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 
       22.95         5.23         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-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-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 
        9.40        63.55        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-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         8.61         8.94        19.59        17.82        10.55 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X 
        7.89         9.67         6.61        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-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X 
        4.11         5.88         5.75         2.53         4.83         7.79 
TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CV TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
        4.11         4.18         2.96         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-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 
       28.27        28.14        22.49        21.63        16.37        11.31 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA 
       15.62        20.05         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 
      103.76        62.37        72.59        70.55        22.92        70.65 
TCGA-S9-A6WL TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ 
       10.88         9.04         7.59         6.15         3.39        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        18.21        13.02 
TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89Z 
       10.39        87.09        17.42        83.80        31.59         5.00 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
       35.93        25.32        22.59        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 

  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 
            15.720             14.945 
[1] "0.2 - 49.5 (15.7)"  "0.0 - 211.2 (14.9)"
[1] "hr=" "3.1"
D61V2, continuous
D61V3, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED     8   9
  11Q LOSS WILD-TYPE 168 215
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      8    9
  11Q LOSS WILD-TYPE  168  215
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE                8                168
  MALE                  9                215
[1] 2 2
[1] FALSE
D61V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  11Q LOSS MUTATED             9                6                 2
  11Q LOSS WILD-TYPE         134               98               151
D61V5, multiclass
                   clus
vv                  11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  ASTROCYTOMA                      9                134
  OLIGOASTROCYTOMA                 6                 98
  OLIGODENDROGLIOMA                2                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"
D61V6, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED     2  15
  11Q LOSS WILD-TYPE  87 296
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      2   15
  11Q LOSS WILD-TYPE   87  296
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  NO                 2                 87
  YES               15                296
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11Q LOSS MUTATED                                  0     0
  11Q LOSS WILD-TYPE                                1     2
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11Q LOSS MUTATED                           0    17
  11Q LOSS WILD-TYPE                        14   359
D61V7, multiclass
                                  clus
vv                                 11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  2
  BLACK OR AFRICAN AMERICAN                       0                 14
  WHITE                                          17                359
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V8, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED     1  16
  11Q LOSS WILD-TYPE  14 343
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      1   16
  11Q LOSS WILD-TYPE   14  343
                        clus
vv                       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 14
  NOT HISPANIC OR LATINO               16                343
[1] 2 2
[1] FALSE

Clustering(62) Variable = 12P LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                  0   1
  12P LOSS MUTATED    15   2
  12P LOSS WILD-TYPE 309  69
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                17                378 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 2                 69 
$`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-P5-A5EW TCGA-S9-A6U1 TCGA-S9-A7R4 
        0.10         2.50         6.71        11.31        17.42 

$`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-DH-5140 TCGA-DH-5141 
       27.81        14.73        13.64        10.92        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        29.62        15.75 
TCGA-DH-A66F TCGA-DH-A66G TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
        7.79         3.85        18.02        14.56        17.46         6.74 
TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5872 TCGA-DU-5874 
       13.38         8.45         6.81       182.33        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-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-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-A6S7 TCGA-DU-A6S8 
        5.65        12.20         8.65         2.70         7.23         5.98 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A7T8 TCGA-E1-5303 TCGA-E1-5304 
       11.41        26.76         7.13       124.50        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-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 
       14.33        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        11.87        15.52        24.46 
TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K 
        0.59         5.26         3.72         9.67         7.04         6.64 
TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A713 
        7.04         4.21         4.08        10.78        22.95         5.23 
TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7471 TCGA-HT-7472 
        0.13         0.10         6.67         7.82         0.13         0.03 
TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7479 
       16.54         3.75        17.42         6.54        24.26         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-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-8018 TCGA-HT-8019 
        1.64        16.24         9.40        63.55        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-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-7493 TCGA-HW-7495 TCGA-HW-8319 
        8.32        19.23        40.18        35.90         4.31         8.61 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
        8.94        19.59        17.82        10.55         7.89         9.67 
TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV 
        6.61        19.00        42.77         5.23         4.73         0.23 
TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F6 
        1.64         2.37         2.30         4.11         5.88         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-A6CV TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 
        2.96         2.20         3.16         0.59         6.31         3.91 
TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-R8-A6MK TCGA-R8-A6ML 
        4.73         1.91         0.23         5.03        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        28.27 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U2 TCGA-S9-A6U5 
       28.14        22.49        21.63        16.37        15.62        20.05 
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       103.76        62.37 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM 
       72.59        70.55        22.92        70.65        10.88         9.30 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
        9.04         7.59         6.15         3.39        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-A7R2 
        8.12         3.58         4.04        18.21        13.02        10.39 
TCGA-S9-A7R3 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 
       87.09        83.80        31.59         5.00        49.45        35.93 
TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F 
       25.32        22.59        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 

  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 
             12.43              15.04 
[1] "0.1 - 78.0 (12.4)"  "0.0 - 211.2 (15.0)"
[1] "hr=" "1.1"
D62V2, continuous
D62V3, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     9   9
  12P LOSS WILD-TYPE 167 215
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      9    9
  12P LOSS WILD-TYPE  167  215
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE                9                167
  MALE                  9                215
[1] 2 2
[1] FALSE
D62V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  12P LOSS MUTATED            10                4                 4
  12P LOSS WILD-TYPE         133              100               149
D62V5, multiclass
                   clus
vv                  12P LOSS MUTATED 12P LOSS WILD-TYPE
  ASTROCYTOMA                     10                133
  OLIGOASTROCYTOMA                 4                100
  OLIGODENDROGLIOMA                4                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"
D62V6, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     5  13
  12P LOSS WILD-TYPE  84 298
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      5   13
  12P LOSS WILD-TYPE   84  298
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  NO                 5                 84
  YES               13                298
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12P LOSS MUTATED                                  0     0
  12P LOSS WILD-TYPE                                1     2
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12P LOSS MUTATED                           0    17
  12P LOSS WILD-TYPE                        14   359
D62V7, multiclass
                                  clus
vv                                 12P LOSS MUTATED 12P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  2
  BLACK OR AFRICAN AMERICAN                       0                 14
  WHITE                                          17                359
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V8, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     0  17
  12P LOSS WILD-TYPE  15 342
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      0   17
  12P LOSS WILD-TYPE   15  342
                        clus
vv                       12P LOSS MUTATED 12P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 15
  NOT HISPANIC OR LATINO               17                342
[1] 2 2
[1] FALSE

Clustering(63) Variable = 12Q LOSS MUTATION ANALYSIS
D63V1, survival
                    sevent
clus2                  0   1
  12Q LOSS MUTATED    32   4
  12Q LOSS WILD-TYPE 292  67
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                36                359 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 4                 67 
$`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        29.62 
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-A618 TCGA-P5-A5EW TCGA-P5-A5EZ TCGA-S9-A6TV TCGA-S9-A6U1 
        2.50         5.33         6.71         2.30        18.77        11.31 
TCGA-S9-A6WQ TCGA-S9-A7QX TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-TM-A84I TCGA-VM-A8C8 
        3.39         4.04        17.42        83.80        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-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 
       13.64        10.92        19.96        31.82        30.31        14.40 
TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DU-5847 
        8.02        30.21        15.75         7.79         3.85        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-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 
      182.33        17.49        15.16       211.17        52.11        22.42 
TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6402 
       49.02        75.16        46.06        65.75         1.22         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-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 
        7.96        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-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT 
       16.96        14.17        14.24        12.59        15.12         4.96 
TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S7 TCGA-DU-A6S8 
        5.65        12.20         8.65         2.70         7.23         5.98 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A7T8 TCGA-E1-5303 TCGA-E1-5304 
       11.41        26.76         7.13       124.50        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-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 
       14.33        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        11.87        15.52        24.46         0.59 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
        5.26         3.72         9.67         7.04         6.64         7.04 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A713 
        4.21         4.08        10.59        10.78        22.95         5.23 
TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7471 TCGA-HT-7472 
        0.13         0.10         6.67         7.82         0.13         0.03 
TCGA-HT-7473 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7479 TCGA-HT-7480 
       16.54        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-7689 
       16.24         0.76        44.68         6.05         0.10        14.96 
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-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 
        1.71        11.28         1.64        16.24         9.40        63.55 
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-HW-7486 TCGA-HW-7487 
        2.70        13.02         1.81        16.14        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         8.61 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
        8.94        19.59        17.82        10.55         7.89         9.67 
TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV 
        6.61        19.00        42.77         5.23         4.73         0.23 
TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F6 TCGA-QH-A65R 
        1.64         2.37         4.11         5.88         1.28         5.75 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CV 
        2.53         4.83         7.79         4.11         4.18         2.96 
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-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO 
        1.91         0.23         5.03        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        28.27        28.14        22.49 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       21.63        16.37        15.62        20.05         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       103.76        62.37        72.59        70.55 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO 
       22.92        70.65        10.88         9.30         9.04         7.59 
TCGA-S9-A6WP TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY TCGA-S9-A7IZ 
        6.15        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        18.21 
TCGA-S9-A7QZ TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R8 TCGA-S9-A89Z TCGA-TM-A7C3 
       13.02        10.39        87.09        31.59         5.00        49.45 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
       35.93        25.32        22.59        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-A8C9 
       29.92        18.90         9.44         4.57        12.00        30.08 
TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH 
       13.51         0.10         7.89        26.79        10.95 

  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 
             16.45              14.96 
[1] "0.1 - 87.5 (16.5)"  "0.0 - 211.2 (15.0)"
[1] "hr=" "1.4"
D63V2, continuous
D63V3, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    17  20
  12Q LOSS WILD-TYPE 159 204
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     17   20
  12Q LOSS WILD-TYPE  159  204
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FEMALE               17                159
  MALE                 20                204
[1] 2 2
[1] FALSE
D63V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  12Q LOSS MUTATED            18               12                 7
  12Q LOSS WILD-TYPE         125               92               146
D63V5, multiclass
                   clus
vv                  12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  ASTROCYTOMA                     18                125
  OLIGOASTROCYTOMA                12                 92
  OLIGODENDROGLIOMA                7                146
[1] 3 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  27
  12Q LOSS WILD-TYPE  79 284
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     10   27
  12Q LOSS WILD-TYPE   79  284
     clus
vv    12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  NO                10                 79
  YES               27                284
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12Q LOSS MUTATED                                  0     0
  12Q LOSS WILD-TYPE                                1     2
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12Q LOSS MUTATED                           0    36
  12Q LOSS WILD-TYPE                        14   340
D63V7, multiclass
                                  clus
vv                                 12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  2
  BLACK OR AFRICAN AMERICAN                       0                 14
  WHITE                                          36                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"
D63V8, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     0  35
  12Q LOSS WILD-TYPE  15 324
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      0   35
  12Q LOSS WILD-TYPE   15  324
                        clus
vv                       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 15
  NOT HISPANIC OR LATINO               35                324
[1] 2 2
[1] FALSE

Clustering(64) Variable = 13Q LOSS MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                  0   1
  13Q LOSS MUTATED    69  24
  13Q LOSS WILD-TYPE 255  47
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                93                302 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                24                 47 
$`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-DU-5847 TCGA-DU-5853 TCGA-DU-6392 TCGA-DU-6399 
       15.75         7.79        18.02        13.38       211.17        65.75 
TCGA-DU-6400 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-7006 TCGA-DU-7008 TCGA-DU-7010 
        1.22        94.52       114.08        11.47       156.23        14.99 
TCGA-DU-7290 TCGA-DU-7299 TCGA-DU-7301 TCGA-DU-8158 TCGA-DU-8165 TCGA-DU-8167 
       10.36        44.02        25.91         5.10        19.13        15.48 
TCGA-DU-8168 TCGA-DU-A5TS TCGA-DU-A6S3 TCGA-DU-A6S7 TCGA-DU-A76R TCGA-DU-A7T8 
       14.17        15.12         2.70         7.23        21.30       124.50 
TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5307 TCGA-E1-5322 TCGA-FG-5962 
       50.14        67.46        41.13        57.93       130.78        47.77 
TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-6689 TCGA-FG-6692 TCGA-FG-7641 TCGA-FG-8188 
       17.98        34.36        14.93        13.58        20.61        14.96 
TCGA-FG-A60J TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J3 TCGA-FG-A70Z TCGA-HT-7469 
        7.04         7.04         4.21        10.59        10.78         7.82 
TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7482 TCGA-HT-7483 
        8.81         0.13         6.54        24.26        60.03       154.19 
TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 
      107.93         4.57        17.29        31.69        14.96         0.10 
TCGA-HT-7692 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7902 TCGA-HT-8106 TCGA-HT-8564 
        2.96        39.09         0.23        31.43         0.10        15.72 
TCGA-HT-A617 TCGA-HW-7489 TCGA-HW-7491 TCGA-KT-A74X TCGA-P5-A5EZ TCGA-QH-A65Z 
       16.14         8.32        40.18         5.23         2.30         4.11 
TCGA-QH-A6CV TCGA-QH-A6CY TCGA-QH-A6X8 TCGA-S9-A6UA TCGA-S9-A7IX TCGA-S9-A7IY 
        2.96         2.20         4.73         5.85        19.63        12.59 
TCGA-S9-A7J0 TCGA-S9-A7J3 TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A84F TCGA-TM-A84I 
        9.37         8.12         5.00        49.45        50.76        19.36 
TCGA-TM-A84R TCGA-TM-A84S TCGA-VM-A8CD 
        9.44         4.57         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-DH-5141 TCGA-DH-5143 
       15.42        27.81        14.73        13.64        31.82        14.40 
TCGA-DH-5144 TCGA-DH-A66B TCGA-DH-A66G TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
        8.02        29.62         3.85        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-6393 TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6401 
       52.11        22.42        49.02        75.16        46.06        87.45 
TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6410 
        7.04        11.64       133.74        19.89        16.83         7.96 
TCGA-DU-6542 TCGA-DU-7007 TCGA-DU-7009 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 
        7.73        62.96       138.28       105.21         6.54         8.84 
TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7292 TCGA-DU-7294 
      117.40        90.77        30.67        26.30         7.96        94.32 
TCGA-DU-7298 TCGA-DU-7300 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 
       18.94        62.01        60.30        23.31        41.98         2.76 
TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-A5TP 
       23.74         3.98        20.68        21.40        16.96        14.24 
TCGA-DU-A5TR TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 
       12.59         4.96         3.65         5.65        12.20         8.65 
TCGA-DU-A6S6 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A76O TCGA-E1-5305 
       77.98         5.98        11.41        26.76         7.13        79.99 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-EZ-7264 TCGA-FG-5965 TCGA-FG-6688 
      134.27        78.21        95.57        14.33        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        11.87 
TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY 
       15.52        24.46         0.59         5.26         3.72         9.67 
TCGA-FG-A60K TCGA-FG-A6J1 TCGA-FG-A710 TCGA-FG-A713 TCGA-FN-7833 TCGA-HT-7467 
        6.64         4.08        22.95         5.23         0.13         0.10 
TCGA-HT-7468 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7478 
        6.67         0.03        16.54         3.75        17.42         6.38 
TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 
        7.10        75.19        59.18         4.01         5.03        29.85 
TCGA-HT-7603 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7611 
       23.18         3.16        22.06        45.99        56.09        57.60 
TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 
        0.23        14.27         0.16        16.24         0.76        44.68 
TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7691 TCGA-HT-7693 TCGA-HT-7694 
        6.05        42.74         0.10         0.10        17.52         6.90 
TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 
       14.53        39.48        19.23        50.63         0.49        23.61 
TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 
       37.15         0.33         0.13         3.68         5.33         2.93 
TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 
        1.71        11.28         1.64        16.24         9.40        63.55 
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-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB 
        0.23        10.49         0.13         0.07        14.70         0.10 
TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A618 TCGA-HW-7486 
        5.33         2.70        13.02         1.81         5.33        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         8.61         8.94 
TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM 
       19.59        17.82        10.55         7.89         9.67         6.61 
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-A5F6 TCGA-QH-A65R TCGA-QH-A65S 
        2.37         4.11         5.88         1.28         5.75         2.53 
TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A6CS TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
        4.83         7.79         4.18         3.16         0.59         6.31 
TCGA-QH-A6X5 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-R8-A6MK TCGA-R8-A6ML 
        3.91         1.91         0.23         5.03        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        28.27 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 
       28.14        22.49        21.63        16.37        11.31        15.62 
TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UB TCGA-S9-A6WD 
       20.05         9.86        94.62        83.70       103.76        62.37 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM 
       72.59        70.55        22.92        70.65        10.88         9.30 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
        9.04         7.59         6.15         3.39        14.27         7.92 
TCGA-S9-A7IZ TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7QY 
        4.21         8.19         2.04         3.58         4.04        18.21 
TCGA-S9-A7QZ TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 
       13.02        10.39        87.09        17.42        83.80        31.59 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
       35.93        25.32        22.59        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 
       26.79        10.95 

  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 
            14.990             14.715 
[1] "0.1 - 211.2 (15.0)" "0.0 - 182.3 (14.7)"
[1] "hr=" "1.4"
D64V2, continuous
D64V3, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    34  60
  13Q LOSS WILD-TYPE 142 164
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     34   60
  13Q LOSS WILD-TYPE  142  164
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE               34                142
  MALE                 60                164
[1] 2 2
[1] FALSE
D64V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  13Q LOSS MUTATED            38               22                34
  13Q LOSS WILD-TYPE         105               82               119
D64V5, multiclass
                   clus
vv                  13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  ASTROCYTOMA                     38                105
  OLIGOASTROCYTOMA                22                 82
  OLIGODENDROGLIOMA               34                119
[1] 3 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  65
  13Q LOSS WILD-TYPE  60 246
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     29   65
  13Q LOSS WILD-TYPE   60  246
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  NO                29                 60
  YES               65                246
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  13Q LOSS MUTATED                                  1     1
  13Q LOSS WILD-TYPE                                0     1
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  13Q LOSS MUTATED                           3    88
  13Q LOSS WILD-TYPE                        11   288
D64V7, multiclass
                                  clus
vv                                 13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           1                  1
  BLACK OR AFRICAN AMERICAN                       3                 11
  WHITE                                          88                288
[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  87
  13Q LOSS WILD-TYPE  13 272
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      2   87
  13Q LOSS WILD-TYPE   13  272
                        clus
vv                       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                 13
  NOT HISPANIC OR LATINO               87                272
[1] 2 2
[1] FALSE

Clustering(65) Variable = 14Q LOSS MUTATION ANALYSIS
D65V1, survival
                    sevent
clus2                  0   1
  14Q LOSS MUTATED    40  21
  14Q LOSS WILD-TYPE 284  50
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                61                334 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                21                 50 
$`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         2.96         3.16        62.17         9.30        19.63 
TCGA-S9-A7QZ TCGA-S9-A7R2 TCGA-S9-A7R8 TCGA-TM-A7C3 TCGA-TM-A84I TCGA-VM-A8CB 
       13.02        10.39        31.59        49.45        19.36         0.10 
TCGA-VM-A8CD 
        7.89 

$`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-DH-5141 
       15.42        27.81        14.73        13.64        10.92        31.82 
TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G 
        8.02        30.21        29.62        15.75         7.79         3.85 
TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 
       14.56        17.46        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-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6403 
       49.02        75.16         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-7006 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7011 TCGA-DU-7013 TCGA-DU-7014 
       11.47       156.23       138.28       105.21         8.84       117.40 
TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 
       90.77        30.67        26.30         7.96        94.32        18.94 
TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 
       44.02        62.01        25.91        23.31        41.98         2.76 
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-A76K 
       12.20         8.65         2.70        77.98         7.23        11.41 
TCGA-DU-A76O TCGA-DU-A7T8 TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5307 
        7.13       124.50        50.14        67.46        41.13        57.93 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 
      134.27        78.21        95.57        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-A4MT 
       14.24        16.01        20.09        14.96        11.87        24.46 
TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K 
        0.59         5.26         3.72         9.67         7.04         6.64 
TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A713 
        7.04         4.21         4.08        10.78        22.95         5.23 
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-7620 
        3.16        22.06        45.99        56.09        57.60        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 
        0.16        16.24         0.76        44.68         6.05        42.74 
TCGA-HT-7687 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 
        0.10         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-8010 TCGA-HT-8011 
        5.33         2.93         1.71        11.28         1.64        16.24 
TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 
        9.40        63.55        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-A5R9 TCGA-HT-A5RA 
        3.88        16.04        10.49         0.13         0.07        14.70 
TCGA-HT-A5RB TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HW-7486 
        0.10         5.33         2.70        13.02         1.81        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         8.61 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KL TCGA-HW-A5KM 
        8.94        19.59        17.82        10.55         9.67         6.61 
TCGA-IK-7675 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EY 
       19.00         5.23         4.73         0.23         6.71         2.37 
TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F6 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V 
        4.11         5.88         1.28         5.75         2.53         4.83 
TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CY TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 
        7.79         4.11         2.20         0.59         6.31         3.91 
TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-R8-A6MK TCGA-R8-A6ML 
        4.73         1.91         0.23         5.03        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        28.27        28.14 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       22.49        21.63        16.37        11.31        15.62        20.05 
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       103.76        62.37 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WN 
       72.59        70.55        22.92        70.65        10.88         9.04 
TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IY 
        7.59         6.15         3.39        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-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A89Z 
        4.04        18.21        87.09        17.42        83.80         5.00 
TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C 
       35.93        25.32        22.59        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-A8CE TCGA-VM-A8CH 
       30.08        13.51        26.79        10.95 

  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 
            14.960             15.025 
[1] "0.1 - 130.8 (15.0)" "0.0 - 211.2 (15.0)"
[1] "hr=" "3"  
D65V2, continuous
D65V3, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    28  35
  14Q LOSS WILD-TYPE 148 189
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     28   35
  14Q LOSS WILD-TYPE  148  189
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE               28                148
  MALE                 35                189
[1] 2 2
[1] FALSE
D65V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  14Q LOSS MUTATED            29               15                19
  14Q LOSS WILD-TYPE         114               89               134
D65V5, multiclass
                   clus
vv                  14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  ASTROCYTOMA                     29                114
  OLIGOASTROCYTOMA                15                 89
  OLIGODENDROGLIOMA               19                134
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V6, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    11  52
  14Q LOSS WILD-TYPE  78 259
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     11   52
  14Q LOSS WILD-TYPE   78  259
     clus
vv    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  NO                11                 78
  YES               52                259
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  14Q LOSS MUTATED                                  1     1
  14Q LOSS WILD-TYPE                                0     1
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  14Q LOSS MUTATED                           2    57
  14Q LOSS WILD-TYPE                        12   319
D65V7, multiclass
                                  clus
vv                                 14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           1                  1
  BLACK OR AFRICAN AMERICAN                       2                 12
  WHITE                                          57                319
[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  56
  14Q LOSS WILD-TYPE  14 303
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      1   56
  14Q LOSS WILD-TYPE   14  303
                        clus
vv                       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 14
  NOT HISPANIC OR LATINO               56                303
[1] 2 2
[1] FALSE

Clustering(66) Variable = 15Q LOSS MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                  0   1
  15Q LOSS MUTATED    25  10
  15Q LOSS WILD-TYPE 299  61
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                35                360 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                10                 61 
$`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-DU-6393 TCGA-DU-6400 TCGA-DU-7007 TCGA-DU-8158 TCGA-DU-A6S3 
       30.21        52.11         1.22        62.96         5.10         2.70 
TCGA-DU-A76R TCGA-E1-5311 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-A4MW TCGA-FG-A6J3 
       21.30       134.27        15.35        17.88         5.26        10.59 
TCGA-HT-7468 TCGA-HT-7480 TCGA-HT-7606 TCGA-HT-7609 TCGA-HT-7616 TCGA-HT-8012 
        6.67        75.19        17.29        45.99         0.23         9.40 
TCGA-HT-A618 TCGA-P5-A5EZ TCGA-QH-A65S TCGA-QH-A6X8 TCGA-S9-A6TS TCGA-S9-A6U2 
        5.33         2.30         2.53         4.73        62.17        15.62 
TCGA-S9-A6WD TCGA-S9-A6WI TCGA-S9-A7QZ TCGA-S9-A89Z TCGA-TM-A7C5 
       62.37        70.65        13.02         5.00        25.32 

$`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-DH-5141 TCGA-DH-5143 TCGA-DH-5144 
       14.73        13.64        10.92        31.82        14.40         8.02 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DU-5847 TCGA-DU-5849 
       29.62        15.75         7.79         3.85        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-6394 TCGA-DU-6395 
       18.94        17.49        15.16       211.17        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-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-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-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 
        5.65        12.20         8.65        77.98         7.23         5.98 
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-E1-5318 TCGA-E1-5319 TCGA-E1-5322 
       41.13        79.99        57.93        78.21        95.57       130.78 
TCGA-EZ-7264 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 
       14.33        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        11.87        15.52        24.46         0.59         3.72 
TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 
        9.67         7.04         6.64         7.04         4.21         4.08 
TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A713 TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7469 
       10.78        22.95         5.23         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-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-7607 TCGA-HT-7608 TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7620 
        4.57         3.16        22.06        56.09        57.60        14.27 
TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 
        0.16        16.24         0.76        44.68         6.05        42.74 
TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 
        0.10        31.69        14.96         0.10         0.10         2.96 
TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 
       17.52         6.90        14.53        39.48        19.23        39.09 
TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 
        0.23        50.63         0.49        23.61        37.15         0.33 
TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 
        0.13         3.68         5.33         2.93         1.71        11.28 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8013 TCGA-HT-8018 TCGA-HT-8019 
       31.43         1.64        16.24        63.55        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-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB 
        0.23        10.49         0.13         0.07        14.70         0.10 
TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HW-7486 
        5.33         2.70        13.02         1.81        16.14        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 
        8.61         8.94        19.59        17.82        10.55         7.89 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 
        9.67         6.61        19.00        42.77         5.23         4.73 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5F0 TCGA-P5-A5F1 
        0.23         6.71         1.64         2.37         4.11         5.88 
TCGA-P5-A5F6 TCGA-QH-A65R TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS 
        1.28         5.75         4.83         7.79         4.11         4.18 
TCGA-QH-A6CV TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 
        2.96         2.20         3.16         0.59         6.31         3.91 
TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO 
        1.91         0.23         5.03        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        28.27        28.14        22.49 
TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       21.63        16.37        11.31        20.05         9.86        94.62 
TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH 
       83.70         5.85       103.76        72.59        70.55        22.92 
TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ 
       10.88         9.30         9.04         7.59         6.15         3.39 
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        18.21 
TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-TM-A7C3 
       10.39        87.09        17.42        83.80        31.59        49.45 
TCGA-TM-A7C4 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F 
       35.93        22.59        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 

  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 
            15.620             14.945 
[1] "0.2 - 134.3 (15.6)" "0.0 - 211.2 (14.9)"
[1] "hr=" "1.5"
D66V2, continuous
D66V3, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED    14  22
  15Q LOSS WILD-TYPE 162 202
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     14   22
  15Q LOSS WILD-TYPE  162  202
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE               14                162
  MALE                 22                202
[1] 2 2
[1] FALSE
D66V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  15Q LOSS MUTATED            11                9                16
  15Q LOSS WILD-TYPE         132               95               137
D66V5, multiclass
                   clus
vv                  15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  ASTROCYTOMA                     11                132
  OLIGOASTROCYTOMA                 9                 95
  OLIGODENDROGLIOMA               16                137
[1] 3 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  28
  15Q LOSS WILD-TYPE  81 283
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      8   28
  15Q LOSS WILD-TYPE   81  283
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  NO                 8                 81
  YES               28                283
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  15Q LOSS MUTATED                                  0     0
  15Q LOSS WILD-TYPE                                1     2
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  15Q LOSS MUTATED                           0    35
  15Q LOSS WILD-TYPE                        14   341
D66V7, multiclass
                                  clus
vv                                 15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  2
  BLACK OR AFRICAN AMERICAN                       0                 14
  WHITE                                          35                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"
D66V8, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     0  35
  15Q LOSS WILD-TYPE  15 324
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      0   35
  15Q LOSS WILD-TYPE   15  324
                        clus
vv                       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 15
  NOT HISPANIC OR LATINO               35                324
[1] 2 2
[1] FALSE

Clustering(67) Variable = 16P LOSS MUTATION ANALYSIS
D67V1, survival
                    sevent
clus2                  0   1
  16P LOSS MUTATED     6   4
  16P LOSS WILD-TYPE 318  67
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                10                385 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 4                 67 
$`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 
        5.26        24.26        15.72        19.63 

$`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-DH-5140 
       15.42        27.81        14.73        13.64        10.92        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        29.62        15.75 
TCGA-DH-A66F TCGA-DH-A66G TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 
        7.79         3.85        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-7019 
      105.21         6.54         8.84       117.40        90.77        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-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-FG-5962 TCGA-FG-5963 TCGA-FG-5964 
       95.57       130.78        14.33        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        11.87 
TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J 
       15.52        24.46         0.59         3.72         9.67         7.04 
TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Z 
        6.64         7.04         4.21         4.08        10.59        10.78 
TCGA-FG-A710 TCGA-FG-A713 TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 
       22.95         5.23         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-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-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 
        9.40        63.55        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-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-HW-7486 TCGA-HW-7487 TCGA-HW-7489 
        1.81        16.14         5.33        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         8.61         8.94 
TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM 
       19.59        17.82        10.55         7.89         9.67         6.61 
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-A5F6 
        1.64         2.37         2.30         4.11         5.88         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-A6CV TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 
        2.96         2.20         3.16         0.59         6.31         3.91 
TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-R8-A6MK TCGA-R8-A6ML 
        4.73         1.91         0.23         5.03        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        28.27 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 
       28.14        22.49        21.63        16.37        11.31        15.62 
TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB 
       20.05         9.86        94.62        83.70         5.85       103.76 
TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL 
       62.37        72.59        70.55        22.92        70.65        10.88 
TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ 
        9.30         9.04         7.59         6.15         3.39        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-A7QZ TCGA-S9-A7R2 
        8.12         3.58         4.04        18.21        13.02        10.39 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89Z TCGA-TM-A7C3 
       87.09        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 
       35.93        25.32        22.59        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 
       10.95 

  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 
            27.235             14.700 
[1] "5.3 - 78.3 (27.2)"  "0.0 - 211.2 (14.7)"
[1] "hr=" "1.9"
D67V2, continuous
D67V3, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     3   7
  16P LOSS WILD-TYPE 173 217
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      3    7
  16P LOSS WILD-TYPE  173  217
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE                3                173
  MALE                  7                217
[1] 2 2
[1] FALSE
D67V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  16P LOSS MUTATED             5                2                 3
  16P LOSS WILD-TYPE         138              102               150
D67V5, multiclass
                   clus
vv                  16P LOSS MUTATED 16P LOSS WILD-TYPE
  ASTROCYTOMA                      5                138
  OLIGOASTROCYTOMA                 2                102
  OLIGODENDROGLIOMA                3                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"
D67V6, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     2   8
  16P LOSS WILD-TYPE  87 303
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      2    8
  16P LOSS WILD-TYPE   87  303
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  NO                 2                 87
  YES                8                303
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16P LOSS MUTATED                                  0     0
  16P LOSS WILD-TYPE                                1     2
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16P LOSS MUTATED                           0    10
  16P LOSS WILD-TYPE                        14   366
D67V7, multiclass
                                  clus
vv                                 16P LOSS MUTATED 16P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  2
  BLACK OR AFRICAN AMERICAN                       0                 14
  WHITE                                          10                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"
D67V8, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     1   9
  16P LOSS WILD-TYPE  14 350
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      1    9
  16P LOSS WILD-TYPE   14  350
                        clus
vv                       16P LOSS MUTATED 16P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 14
  NOT HISPANIC OR LATINO                9                350
[1] 2 2
[1] FALSE

Clustering(68) Variable = 16Q LOSS MUTATION ANALYSIS
D68V1, survival
                    sevent
clus2                  0   1
  16Q LOSS MUTATED    11   7
  16Q LOSS WILD-TYPE 313  64
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                18                377 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 7                 64 
$`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-A89Z 
       15.72         0.23        83.70        22.92        19.63         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-DH-5140 
       15.42        27.81        14.73        13.64        10.92        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        29.62        15.75 
TCGA-DH-A66F TCGA-DH-A66G TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 
        7.79         3.85        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-7013 TCGA-DU-7015 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 
        8.84        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-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-8166 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS 
       21.40        16.96        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-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 
       21.30       124.50        50.14        67.46        41.13        79.99 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 TCGA-FG-5962 
      134.27        78.21        95.57       130.78        14.33        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-A4MX 
       14.96        11.87        15.52        24.46         0.59         3.72 
TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 
        9.67         7.04         6.64         7.04         4.21         4.08 
TCGA-FG-A6J3 TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A713 TCGA-FN-7833 TCGA-HT-7467 
       10.59        10.78        22.95         5.23         0.13         0.10 
TCGA-HT-7468 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 
        6.67         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-8018 TCGA-HT-8019 
        1.64        16.24         9.40        63.55        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-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-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-7493 TCGA-HW-7495 TCGA-HW-8319 
        8.32        19.23        40.18        35.90         4.31         8.61 
TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL 
        8.94        19.59        17.82        10.55         7.89         9.67 
TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 TCGA-P5-A5EV 
        6.61        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-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-A6CV TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
        4.18         2.96         2.20         3.16         0.59         6.31 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-R8-A6MK 
        3.91         4.73         1.91         0.23         5.03        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 
       28.27        28.14        22.49        21.63        16.37        11.31 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6UA TCGA-S9-A6UB 
       15.62        20.05         9.86        94.62         5.85       103.76 
TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM 
       62.37        72.59        70.55        70.65        10.88         9.30 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
        9.04         7.59         6.15         3.39        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-A7R2 TCGA-S9-A7R3 
        3.58         4.04        18.21        13.02        10.39        87.09 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 
       17.42        83.80        31.59        49.45        35.93        25.32 
TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G 
       22.59        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 
       13.51         0.10         7.89        26.79        10.95 

  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 
             19.38              14.70 
[1] "0.2 - 117.4 (19.4)" "0.0 - 211.2 (14.7)"
[1] "hr=" "1.8"
D68V2, continuous
D68V3, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED     8  10
  16Q LOSS WILD-TYPE 168 214
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      8   10
  16Q LOSS WILD-TYPE  168  214
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE                8                168
  MALE                 10                214
[1] 2 2
[1] FALSE
D68V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  16Q LOSS MUTATED             9                4                 5
  16Q LOSS WILD-TYPE         134              100               148
D68V5, multiclass
                   clus
vv                  16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  ASTROCYTOMA                      9                134
  OLIGOASTROCYTOMA                 4                100
  OLIGODENDROGLIOMA                5                148
[1] 3 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  13
  16Q LOSS WILD-TYPE  84 298
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      5   13
  16Q LOSS WILD-TYPE   84  298
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  NO                 5                 84
  YES               13                298
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16Q LOSS MUTATED                                  0     0
  16Q LOSS WILD-TYPE                                1     2
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16Q LOSS MUTATED                           1    17
  16Q LOSS WILD-TYPE                        13   359
D68V7, multiclass
                                  clus
vv                                 16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  2
  BLACK OR AFRICAN AMERICAN                       1                 13
  WHITE                                          17                359
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V8, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED     1  17
  16Q LOSS WILD-TYPE  14 342
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      1   17
  16Q LOSS WILD-TYPE   14  342
                        clus
vv                       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 14
  NOT HISPANIC OR LATINO               17                342
[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 315  68
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                12                383 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 3                 68 
$`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         9.67 
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-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 
       10.92        19.96        31.82        30.31        14.40         8.02 
TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DU-5847 
       30.21        29.62        15.75         7.79         3.85        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-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-7007 TCGA-DU-7008 
      114.08         7.96         7.73        11.47        62.96       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-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8166 
        2.76         5.10         3.98        20.68        21.40        16.96 
TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU 
       15.48        14.17        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-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-FG-5962 TCGA-FG-5963 
       78.21        95.57       130.78        14.33        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 
       11.87        15.52        24.46         0.59         5.26         3.72 
TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 
        7.04         6.64         7.04         4.21         4.08        10.59 
TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A713 TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 
       10.78        22.95         5.23         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-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 
       31.69         0.10         0.10         2.96        17.52         6.90 
TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 
       14.53        39.48        19.23        39.09         0.23        50.63 
TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 
        0.49        23.61        37.15         0.33         0.13         3.68 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 
        5.33         2.93         1.71        11.28        31.43         1.64 
TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 
       16.24         9.40        63.55        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-A5R9 
       29.59         3.88        16.04        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-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 
       16.14         5.33        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         8.61         8.94        19.59 
TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 
       17.82        10.55         7.89         9.67         6.61        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-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-A6CS TCGA-QH-A6CV TCGA-QH-A6CY TCGA-QH-A6CZ 
        7.79         4.11         4.18         2.96         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-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TS 
        5.03        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        28.27        28.14        22.49        21.63 
TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       16.37        11.31        15.62        20.05         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       103.76        62.37        72.59        70.55 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO 
       22.92        70.65        10.88         9.30         9.04         7.59 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY 
        6.15         3.39        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-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 
        4.04        18.21        13.02        10.39        87.09        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        35.93        25.32 
TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84G 
       22.59        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 
       13.51         0.10         7.89        26.79        10.95 

  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 
            11.955             15.120 
[1] "0.1 - 23.7 (12.0)"  "0.0 - 211.2 (15.1)"
[1] "hr=" "4.4"
D69V2, continuous
D69V3, binary
                    cls
clus                   0   1
  17P LOSS MUTATED     7   5
  17P LOSS WILD-TYPE 169 219
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      7    5
  17P LOSS WILD-TYPE  169  219
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE                7                169
  MALE                  5                219
[1] 2 2
[1] FALSE
D69V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  17P LOSS MUTATED             6                2                 4
  17P LOSS WILD-TYPE         137              102               149
D69V5, multiclass
                   clus
vv                  17P LOSS MUTATED 17P LOSS WILD-TYPE
  ASTROCYTOMA                      6                137
  OLIGOASTROCYTOMA                 2                102
  OLIGODENDROGLIOMA                4                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"
D69V6, binary
                    cls
clus                   0   1
  17P LOSS MUTATED     1  11
  17P LOSS WILD-TYPE  88 300
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      1   11
  17P LOSS WILD-TYPE   88  300
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  NO                 1                 88
  YES               11                300
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17P LOSS MUTATED                                  0     0
  17P LOSS WILD-TYPE                                1     2
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17P LOSS MUTATED                           0    12
  17P LOSS WILD-TYPE                        14   364
D69V7, multiclass
                                  clus
vv                                 17P LOSS MUTATED 17P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  2
  BLACK OR AFRICAN AMERICAN                       0                 14
  WHITE                                          12                364
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V8, binary
                    cls
clus                   0   1
  17P LOSS MUTATED     2  10
  17P LOSS WILD-TYPE  13 349
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      2   10
  17P LOSS WILD-TYPE   13  349
                        clus
vv                       17P LOSS MUTATED 17P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                 13
  NOT HISPANIC OR LATINO               10                349
[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 317  70
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 8                387 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 1                 70 
$`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         9.67        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-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 
       10.92        19.96        31.82        30.31        14.40         8.02 
TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DU-5847 
       30.21        29.62        15.75         7.79         3.85        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-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-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-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-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-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-E1-5302 TCGA-E1-5303 TCGA-E1-5304 
        7.13        21.30       124.50        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-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 
       14.33        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        11.87        15.52        24.46 
TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
        0.59         5.26         3.72         7.04         6.64         7.04 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A713 
        4.21         4.08        10.59        10.78        22.95         5.23 
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-7690 TCGA-HT-7691 
        6.05        42.74         0.10        31.69         0.10         0.10 
TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 
        2.96        17.52         6.90        14.53        39.48        19.23 
TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 
       39.09         0.23        50.63         0.49        23.61        37.15 
TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 
        0.33         0.13         3.68         5.33         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-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-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB 
        0.23        10.49         0.13         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-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         8.61         8.94        19.59        17.82        10.55 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X 
        7.89         9.67         6.61        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-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-A6CV TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
        4.18         2.96         2.20         3.16         0.59         6.31 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-R8-A6MK 
        3.91         4.73         1.91         0.23         5.03        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 
       28.27        28.14        22.49        21.63        16.37        11.31 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA 
       15.62        20.05         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 
      103.76        62.37        72.59        70.55        22.92        70.65 
TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ 
       10.88         9.30         9.04         7.59         6.15         3.39 
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        18.21 
TCGA-S9-A7QZ TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 
       13.02        10.39        87.09        17.42        83.80        31.59 
TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF 
        5.00        49.45        35.93        25.32        22.59        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 
        7.89        26.79        10.95 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              0.10               0.03 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             19.13             211.17 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             5.985             15.090 
[1] "0.1 - 19.1 (6.0)"   "0.0 - 211.2 (15.1)"
[1] "hr=" "2.7"
D70V2, continuous
D70V3, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     4   4
  17Q LOSS WILD-TYPE 172 220
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      4    4
  17Q LOSS WILD-TYPE  172  220
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE                4                172
  MALE                  4                220
[1] 2 2
[1] FALSE
D70V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  17Q LOSS MUTATED             3                1                 4
  17Q LOSS WILD-TYPE         140              103               149
D70V5, multiclass
                   clus
vv                  17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  ASTROCYTOMA                      3                140
  OLIGOASTROCYTOMA                 1                103
  OLIGODENDROGLIOMA                4                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"
D70V6, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     1   7
  17Q LOSS WILD-TYPE  88 304
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      1    7
  17Q LOSS WILD-TYPE   88  304
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  NO                 1                 88
  YES                7                304
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17Q LOSS MUTATED                                  0     0
  17Q LOSS WILD-TYPE                                1     2
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17Q LOSS MUTATED                           0     8
  17Q LOSS WILD-TYPE                        14   368
D70V7, multiclass
                                  clus
vv                                 17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  2
  BLACK OR AFRICAN AMERICAN                       0                 14
  WHITE                                           8                368
[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  13 353
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      2    6
  17Q LOSS WILD-TYPE   13  353
                        clus
vv                       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                 13
  NOT HISPANIC OR LATINO                6                353
[1] 2 2
[1] FALSE

Clustering(71) Variable = 18P LOSS MUTATION ANALYSIS
D71V1, survival
                    sevent
clus2                  0   1
  18P LOSS MUTATED    46  12
  18P LOSS WILD-TYPE 278  59
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                58                337 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                12                 59 
$`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        29.62 
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         8.94         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        28.27        28.14         5.85        62.37 
TCGA-S9-A6WH TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WP TCGA-S9-A7QY 
       22.92        10.88         9.30         9.04         6.15        18.21 
TCGA-S9-A7R2 TCGA-TM-A84G TCGA-TM-A84I TCGA-VM-A8CA 
       10.39        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-DH-5141 
       15.42        27.81        14.73        13.64        10.92        31.82 
TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DU-5847 
       14.40         8.02        15.75         7.79         3.85        18.02 
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-6394 TCGA-DU-6395 
       18.94        17.49        15.16       211.17        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-6408 TCGA-DU-6410 
       11.64       133.74        19.89        16.83       114.08         7.96 
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-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-7301 TCGA-DU-7302 
        7.96        94.32        18.94        44.02        25.91        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-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-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-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 
       21.30       124.50        50.14        67.46        41.13        79.99 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 TCGA-FG-5962 
      134.27        78.21        95.57       130.78        14.33        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-8189 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX 
       11.87        15.52        24.46         0.59         5.26         3.72 
TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 
        9.67         7.04         6.64         7.04         4.21         4.08 
TCGA-FG-A6J3 TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A713 TCGA-FN-7833 TCGA-HT-7467 
       10.59        10.78        22.95         5.23         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-7478 TCGA-HT-7479 TCGA-HT-7481 TCGA-HT-7482 
        3.75        17.42         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-7610 TCGA-HT-7611 
        4.57        17.29         3.16        22.06        56.09        57.60 
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-7693 
       42.74         0.10        14.96         0.10         0.10        17.52 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7860 
        6.90        14.53        39.48        19.23        39.09         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-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 
        9.40        63.55        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-A5R9 TCGA-HT-A5RA TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A618 
        0.07        14.70         5.33         2.70        13.02         5.33 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7493 TCGA-HW-7495 
       29.92        13.45         8.32        19.23        35.90         4.31 
TCGA-HW-8319 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KL TCGA-HW-A5KM 
        8.61        19.59        17.82        10.55         9.67         6.61 
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-A5EY TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F6 TCGA-QH-A65S TCGA-QH-A65V 
        2.37         4.11         5.88         1.28         2.53         4.83 
TCGA-QH-A65X TCGA-QH-A6CS TCGA-QH-A6CV TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 
        7.79         4.18         2.96         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-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-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       22.49        21.63        16.37        11.31        15.62        20.05 
TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UB TCGA-S9-A6WE TCGA-S9-A6WG 
        9.86        94.62        83.70       103.76        72.59        70.55 
TCGA-S9-A6WI TCGA-S9-A6WO TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX 
       70.65         7.59         3.39        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-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 
        3.58         4.04        13.02        87.09        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        35.93        25.32        22.59 
TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84H TCGA-TM-A84J 
       48.39        12.00        15.09        50.76        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-A8CB TCGA-VM-A8CD TCGA-VM-A8CE 
       12.00        33.07        30.08         0.10         7.89        26.79 
TCGA-VM-A8CH 
       10.95 

  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 
            17.145             14.730 
[1] "0.1 - 138.3 (17.1)" "0.0 - 211.2 (14.7)"
[1] "hr=" "1.1"
D71V2, continuous
D71V3, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    19  39
  18P LOSS WILD-TYPE 157 185
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     19   39
  18P LOSS WILD-TYPE  157  185
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE               19                157
  MALE                 39                185
[1] 2 2
[1] FALSE
D71V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  18P LOSS MUTATED            23               10                25
  18P LOSS WILD-TYPE         120               94               128
D71V5, multiclass
                   clus
vv                  18P LOSS MUTATED 18P LOSS WILD-TYPE
  ASTROCYTOMA                     23                120
  OLIGOASTROCYTOMA                10                 94
  OLIGODENDROGLIOMA               25                128
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V6, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    11  47
  18P LOSS WILD-TYPE  78 264
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     11   47
  18P LOSS WILD-TYPE   78  264
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  NO                11                 78
  YES               47                264
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18P LOSS MUTATED                                  1     0
  18P LOSS WILD-TYPE                                0     2
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18P LOSS MUTATED                           0    55
  18P LOSS WILD-TYPE                        14   321
D71V7, multiclass
                                  clus
vv                                 18P LOSS MUTATED 18P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           0                  2
  BLACK OR AFRICAN AMERICAN                       0                 14
  WHITE                                          55                321
[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  49
  18P LOSS WILD-TYPE  12 310
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      3   49
  18P LOSS WILD-TYPE   12  310
                        clus
vv                       18P LOSS MUTATED 18P LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                 12
  NOT HISPANIC OR LATINO               49                310
[1] 2 2
[1] FALSE

Clustering(72) Variable = 18Q LOSS MUTATION ANALYSIS
D72V1, survival
                    sevent
clus2                  0   1
  18Q LOSS MUTATED    42  11
  18Q LOSS WILD-TYPE 282  60
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                53                342 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                11                 60 
$`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-DU-5849 
       11.01        19.96        30.31        30.21        29.62        14.56 
TCGA-DU-5870 TCGA-DU-6393 TCGA-DU-6407 TCGA-DU-7009 TCGA-DU-7014 TCGA-DU-7300 
      182.33        52.11        94.52       138.28       117.40        62.01 
TCGA-DU-8158 TCGA-DU-A5TT TCGA-E1-5307 TCGA-FG-8188 TCGA-HT-7476 TCGA-HT-7477 
        5.10         4.96        57.93        14.96         6.54        24.26 
TCGA-HT-7480 TCGA-HT-7606 TCGA-HT-7609 TCGA-HT-7616 TCGA-HT-7688 TCGA-HT-7692 
       75.19        17.29        45.99         0.23        31.69         2.96 
TCGA-HT-7857 TCGA-HT-8564 TCGA-HT-A5RB TCGA-HT-A617 TCGA-HW-7491 TCGA-HW-8320 
        0.23        15.72         0.10        16.14        40.18         8.94 
TCGA-P5-A5EX TCGA-QH-A65R TCGA-QH-A65Z TCGA-S9-A6TS TCGA-S9-A6TW TCGA-S9-A6TX 
        1.64         5.75         4.11        62.17        28.27        28.14 
TCGA-S9-A6WD TCGA-S9-A6WH TCGA-S9-A6WL TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WP 
       62.37        22.92        10.88         9.30         9.04         6.15 
TCGA-S9-A7QY TCGA-S9-A7R2 TCGA-TM-A84G TCGA-TM-A84I TCGA-VM-A8CA 
       18.21        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-DH-5141 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G 
       31.82        14.40         8.02        15.75         7.79         3.85 
TCGA-DU-5847 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 
       18.02        17.46         6.74        13.38         8.45         6.81 
TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6394 TCGA-DU-6395 
       18.94        17.49        15.16       211.17        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-6408 TCGA-DU-6410 
       11.64       133.74        19.89        16.83       114.08         7.96 
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-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-7301 TCGA-DU-7302 
        7.96        94.32        18.94        44.02        25.91        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-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-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-E1-5302 TCGA-E1-5303 TCGA-E1-5304 
        7.13        21.30       124.50        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-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        11.87        15.52        24.46         0.59         5.26 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ 
        3.72         9.67         7.04         6.64         7.04         4.21 
TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A713 TCGA-FN-7833 
        4.08        10.59        10.78        22.95         5.23         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-7478 TCGA-HT-7479 TCGA-HT-7481 
       16.54         3.75        17.42         6.38         7.10        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-7610 TCGA-HT-7611 
      107.93         4.57         3.16        22.06        56.09        57.60 
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-7693 
       42.74         0.10        14.96         0.10         0.10        17.52 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7858 
        6.90        14.53        39.48        19.23        39.09        50.63 
TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 
        0.49        23.61        37.15         0.33         0.13         3.68 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 
        5.33         2.93         1.71        11.28        31.43         1.64 
TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 
       16.24         9.40        63.55        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-A4DS TCGA-HT-A4DV 
        0.23        29.59         3.88        16.04         0.23        10.49 
TCGA-HT-A5R5 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 
        0.13         0.07        14.70         5.33         2.70        13.02 
TCGA-HT-A616 TCGA-HT-A618 TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 
        1.81         5.33        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         8.61        19.59        17.82        10.55 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X 
        7.89         9.67         6.61        19.00        42.77         5.23 
TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F0 
        4.73         0.23         6.71         2.37         2.30         4.11 
TCGA-P5-A5F1 TCGA-P5-A5F6 TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A6CS 
        5.88         1.28         2.53         4.83         7.79         4.18 
TCGA-QH-A6CV TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 
        2.96         2.20         3.16         0.59         6.31         3.91 
TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-R8-A6MK TCGA-R8-A6ML 
        4.73         1.91         0.23         5.03        88.83        94.03 
TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TY TCGA-S9-A6TZ 
       32.65        59.38        69.07        18.77        22.49        21.63 
TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 
       16.37        11.31        15.62        20.05         9.86        94.62 
TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WI 
       83.70         5.85       103.76        72.59        70.55        70.65 
TCGA-S9-A6WO TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IX TCGA-S9-A7IY 
        7.59         3.39        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-A7QZ TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 
        4.04        13.02        87.09        17.42        83.80        31.59 
TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF 
        5.00        49.45        35.93        25.32        22.59        48.39 
TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84H TCGA-TM-A84J TCGA-TM-A84L 
       12.00        15.09        50.76        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-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 

  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 
            19.360             14.465 
[1] "0.1 - 182.3 (19.4)" "0.0 - 211.2 (14.5)"
[1] "hr=" "1.2"
D72V2, continuous
D72V3, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED    20  33
  18Q LOSS WILD-TYPE 156 191
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     20   33
  18Q LOSS WILD-TYPE  156  191
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE               20                156
  MALE                 33                191
[1] 2 2
[1] FALSE
D72V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  18Q LOSS MUTATED            18                9                26
  18Q LOSS WILD-TYPE         125               95               127
D72V5, multiclass
                   clus
vv                  18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  ASTROCYTOMA                     18                125
  OLIGOASTROCYTOMA                 9                 95
  OLIGODENDROGLIOMA               26                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"
D72V6, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED    11  42
  18Q LOSS WILD-TYPE  78 269
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     11   42
  18Q LOSS WILD-TYPE   78  269
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  NO                11                 78
  YES               42                269
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18Q LOSS MUTATED                                  1     0
  18Q LOSS WILD-TYPE                                0     2
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18Q LOSS MUTATED                           0    50
  18Q LOSS WILD-TYPE                        14   326
D72V7, multiclass
                                  clus
vv                                 18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           0                  2
  BLACK OR AFRICAN AMERICAN                       0                 14
  WHITE                                          50                326
[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  46
  18Q LOSS WILD-TYPE  12 313
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      3   46
  18Q LOSS WILD-TYPE   12  313
                        clus
vv                       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                 12
  NOT HISPANIC OR LATINO               46                313
[1] 2 2
[1] FALSE

Clustering(73) Variable = 19P LOSS MUTATION ANALYSIS
D73V1, survival
                    sevent
clus2                  0   1
  19P LOSS MUTATED    13   5
  19P LOSS WILD-TYPE 311  66
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                18                377 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 5                 66 
$`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        29.62 
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-A6WI TCGA-S9-A7IS TCGA-TM-A84M 
       15.72         1.28        32.65        70.65         7.92        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-DH-5141 
       15.42        27.81        14.73        13.64        10.92        31.82 
TCGA-DH-5143 TCGA-DH-A669 TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DU-5847 
       14.40        30.21        15.75         7.79         3.85        18.02 
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-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-6399 TCGA-DU-6400 TCGA-DU-6401 
       49.02        75.16        46.06        65.75         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-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-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-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 
       12.59         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-E1-5302 TCGA-E1-5303 TCGA-E1-5304 
        7.13        21.30       124.50        50.14        67.46        41.13 
TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 
       79.99        57.93       134.27        95.57       130.78        14.33 
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        11.87        15.52        24.46         0.59 
TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
        5.26         3.72         9.67         7.04         6.64         7.04 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A713 
        4.21         4.08        10.59        10.78        22.95         5.23 
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-7689 TCGA-HT-7690 TCGA-HT-7691 
        6.05        42.74         0.10        14.96         0.10         0.10 
TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 
        2.96        17.52         6.90        14.53        39.48        19.23 
TCGA-HT-7856 TCGA-HT-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-8018 
       31.43         1.64        16.24         9.40        63.55        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-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-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-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 
        8.61         8.94        19.59        17.82        10.55         7.89 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X TCGA-KT-A7W1 
        9.67         6.61        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-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-A6CV TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
        4.18         2.96         2.20         3.16         0.59         6.31 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-R8-A6MK 
        3.91         4.73         1.91         0.23         5.03        88.83 
TCGA-R8-A6ML TCGA-R8-A73M TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW 
       94.03        59.38        62.17        69.07        18.77        28.27 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 
       28.14        22.49        21.63        16.37        11.31        15.62 
TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB 
       20.05         9.86        94.62        83.70         5.85       103.76 
TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WL TCGA-S9-A6WM 
       62.37        72.59        70.55        22.92        10.88         9.30 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IX 
        9.04         7.59         6.15         3.39        14.27        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-A7R2 TCGA-S9-A7R3 
        3.58         4.04        18.21        13.02        10.39        87.09 
TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A7C4 
       17.42        83.80        31.59         5.00        49.45        35.93 
TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F 
       25.32        22.59        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-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH 
       13.51         0.10         7.89        26.79        10.95 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              0.23               0.03 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             78.21             211.17 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             18.23              14.73 
[1] "0.2 - 78.2 (18.2)"  "0.0 - 211.2 (14.7)"
[1] "hr=" "1.7"
D73V2, continuous
D73V3, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     9   9
  19P LOSS WILD-TYPE 167 215
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      9    9
  19P LOSS WILD-TYPE  167  215
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE                9                167
  MALE                  9                215
[1] 2 2
[1] FALSE
D73V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  19P LOSS MUTATED             7                4                 7
  19P LOSS WILD-TYPE         136              100               146
D73V5, multiclass
                   clus
vv                  19P LOSS MUTATED 19P LOSS WILD-TYPE
  ASTROCYTOMA                      7                136
  OLIGOASTROCYTOMA                 4                100
  OLIGODENDROGLIOMA                7                146
[1] 3 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  11
  19P LOSS WILD-TYPE  82 300
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      7   11
  19P LOSS WILD-TYPE   82  300
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  NO                 7                 82
  YES               11                300
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19P LOSS MUTATED                                  0     1
  19P LOSS WILD-TYPE                                1     1
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19P LOSS MUTATED                           2    15
  19P LOSS WILD-TYPE                        12   361
D73V7, multiclass
                                  clus
vv                                 19P LOSS MUTATED 19P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  1
  BLACK OR AFRICAN AMERICAN                       2                 12
  WHITE                                          15                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"
D73V8, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     1  15
  19P LOSS WILD-TYPE  14 344
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      1   15
  19P LOSS WILD-TYPE   14  344
                        clus
vv                       19P LOSS MUTATED 19P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 14
  NOT HISPANIC OR LATINO               15                344
[1] 2 2
[1] FALSE

Clustering(74) Variable = 19Q LOSS MUTATION ANALYSIS
D74V1, survival
                    sevent
clus2                  0   1
  19Q LOSS MUTATED   140  24
  19Q LOSS WILD-TYPE 184  47
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
               164                231 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                24                 47 
$`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-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5144 
       14.73        13.64        19.96        31.82        30.31         8.02 
TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DU-5849 
       30.21        29.62        15.75         7.79         3.85        14.56 
TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6397 
        6.81       182.33        15.16        52.11        22.42        46.06 
TCGA-DU-6400 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-7009 TCGA-DU-7014 TCGA-DU-7018 
        1.22       114.08         7.96       138.28       117.40        30.67 
TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7300 TCGA-DU-7302 TCGA-DU-8164 TCGA-DU-8168 
       94.32        18.94        62.01        60.30        21.40        14.17 
TCGA-DU-A5TS TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S8 TCGA-DU-A76R 
       15.12         8.65         2.70        77.98         5.98        21.30 
TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 
       41.13        79.99       134.27        78.21        95.57       130.78 
TCGA-EZ-7264 TCGA-FG-5962 TCGA-FG-5964 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 
       14.33        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        24.46         6.64 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A710 TCGA-FG-A713 TCGA-HT-7467 TCGA-HT-7468 
        4.21         4.08        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 
       10.55        42.77         5.23         1.64         4.11         1.28 
TCGA-QH-A65R TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CY TCGA-QH-A6CZ 
        5.75         4.83         7.79         4.11         2.20         3.16 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO 
        6.31         3.91         4.73        88.83        94.03        32.65 
TCGA-R8-A73M TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6U2 TCGA-S9-A6U5 
       59.38        28.27        28.14        22.49        15.62        20.05 
TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL 
      103.76        62.37        72.59        22.92        70.65        10.88 
TCGA-S9-A6WN TCGA-S9-A6WP TCGA-S9-A7IQ TCGA-S9-A7IS TCGA-S9-A7IY TCGA-S9-A7J1 
        9.04         6.15        14.27         7.92        12.59         8.19 
TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-TM-A7C5 TCGA-TM-A84G 
        2.04         8.12        18.21        13.02        25.32        34.36 
TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84R TCGA-TM-A84S TCGA-VM-A8C8 TCGA-VM-A8CA 
       16.50        29.92         9.44         4.57        33.07        13.51 
TCGA-VM-A8CB TCGA-VM-A8CE 
        0.10        26.79 

$`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-DH-5143 
       18.84        18.38        18.84        15.42        10.92        14.40 
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-FG-5963 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 
       67.46        57.93        17.98        32.19        18.77        14.93 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 
       24.99        23.97        13.58        20.09        12.95        13.68 
TCGA-FG-8185 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX 
       14.24        11.87        15.52         0.59         5.26         3.72 
TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60L TCGA-FG-A6J3 TCGA-FG-A70Z TCGA-FN-7833 
        9.67         7.04         7.04        10.59        10.78         0.13 
TCGA-HT-7470 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 
        8.81         0.03        16.54         3.75        17.42         6.54 
TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 
       24.26         6.38         7.10        60.03       154.19         4.01 
TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7606 TCGA-HT-7609 
        5.03        29.85        23.18       107.93        17.29        45.99 
TCGA-HT-7610 TCGA-HT-7611 TCGA-HT-7676 TCGA-HT-7680 TCGA-HT-7684 TCGA-HT-7686 
       56.09        57.60         0.16         0.76         6.05        42.74 
TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7693 TCGA-HT-7854 TCGA-HT-7855 
       14.96         0.10         0.10        17.52        39.48        19.23 
TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7882 
       50.63         0.49        23.61         3.68         5.33         1.71 
TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8011 TCGA-HT-8013 TCGA-HT-8018 TCGA-HT-8019 
       11.28        31.43        16.24        63.55        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-A5RA TCGA-HT-A5RB 
        3.88        16.04         0.23         0.13        14.70         0.10 
TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HW-7489 
        5.33         2.70         1.81        16.14         5.33         8.32 
TCGA-HW-7490 TCGA-HW-7493 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-A5KK 
       19.23        35.90         8.61         8.94        19.59         7.89 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW 
        9.67         6.61        19.00         4.73         0.23         6.71 
TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-P5-A5F1 TCGA-QH-A65S TCGA-QH-A6CS TCGA-QH-A6CV 
        2.37         2.30         5.88         2.53         4.18         2.96 
TCGA-QH-A6X3 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-S9-A6TS TCGA-S9-A6TU 
        0.59         1.91         0.23         5.03        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        11.31         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        70.55         9.30         7.59         3.39 
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-A89Z TCGA-TM-A7C3 
       87.09        17.42        83.80        31.59         5.00        49.45 
TCGA-TM-A7C4 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F 
       35.93        22.59        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-A8C9 TCGA-VM-A8CD TCGA-VM-A8CH 
       30.08         7.89        10.95 

  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 
            15.255             14.700 
[1] "0.1 - 182.3 (15.3)" "0.0 - 211.2 (14.7)"
[1] "hr=" "1.6"
D74V2, continuous
D74V3, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    74  92
  19Q LOSS WILD-TYPE 102 132
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     74   92
  19Q LOSS WILD-TYPE  102  132
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE               74                102
  MALE                 92                132
[1] 2 2
[1] FALSE
D74V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  19Q LOSS MUTATED            17               33               116
  19Q LOSS WILD-TYPE         126               71                37
D74V5, multiclass
                   clus
vv                  19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  ASTROCYTOMA                     17                126
  OLIGOASTROCYTOMA                33                 71
  OLIGODENDROGLIOMA              116                 37
[1] 3 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    31 135
  19Q LOSS WILD-TYPE  58 176
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     31  135
  19Q LOSS WILD-TYPE   58  176
     clus
vv    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  NO                31                 58
  YES              135                176
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19Q LOSS MUTATED                                  0     1
  19Q LOSS WILD-TYPE                                1     1
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19Q LOSS MUTATED                           6   154
  19Q LOSS WILD-TYPE                         8   222
D74V7, multiclass
                                  clus
vv                                 19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  1
  BLACK OR AFRICAN AMERICAN                       6                  8
  WHITE                                         154                222
[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     7 146
  19Q LOSS WILD-TYPE   8 213
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      7  146
  19Q LOSS WILD-TYPE    8  213
                        clus
vv                       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    7                  8
  NOT HISPANIC OR LATINO              146                213
[1] 2 2
[1] FALSE

Clustering(75) Variable = 20P LOSS MUTATION ANALYSIS
D75V1, survival
                    sevent
clus2                  0   1
  20P LOSS MUTATED     2   1
  20P LOSS WILD-TYPE 322  70
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 3                392 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 1                 70 
$`20P LOSS MUTATED`
TCGA-DB-5277 TCGA-DU-8166 TCGA-HT-7693 
       46.65        16.96        17.52 

$`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-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-DU-5847 TCGA-DU-5849 
       29.62        15.75         7.79         3.85        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-6399 TCGA-DU-6400 TCGA-DU-6401 
       49.02        75.16        46.06        65.75         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-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-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-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR 
       21.40        19.13        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-E1-5302 TCGA-E1-5303 TCGA-E1-5304 
        7.13        21.30       124.50        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-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 
       14.33        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        11.87        15.52        24.46 
TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K 
        0.59         5.26         3.72         9.67         7.04         6.64 
TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Z TCGA-FG-A710 
        7.04         4.21         4.08        10.59        10.78        22.95 
TCGA-FG-A713 TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 
        5.23         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-7694 TCGA-HT-7695 TCGA-HT-7854 
        0.10         0.10         2.96         6.90        14.53        39.48 
TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 
       19.23        39.09         0.23        50.63         0.49        23.61 
TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 TCGA-HT-7881 
       37.15         0.33         0.13         3.68         5.33         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-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 
       63.55        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-HW-7486 TCGA-HW-7487 TCGA-HW-7489 
        1.81        16.14         5.33        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         8.61         8.94 
TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM 
       19.59        17.82        10.55         7.89         9.67         6.61 
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-A5F6 
        1.64         2.37         2.30         4.11         5.88         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-A6CV TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 
        2.96         2.20         3.16         0.59         6.31         3.91 
TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-R8-A6MK TCGA-R8-A6ML 
        4.73         1.91         0.23         5.03        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        28.27 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 
       28.14        22.49        21.63        16.37        11.31        15.62 
TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB 
       20.05         9.86        94.62        83.70         5.85       103.76 
TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL 
       62.37        72.59        70.55        22.92        70.65        10.88 
TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ 
        9.30         9.04         7.59         6.15         3.39        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        18.21        13.02 
TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89Z 
       10.39        87.09        17.42        83.80        31.59         5.00 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B 
       49.45        35.93        25.32        22.59        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 
       26.79        10.95 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             16.96               0.03 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             46.65             211.17 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
            17.520             14.945 
[1] "17.0 - 46.6 (17.5)" "0.0 - 211.2 (14.9)"
[1] "hr=" "2"  
D75V2, continuous
D75V3, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     2   1
  20P LOSS WILD-TYPE 174 223
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      2    1
  20P LOSS WILD-TYPE  174  223
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  FEMALE                2                174
  MALE                  1                223
[1] 2 2
[1] FALSE
D75V4, continuous
[1] "Remove cluster labels:" "20P LOSS MUTATED"      
clus
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 1                233 
        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-DH-5140         TCGA-DH-5142 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DH-5143         TCGA-DH-5144         TCGA-DH-A66B 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DH-A66D         TCGA-DH-A66F         TCGA-DH-A66G 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DU-5851         TCGA-DU-5852         TCGA-DU-5853 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DU-5854         TCGA-DU-5855         TCGA-DU-5870 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DU-5871         TCGA-DU-5874         TCGA-DU-6396 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DU-6403         TCGA-DU-6404         TCGA-DU-6405 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DU-6407         TCGA-DU-6408         TCGA-DU-6410 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DU-7011         TCGA-DU-7013         TCGA-DU-7014 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DU-7015         TCGA-DU-7018         TCGA-DU-7019 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DU-7294         TCGA-DU-7298         TCGA-DU-7299 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DU-7300         TCGA-DU-7301         TCGA-DU-7302 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DU-7304         TCGA-DU-7306         TCGA-DU-7309 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DU-8158         TCGA-DU-8161         TCGA-DU-8162 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DU-8163         TCGA-DU-8165         TCGA-DU-8167 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DU-8168         TCGA-DU-A5TP         TCGA-DU-A5TR 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DU-A5TS         TCGA-DU-A5TU         TCGA-DU-A5TW 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DU-A6S2         TCGA-DU-A6S6         TCGA-DU-A6S7 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DU-A6S8         TCGA-DU-A76R         TCGA-DU-A7T8 
"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-A713         TCGA-HT-7468         TCGA-HT-7470 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-HT-7475         TCGA-HT-7477         TCGA-HT-7485 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-HT-7607         TCGA-HT-7609         TCGA-HT-7611 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-HT-7689         TCGA-HT-7692         TCGA-HT-7694 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-HT-7854         TCGA-HT-7875         TCGA-HT-7884 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-HT-8564         TCGA-HT-A4DV         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-A5F6         TCGA-QH-A65R         TCGA-QH-A65S 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-QH-A65V         TCGA-QH-A65X         TCGA-QH-A65Z 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-QH-A6CS         TCGA-QH-A6CU         TCGA-QH-A6CV 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-QH-A6CW         TCGA-QH-A6CX         TCGA-QH-A6CY 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-QH-A6CZ         TCGA-QH-A6X3         TCGA-QH-A6X4 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-QH-A6X5         TCGA-QH-A6X8         TCGA-QH-A6X9 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-QH-A6XA         TCGA-QH-A6XC         TCGA-S9-A6TS 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-S9-A6TU         TCGA-S9-A6TV         TCGA-S9-A6TW 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-S9-A6TX         TCGA-S9-A6TY         TCGA-S9-A6TZ 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-S9-A6U0         TCGA-S9-A6U1         TCGA-S9-A6U2 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-S9-A6U5         TCGA-S9-A6U6         TCGA-S9-A6U8 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-S9-A6UA         TCGA-S9-A6UB         TCGA-S9-A6WD 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-S9-A6WE         TCGA-S9-A6WG         TCGA-S9-A6WH 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-S9-A6WI         TCGA-S9-A6WL         TCGA-S9-A6WM 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-S9-A6WN         TCGA-S9-A6WO         TCGA-S9-A6WP 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-S9-A6WQ         TCGA-S9-A7IQ         TCGA-S9-A7IS 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-S9-A7IX         TCGA-S9-A7IY         TCGA-S9-A7IZ 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-S9-A7J0         TCGA-S9-A7J1         TCGA-S9-A7J2 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-S9-A7J3         TCGA-S9-A7QW         TCGA-S9-A7QX 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-S9-A7QY         TCGA-S9-A7QZ         TCGA-S9-A7R2 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-S9-A7R3         TCGA-S9-A7R4         TCGA-S9-A7R7 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-S9-A7R8         TCGA-S9-A89Z         TCGA-TM-A7C3 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-TM-A7C4         TCGA-TM-A7C5         TCGA-TM-A7CA 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-TM-A7CF         TCGA-TM-A84B         TCGA-TM-A84C 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-TM-A84F         TCGA-TM-A84G         TCGA-TM-A84H 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-TM-A84I         TCGA-TM-A84J         TCGA-TM-A84L 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-TM-A84M         TCGA-TM-A84O         TCGA-TM-A84Q 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-TM-A84R         TCGA-TM-A84S         TCGA-TM-A84T 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-VM-A8C8         TCGA-VM-A8CA         TCGA-VM-A8CD 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-VM-A8CE         TCGA-VM-A8CH 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  20P LOSS MUTATED             1                1                 1
  20P LOSS WILD-TYPE         142              103               152
D75V5, multiclass
                   clus
vv                  20P LOSS MUTATED 20P LOSS WILD-TYPE
  ASTROCYTOMA                      1                142
  OLIGOASTROCYTOMA                 1                103
  OLIGODENDROGLIOMA                1                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"
D75V6, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     1   2
  20P LOSS WILD-TYPE  88 309
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      1    2
  20P LOSS WILD-TYPE   88  309
     clus
vv    20P LOSS MUTATED 20P LOSS WILD-TYPE
  NO                 1                 88
  YES                2                309
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20P LOSS MUTATED                                  0     0
  20P LOSS WILD-TYPE                                1     2
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20P LOSS MUTATED                           0     3
  20P LOSS WILD-TYPE                        14   373
D75V7, multiclass
                                  clus
vv                                 20P LOSS MUTATED 20P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  2
  BLACK OR AFRICAN AMERICAN                       0                 14
  WHITE                                           3                373
[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   3
  20P LOSS WILD-TYPE  15 356
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      0    3
  20P LOSS WILD-TYPE   15  356
                        clus
vv                       20P LOSS MUTATED 20P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 15
  NOT HISPANIC OR LATINO                3                356
[1] 2 2
[1] FALSE

Clustering(76) Variable = 21Q LOSS MUTATION ANALYSIS
D76V1, survival
                    sevent
clus2                  0   1
  21Q LOSS MUTATED    21   3
  21Q LOSS WILD-TYPE 303  68
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                24                371 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 3                 68 
$`21Q LOSS MUTATED`
TCGA-CS-4943 TCGA-DB-5279 TCGA-DH-5140 TCGA-DH-5142 TCGA-DU-5871 TCGA-DU-7010 
       18.15        44.52        19.96        30.31        18.94        14.99 
TCGA-DU-8165 TCGA-DU-8167 TCGA-DU-A5TU TCGA-E1-5307 TCGA-FG-7636 TCGA-FG-A60J 
       19.13        15.48         3.65        57.93        17.88         7.04 
TCGA-HT-7689 TCGA-HT-7857 TCGA-HT-7902 TCGA-HT-8106 TCGA-HT-8564 TCGA-HW-7490 
       14.96         0.23        31.43         0.10        15.72        19.23 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EZ TCGA-P5-A5F6 TCGA-S9-A89Z TCGA-TM-A84Q 
        0.23         6.71         2.30         1.28         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-DH-5141 
       15.42        27.81        14.73        13.64        10.92        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        29.62        15.75         7.79 
TCGA-DH-A66G TCGA-DU-5847 TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 
        3.85        18.02        14.56        17.46         6.74        13.38 
TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 
        8.45         6.81       182.33        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-8168 TCGA-DU-A5TP TCGA-DU-A5TR 
       20.68        21.40        16.96        14.17        14.24        12.59 
TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S2 TCGA-DU-A6S3 
       15.12         4.96         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-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 
       21.30       124.50        50.14        67.46        41.13        79.99 
TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 TCGA-FG-5962 
      134.27        78.21        95.57       130.78        14.33        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 
       11.87        15.52        24.46         0.59         5.26         3.72 
TCGA-FG-A4MY TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 
        9.67         6.64         7.04         4.21         4.08        10.59 
TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A713 TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 
       10.78        22.95         5.23         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-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 
       31.69         0.10         0.10         2.96        17.52         6.90 
TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7858 TCGA-HT-7860 
       14.53        39.48        19.23        39.09        50.63         0.49 
TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 
       23.61        37.15         0.33         0.13         3.68         5.33 
TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 
        2.93         1.71        11.28         1.64        16.24         9.40 
TCGA-HT-8013 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8107 
       63.55        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-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-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-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7491 TCGA-HW-7493 
        5.33        29.92        13.45         8.32        40.18        35.90 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ 
        4.31         8.61         8.94        19.59        17.82        10.55 
TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X 
        7.89         9.67         6.61        19.00        42.77         5.23 
TCGA-KT-A7W1 TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-QH-A65R 
        4.73         1.64         2.37         4.11         5.88         5.75 
TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CV 
        2.53         4.83         7.79         4.11         4.18         2.96 
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-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO 
        1.91         0.23         5.03        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        28.27        28.14 
TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 
       22.49        21.63        16.37        11.31        15.62        20.05 
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       103.76        62.37 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM 
       72.59        70.55        22.92        70.65        10.88         9.30 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
        9.04         7.59         6.15         3.39        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-A7R2 
        8.12         3.58         4.04        18.21        13.02        10.39 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-TM-A7C3 TCGA-TM-A7C4 
       87.09        17.42        83.80        31.59        49.45        35.93 
TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F 
       25.32        22.59        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-A8CA TCGA-VM-A8CB TCGA-VM-A8CD TCGA-VM-A8CE TCGA-VM-A8CH 
       13.51         0.10         7.89        26.79        10.95 

  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 
             15.60              14.73 
[1] "0.1 - 57.9 (15.6)"  "0.0 - 211.2 (14.7)"
[1] "hr=" "1.3"
D76V2, continuous
D76V3, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    12  12
  21Q LOSS WILD-TYPE 164 212
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     12   12
  21Q LOSS WILD-TYPE  164  212
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE               12                164
  MALE                 12                212
[1] 2 2
[1] FALSE
D76V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  21Q LOSS MUTATED            15                5                 4
  21Q LOSS WILD-TYPE         128               99               149
D76V5, multiclass
                   clus
vv                  21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  ASTROCYTOMA                     15                128
  OLIGOASTROCYTOMA                 5                 99
  OLIGODENDROGLIOMA                4                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"
D76V6, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED     4  20
  21Q LOSS WILD-TYPE  85 291
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      4   20
  21Q LOSS WILD-TYPE   85  291
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  NO                 4                 85
  YES               20                291
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  21Q LOSS MUTATED                                  0     0
  21Q LOSS WILD-TYPE                                1     2
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  21Q LOSS MUTATED                           0    23
  21Q LOSS WILD-TYPE                        14   353
D76V7, multiclass
                                  clus
vv                                 21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  2
  BLACK OR AFRICAN AMERICAN                       0                 14
  WHITE                                          23                353
[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  21
  21Q LOSS WILD-TYPE  14 338
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      1   21
  21Q LOSS WILD-TYPE   14  338
                        clus
vv                       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 14
  NOT HISPANIC OR LATINO               21                338
[1] 2 2
[1] FALSE

Clustering(77) Variable = 22Q LOSS MUTATION ANALYSIS
D77V1, survival
                    sevent
clus2                  0   1
  22Q LOSS MUTATED    28  17
  22Q LOSS WILD-TYPE 296  54
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                45                350 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                17                 54 
$`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         9.67        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-A89Z TCGA-TM-A84G TCGA-VM-A8CD 
        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-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 
       10.92        19.96        31.82        30.31        14.40         8.02 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DU-5849 TCGA-DU-5851 
       29.62        15.75         7.79         3.85        14.56        17.46 
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-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-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 
       62.96       138.28        14.99       105.21         6.54         8.84 
TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7292 TCGA-DU-7294 
      117.40        90.77        30.67        26.30         7.96        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-A5TW TCGA-DU-A6S2 TCGA-DU-A6S3 
       14.24        12.59        15.12         5.65         8.65         2.70 
TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76O TCGA-DU-A76R TCGA-DU-A7T8 
       77.98         7.23         5.98         7.13        21.30       124.50 
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-EZ-7264 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 
       95.57        14.33        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-8181 TCGA-FG-8182 TCGA-FG-8185 
       17.88        22.55        20.61        12.95        13.68        14.24 
TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT 
       16.01        20.09        14.96        11.87        15.52        24.46 
TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L 
        0.59         5.26         3.72         7.04         6.64         7.04 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Z TCGA-FG-A710 TCGA-FG-A713 
        4.21         4.08        10.59        10.78        22.95         5.23 
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-7687 TCGA-HT-7689 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 
        0.10        14.96         0.10         2.96        17.52         6.90 
TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 
       14.53        39.48        19.23        39.09         0.23        50.63 
TCGA-HT-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-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 
        9.40        63.55        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-A615 
        0.13         0.07        14.70         0.10         5.33        13.02 
TCGA-HT-A616 TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 
        1.81        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         8.61         8.94        19.59        17.82 
TCGA-HW-A5KJ TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-KT-A74X 
       10.55         9.67         6.61        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-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X 
        4.11         5.88         5.75         2.53         4.83         7.79 
TCGA-QH-A65Z TCGA-QH-A6CV TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
        4.11         2.96         2.20         3.16         0.59         6.31 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-R8-A6MK 
        3.91         4.73         1.91         0.23         5.03        88.83 
TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW 
       94.03        32.65        59.38        69.07        18.77        28.27 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 
       28.14        22.49        21.63        16.37        11.31        15.62 
TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UB TCGA-S9-A6WD 
       20.05         9.86        94.62        83.70       103.76        62.37 
TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WM 
       72.59        70.55        22.92        70.65        10.88         9.30 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
        9.04         7.59         6.15         3.39        14.27         7.92 
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-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 
        4.04        18.21        13.02        10.39        87.09        17.42 
TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA 
       83.80        31.59        49.45        35.93        25.32        22.59 
TCGA-TM-A7CF TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84F TCGA-TM-A84H TCGA-TM-A84I 
       48.39        12.00        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-A8CA TCGA-VM-A8CB 
        4.57        12.00        33.07        30.08        13.51         0.10 
TCGA-VM-A8CE TCGA-VM-A8CH 
       26.79        10.95 

  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 
             15.48              14.96 
[1] "0.1 - 156.2 (15.5)" "0.0 - 211.2 (15.0)"
[1] "hr=" "2.7"
D77V2, continuous
D77V3, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    22  23
  22Q LOSS WILD-TYPE 154 201
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     22   23
  22Q LOSS WILD-TYPE  154  201
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE               22                154
  MALE                 23                201
[1] 2 2
[1] FALSE
D77V4, continuous
                    vv
clus                 ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  22Q LOSS MUTATED            21               11                13
  22Q LOSS WILD-TYPE         122               93               140
D77V5, multiclass
                   clus
vv                  22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  ASTROCYTOMA                     21                122
  OLIGOASTROCYTOMA                11                 93
  OLIGODENDROGLIOMA               13                140
[1] 3 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  36
  22Q LOSS WILD-TYPE  80 275
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      9   36
  22Q LOSS WILD-TYPE   80  275
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  NO                 9                 80
  YES               36                275
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  22Q LOSS MUTATED                                  1     0
  22Q LOSS WILD-TYPE                                0     2
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  22Q LOSS MUTATED                           1    43
  22Q LOSS WILD-TYPE                        13   333
D77V7, multiclass
                                  clus
vv                                 22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           0                  2
  BLACK OR AFRICAN AMERICAN                       1                 13
  WHITE                                          43                333
[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  40
  22Q LOSS WILD-TYPE  14 319
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      1   40
  22Q LOSS WILD-TYPE   14  319
                        clus
vv                       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 14
  NOT HISPANIC OR LATINO               40                319
[1] 2 2
[1] FALSE

Clustering(78) Variable = XQ LOSS MUTATION ANALYSIS
D78V1, survival
                   sevent
clus2                 0   1
  XQ LOSS MUTATED    37  15
  XQ LOSS WILD-TYPE 287  56
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               52               343 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               15                56 
$`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-FG-5964 
        5.98        21.30        50.14       134.27        14.33        34.36 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-HT-7469 TCGA-HT-7471 TCGA-HT-7477 TCGA-HT-7616 
        4.21         4.08         7.82         0.13        24.26         0.23 
TCGA-HT-7690 TCGA-HT-7692 TCGA-HT-7855 TCGA-HT-8104 TCGA-HT-8564 TCGA-HW-7491 
        0.10         2.96        19.23        12.23        15.72        40.18 
TCGA-HW-8321 TCGA-IK-7675 TCGA-KT-A74X TCGA-P5-A5EZ TCGA-P5-A5F6 TCGA-QH-A65Z 
       19.59        19.00         5.23         2.30         1.28         4.11 
TCGA-QH-A6X4 TCGA-QH-A6X8 TCGA-S9-A6TV TCGA-S9-A6WP TCGA-S9-A7IS TCGA-S9-A7QW 
        6.31         4.73        18.77         6.15         7.92         3.58 
TCGA-S9-A89Z TCGA-TM-A7C5 TCGA-TM-A84I TCGA-VM-A8CD 
        5.00        25.32        19.36         7.89 

$`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-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 
       10.92        31.82        30.31        14.40         8.02        30.21 
TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DU-5849 TCGA-DU-5851 
       29.62        15.75         7.79         3.85        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-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-7007 
       11.64        19.89        16.83        94.52       114.08        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-7298 
      117.40        90.77        26.30        10.36         7.96        18.94 
TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7304 TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8161 
       62.01        25.91        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-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-A76K 
       12.20         8.65         2.70        77.98         7.23        11.41 
TCGA-DU-A76L TCGA-DU-A76O TCGA-DU-A7T8 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 
       26.76         7.13       124.50        67.46        41.13        79.99 
TCGA-E1-5307 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-FG-5962 TCGA-FG-5963 
       57.93        78.21        95.57       130.78        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        11.87 
TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY 
       15.52        24.46         0.59         5.26         3.72         9.67 
TCGA-FG-A60J TCGA-FG-A60K TCGA-FG-A60L TCGA-FG-A6J3 TCGA-FG-A70Z TCGA-FG-A710 
        7.04         6.64         7.04        10.59        10.78        22.95 
TCGA-FG-A713 TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7470 TCGA-HT-7472 
        5.23         0.13         0.10         6.67         8.81         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-7688 TCGA-HT-7689 TCGA-HT-7691 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 
       31.69        14.96         0.10        17.52         6.90        14.53 
TCGA-HT-7854 TCGA-HT-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-8018 TCGA-HT-8019 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 
       63.55        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-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-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-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7493 
        5.33        29.92        13.45         8.32        19.23        35.90 
TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
        4.31         8.61         8.94        17.82        10.55         7.89 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-8125 TCGA-KT-A7W1 TCGA-P5-A5EV TCGA-P5-A5EW 
        9.67         6.61        42.77         4.73         0.23         6.71 
TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-QH-A65R TCGA-QH-A65S 
        1.64         2.37         4.11         5.88         5.75         2.53 
TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A6CS TCGA-QH-A6CV TCGA-QH-A6CY TCGA-QH-A6CZ 
        4.83         7.79         4.18         2.96         2.20         3.16 
TCGA-QH-A6X3 TCGA-QH-A6X5 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC TCGA-R8-A6MK 
        0.59         3.91         1.91         0.23         5.03        88.83 
TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TW 
       94.03        32.65        59.38        62.17        69.07        28.27 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 TCGA-S9-A6U2 
       28.14        22.49        21.63        16.37        11.31        15.62 
TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB 
       20.05         9.86        94.62        83.70         5.85       103.76 
TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL 
       62.37        72.59        70.55        22.92        70.65        10.88 
TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IX 
        9.30         9.04         7.59         3.39        14.27        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-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R4 
        4.04        18.21        13.02        10.39        87.09        17.42 
TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7CA TCGA-TM-A7CF 
       83.80        31.59        49.45        35.93        22.59        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-A8CE 
       12.00        33.07        30.08        13.51         0.10        26.79 
TCGA-VM-A8CH 
       10.95 

  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 
           13.115            15.120 
[1] "0.1 - 134.3 (13.1)" "0.0 - 211.2 (15.1)"
[1] "hr=" "2"  
D78V2, continuous
D78V3, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    20  33
  XQ LOSS WILD-TYPE 156 191
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     20   33
  XQ LOSS WILD-TYPE  156  191
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE              20               156
  MALE                33               191
[1] 2 2
[1] FALSE
D78V4, continuous
                   vv
clus                ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  XQ LOSS MUTATED            19               12                22
  XQ LOSS WILD-TYPE         124               92               131
D78V5, multiclass
                   clus
vv                  XQ LOSS MUTATED XQ LOSS WILD-TYPE
  ASTROCYTOMA                    19               124
  OLIGOASTROCYTOMA               12                92
  OLIGODENDROGLIOMA              22               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"
D78V6, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    12  41
  XQ LOSS WILD-TYPE  77 270
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     12   41
  XQ LOSS WILD-TYPE   77  270
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  NO               12                77
  YES              41               270
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XQ LOSS MUTATED                                  0     0
  XQ LOSS WILD-TYPE                                1     2
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XQ LOSS MUTATED                           0    52
  XQ LOSS WILD-TYPE                        14   324
D78V7, multiclass
                                  clus
vv                                 XQ LOSS MUTATED XQ LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 2
  BLACK OR AFRICAN AMERICAN                      0                14
  WHITE                                         52               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"
D78V8, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     2  48
  XQ LOSS WILD-TYPE  13 311
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      2   48
  XQ LOSS WILD-TYPE   13  311
                        clus
vv                       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                13
  NOT HISPANIC OR LATINO              48               311
[1] 2 2
[1] FALSE
