[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"        "-oTKIRC-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/KIRC-TP/10005959/KIRC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/KIRC-TP/10013767/transformed.cor.cli.txt"

nPatients in clinical file=515, in cluster file=527, common to both=505
[1] "Reduce the number of clustering variables from 80 to 79."
[1]  79 505
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               23               482 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               23               482 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               50               455 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               50               455 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               75               430 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               75               430 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               77               428 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               77               428 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               19               486 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               19               486 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               60               445 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               60               445 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               13               492 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               13               492 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               13               492 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               13               492 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              187               318 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              187               318 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
              200               305 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
              200               305 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               11               494 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               11               494 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                9               496 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                9               496 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              167               338 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              167               338 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              168               337 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              168               337 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               29               476 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               29               476 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               60               445 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               60               445 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               13               492 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               13               492 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               12               493 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               12               493 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                17                488 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                17                488 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                12                493 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                12                493 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                31                474 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                31                474 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                29                476 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                29                476 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               119                386 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               119                386 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
               120                385 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
               120                385 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                22                483 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                22                483 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                16                489 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                16                489 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                26                479 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                26                479 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
               104                401 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
               104                401 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                96                409 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                96                409 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                25                480 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                25                480 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                31                474 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                31                474 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                25                480 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                25                480 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                25                480 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                25                480 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                51                454 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                51                454 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                57                448 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                57                448 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               110                395 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               110                395 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               113                392 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               113                392 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                49                456 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                49                456 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                40                465 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                40                465 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               29               476 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               29               476 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               55               450 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               55               450 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               36               469 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               36               469 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               14               491 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               14               491 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               14               491 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               14               491 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
              364               141 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
              364               141 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               96               409 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               96               409 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               71               434 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               71               434 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               65               440 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               65               440 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                7               498 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                7               498 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                6               499 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                6               499 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               98               407 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               98               407 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              125               380 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              125               380 
[1] "7Q LOSS MUTATION ANALYSIS"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                3               502 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                3               502 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              134               371 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              134               371 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               62               443 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               62               443 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              144               361 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              144               361 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              145               360 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              145               360 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                65                440 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                65                440 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                87                418 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                87                418 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                18                487 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                18                487 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                23                482 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                23                482 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 3                502 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 3                502 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 4                501 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 4                501 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                69                436 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                69                436 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               211                294 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               211                294 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                35                470 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                35                470 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 9                496 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 9                496 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                13                492 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                13                492 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                44                461 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                44                461 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                28                477 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                28                477 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                91                414 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                91                414 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                93                412 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                93                412 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                11                494 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                11                494 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 4                501 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 4                501 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 8                497 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 8                497 
[1] "20Q LOSS MUTATION ANALYSIS"
[1] 3
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 3                502 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 3                502 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                53                452 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                53                452 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                38                467 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                38                467 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               45               460 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               45               460 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDESEASE"                  
 [6] "NEOPLASM.DISEASESTAGE"                 
 [7] "PATHOLOGY.T.STAGE"                     
 [8] "PATHOLOGY.N.STAGE"                     
 [9] "PATHOLOGY.M.STAGE"                     
[10] "DCCUPLOADDATE"                         
[11] "GENDER"                                
[12] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[13] "DAYSTOLASTKNOWNALIVE"                  
[14] "RADIATIONTHERAPY"                      
[15] "KARNOFSKYPERFORMANCESCORE"             
[16] "HISTOLOGICALTYPE"                      
[17] "RADIATIONS.RADIATION.REGIMENINDICATION"
[18] "NUMBERPACKYEARSSMOKED"                 
[19] "YEAROFTOBACCOSMOKINGONSET"             
[20] "RACE"                                  
[21] "ETHNICITY"                             
[22] "BATCHNUMBER"                           

Input Data has 22 rows and 505 columns.

[1] "Batch" "22"   
[1] "Last Follow UP"
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3316 
        1120         1436           16           NA          735         1493 
TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 
        1491         1130         1508         1478         1106         1186 
TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 
         751         1137         1485          665         1043          945 
TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 
          NA         1610         1385          910           NA         2688 
TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 
        1307         2504         1559          319          873         2270 
TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 
        2274          735         1621         1314         1070          630 
TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A8CQ 
         567          574          861         1993          617            3 
TCGA-A3-A8OX TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
          NA         3343           NA         2566         2223         2017 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
         480         1853         2192         2087         2044         1745 
TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 
        1423         1471         1280         1217         1779         1481 
TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
        1397          874           NA         1143         1168          951 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4690 
         853          369         1238           43           NA           NA 
TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4698 
          NA           NA           NA           NA           NA           NA 
TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 
         110           NA           NA           NA           26           NA 
TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
          96           NA           NA           NA          616           NA 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 
          NA           18           NA           NA           NA           NA 
TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 
          NA          183           NA           NA           NA           NA 
TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 
          NA           NA           NA           NA           NA           NA 
TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 
          NA           NA           NA           NA           NA           NA 
TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 
          NA           NA           NA           NA           NA           NA 
TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 
          NA           NA           NA           NA           NA           NA 
TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 
          NA           NA           NA           NA           NA           NA 
TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 
         665           NA           NA           NA           NA           NA 
TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 
          NA           NA          911           NA         1092          359 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
         797          657          535           59          493          554 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 
         652         1132          449         2408         3431         1487 
TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 
        3076           NA         1420         1727         1835         2583 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
        2741         1732         1605         1203         3668         2414 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 
        3117         1459         2931         2722         1865         2963 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 
         992         1092           51          374          648          952 
TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 
         358          315          417          656          507          291 
TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
         175            7           38           16          141          166 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
          11            7           NA          511          826          838 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 
         762          750          523          777          788          700 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
         636          722           36          822           26          737 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
         522          505          194          434           15         1046 
TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I 
         435          830          519           53          256          150 
TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 
          66          110         3377           NA         2881         2746 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 
        3074         2839           NA         3037           13         2718 
TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 
         701           NA         1893         1879         1955         1670 
TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 
        2964         1625           NA          845         1888           NA 
TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 
        1133          645          461           NA         2859           NA 
TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 
          NA           NA           NA         1666           NA         1367 
TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 
         372          970           NA           NA           NA           NA 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 
         374         2208         2372         2361          182           NA 
TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4770 
          NA         2184         1462          400         1876           NA 
TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 
          NA         1885         1843          411         1731         2080 
TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 
         354         1854           NA         1489           NA          620 
TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 
        1107           NA           NA         1124          204         1459 
TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
         211         2660         2172         1935         1785         1834 
TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 
        1862         1871          205         1746         1794          433 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 
        1487         1502         1384           NA         1433         1632 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 
         454           NA         1014         1413           NA          785 
TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 
        1124           NA          118         1413          501          177 
TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 
        1308         1371          932         1266          563         1177 
TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 
        1126          840         1140         1071           NA           NA 
TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 
          NA          193         2412           NA         2257          932 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 
          NA          293           NA         2263         1495         1165 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 
        1291         1133         1132          693          406          822 
TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
        1011          967          714          408          749         1018 
TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 
         603         1355         1063          951           29         1820 
TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 
        1416         1924           NA           NA         2308         1998 
TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 
          NA         1628         1793           NA          646         2554 
TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 
        1498         2423         1435         2259         2283         2353 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
        1955         2186         2014         1883         1759         2125 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 
        1952           NA           NA         1946         2085           NA 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 
        1521          750          841           NA         1808         1528 
TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 
          NA         1450         1520         1560         1792         1496 
TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 
        1499         1531         1657           NA         1373           NA 
TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 
          NA           NA         1943           NA         2430         2575 
TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 
          NA           NA           NA           NA          552         1883 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6028 
        1889         2231         2038           NA         1855           NA 
TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 
          NA         1906         2548           NA           NA         2799 
TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 
        2489           NA         2609         2226         2017         2378 
TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 
        2271           NA         3222         2552         3146           NA 
TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 
         774         1404           18           NA         1943         1787 
TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 
          NA           NA         1843         1928         2830           NA 
TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 
        1868         1929         1789           25           NA           NA 
TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 
        1712         1683         1732         1683         1430          330 
TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 
          NA          662         1740         1446          685           NA 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
          59          946          386         2439         2067         1997 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
         373          435          693         1905         1329         1398 
TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 
        1470          370          355         1130          723         1729 
TCGA-DV-5576 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC 
          NA          551          119          206          127           NA 
TCGA-GK-A6C7 
          61 
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=157,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=335,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'NEOPLASM.DISEASESTAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY.M.STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=16,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=56,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 14:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=5,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'HISTOLOGICAL.TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 17:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 18:'NUMBERPACKYEARSSMOKED':	nDistinctValues=6,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'YEAROFTOBACCOSMOKINGONSET':	nDistinctValues=2,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 20:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 22:'BATCH.NUMBER':	nDistinctValues=14,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                         "NEOPLASM.DISEASESTAGE"      
 [3] "PATHOLOGY.T.STAGE"           "PATHOLOGY.N.STAGE"          
 [5] "PATHOLOGY.M.STAGE"           "GENDER"                     
 [7] "KARNOFSKY.PERFORMANCE.SCORE" "NUMBERPACKYEARSSMOKED"      
 [9] "RACE"                        "ETHNICITY"                  
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 505 columns, 1 survival variables, and 10 non-survival variables.
AGE, nv=59, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=4, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
250  67 177  11 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
250  67 177  11 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
 T1  T2  T3  T4 
250  67 177  11 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
250  67 177  11 
PATHOLOGY.N.STAGE, nv=2, binary=FALSE, numeric=TRUE
PATHOLOGY.M.STAGE, nv=3, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY.PERFORMANCE.SCORE, nv=5, binary=FALSE, numeric=TRUE
NUMBERPACKYEARSSMOKED, nv=6, binary=FALSE, numeric=TRUE
RACE, nv=3, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1P GAIN MUTATION ANALYSIS
D1V1, survival
                   sevent
clus2                 0   1
  1P GAIN MUTATED    10   2
  1P GAIN WILD-TYPE 328  24
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               12               352 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                2                24 
$`1P GAIN MUTATED`
TCGA-A3-3316 TCGA-A3-3372 TCGA-AK-3430 TCGA-B8-5551 TCGA-BP-4756 TCGA-BP-5175 
        1493          735          480           15          374          932 
TCGA-CJ-4635 TCGA-CJ-4873 TCGA-CJ-6027 TCGA-CW-6090 TCGA-CZ-4858 TCGA-CZ-5452 
        1416         2259         1855         2552         1943         1789 

$`1P GAIN WILD-TYPE`
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3319 
        1120         1436           16          735         1491         1130 
TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 
        1508         1478         1106         1186          751         1137 
TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3347 TCGA-A3-3349 
        1485          665         1043          945         1610         1385 
TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 
         910         2688         1307         2504         1559          319 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 
         873         2270         2274         1621         1314         1070 
TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 
         630          567          574          861         1993          617 
TCGA-A3-A8CQ TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3431 
           3         3343         2566         2223         2017         1853 
TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 
        2192         2087         2044         1745         1423         1471 
TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 
        1280         1217         1779         1481         1397          874 
TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 
        1143         1168          951          853          369         1238 
TCGA-AS-3778 TCGA-B0-4699 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4718 TCGA-B0-4813 
          43          110           26           96          616           18 
TCGA-B0-4819 TCGA-B0-5097 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 
         183          665          911         1092          359          797 
TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
         657          535           59          493          554          652 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 
        1132          449         2408         3431         1487         3076 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 
        1420         1727         1835         2583         2741         1732 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 
        1605         1203         3668         2414         3117         1459 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 
        2931         2722         1865         2963          992         1092 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 
          51          374          648          952          358          315 
TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 
         417          656          507          291          175            7 
TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 
          38           16          141          166           11            7 
TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 
         511          826          838          762          750          523 
TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 
         777          788          700          636          722           36 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 
         822           26          737          522          505          194 
TCGA-B8-5550 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G 
         434         1046          435          830          519           53 
TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4158 TCGA-BP-4160 
         256          150           66          110         3377         2881 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 
        2746         3074         2839         3037           13         2718 
TCGA-BP-4169 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 
         701         1893         1879         1955         1670         2964 
TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 
        1625          845         1888         1133          645          461 
TCGA-BP-4338 TCGA-BP-4344 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4758 
        2859         1666         1367          372          970         2208 
TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 
        2372         2361          182         2184         1462          400 
TCGA-BP-4769 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 
        1876         1885         1843          411         1731         2080 
TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4801 
         354         1854         1489          620         1107         1124 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 
         204         1459          211         2660         2172         1935 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 
        1785         1834         1862         1871          205         1746 
TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4975 
        1794          433         1487         1502         1384         1433 
TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4987 
        1632          454         1014         1413          785         1124 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 
         118         1413          501          177         1308         1371 
TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 
         932         1266          563         1177         1126          840 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5177 
        1140         1071          193         2412         2257          293 
TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 
        2263         1495         1165         1291         1133         1132 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 
         693          406          822         1011          967          714 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 
         408          749         1018          603         1355         1063 
TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4636 TCGA-CJ-4639 TCGA-CJ-4640 
         951           29         1820         1924         2308         1998 
TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
        1628         1793          646         2554         1498         2423 
TCGA-CJ-4872 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 
        1435         2283         2353         1955         2186         2014 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4889 TCGA-CJ-4890 
        1883         1759         2125         1952         1946         2085 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4901 
        1521          750          841         1808         1528         1450 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 
        1520         1560         1792         1496         1499         1531 
TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-5671 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5681 
        1657         1373         1943         2430         2575          552 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6031 TCGA-CJ-6032 
        1883         1889         2231         2038         1906         2548 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 
        2799         2489         2609         2226         2017         2378 
TCGA-CW-5591 TCGA-CW-6088 TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 
        2271         3222         3146          774         1404           18 
TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 
        1787         1843         1928         2830         1868         1929 
TCGA-CZ-5453 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
          25         1712         1683         1732         1683         1430 
TCGA-CZ-5461 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5468 
         330          662         1740         1446          685           59 
TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
         946          386         2439         2067         1997          373 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 
         435          693         1905         1329         1398         1470 
TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-EU-5904 
         370          355         1130          723         1729          551 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-GK-A6C7 
         119          206          127           61 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               15                 3 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             2552              3668 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
           1454.5            1285.5 
[1] "15.0 - 2552.0 (1454.5)" "3.0 - 3668.0 (1285.5)" 
[1] "hr=" "2.5"
D1V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  1P GAIN MUTATED         7        3         8        5
  1P GAIN WILD-TYPE     237       53       118       74
D1V3, multiclass
           clus
vv          1P GAIN MUTATED 1P GAIN WILD-TYPE
  STAGE I                 7               237
  STAGE II                3                53
  STAGE III               8               118
  STAGE IV                5                74
[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"
                   vv
clus                 T1  T2  T3  T4
  1P GAIN MUTATED     8   3  12   0
  1P GAIN WILD-TYPE 242  64 165  11
D1V4, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  T1               8               242
  T2               3                64
  T3              12               165
  T4               0                11
[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"
D1V5, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    10   2
  1P GAIN WILD-TYPE 220  16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     10    2
  1P GAIN WILD-TYPE  220   16
   clus
vv  1P GAIN MUTATED 1P GAIN WILD-TYPE
  0              10               220
  1               2                16
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  1P GAIN MUTATED    18   5   0
  1P GAIN WILD-TYPE 399  73   9
D1V6, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  M0              18               399
  M1               5                73
  MX               0                 9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V7, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     8  15
  1P GAIN WILD-TYPE 170 312
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      8   15
  1P GAIN WILD-TYPE  170  312
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE               8               170
  MALE                15               312
[1] 2 2
[1] FALSE
D1V8, continuous
D1V9, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1P GAIN MUTATED       1                         1    21
  1P GAIN WILD-TYPE     7                        32   436
D1V10, multiclass
                           clus
vv                          1P GAIN MUTATED 1P GAIN WILD-TYPE
  ASIAN                                   1                 7
  BLACK OR AFRICAN AMERICAN               1                32
  WHITE                                  21               436
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V11, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     1  14
  1P GAIN WILD-TYPE  23 316
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      1   14
  1P GAIN WILD-TYPE   23  316
                        clus
vv                       1P GAIN MUTATED 1P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                23
  NOT HISPANIC OR LATINO              14               316
[1] 2 2
[1] FALSE

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                 0   1
  1Q GAIN MUTATED    27   3
  1Q GAIN WILD-TYPE 311  23
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               30               334 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                3                23 
$`1Q GAIN MUTATED`
TCGA-A3-3316 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3372 TCGA-A3-3382 TCGA-AK-3430 
        1493         1043          945          735          574          480 
TCGA-AK-3450 TCGA-B0-5115 TCGA-B0-5701 TCGA-B4-5843 TCGA-B8-5551 TCGA-BP-4161 
        1779          797         1732           11           15         2746 
TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4756 TCGA-BP-4781 TCGA-BP-5175 TCGA-CJ-4635 
        1879         1955          374         2080          932         1416 
TCGA-CJ-4640 TCGA-CJ-4873 TCGA-CJ-4876 TCGA-CJ-4881 TCGA-CJ-4916 TCGA-CJ-5675 
        1998         2259         1955         2014         1373         2430 
TCGA-CJ-6027 TCGA-CW-5587 TCGA-CW-6090 TCGA-CZ-4854 TCGA-CZ-4858 TCGA-CZ-5452 
        1855         2226         2552         1404         1943         1789 

$`1Q GAIN WILD-TYPE`
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3319 
        1120         1436           16          735         1491         1130 
TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 
        1508         1478         1106         1186          751         1137 
TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 
        1485          665         1610         1385          910         2688 
TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 
        1307         2504         1559          319          873         2270 
TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 
        2274         1621         1314         1070          630          567 
TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A8CQ TCGA-AK-3425 TCGA-AK-3427 
         861         1993          617            3         3343         2566 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 
        2223         2017         1853         2192         2087         2044 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3451 
        1745         1423         1471         1280         1217         1481 
TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
        1397          874         1143         1168          951          853 
TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4699 TCGA-B0-4706 TCGA-B0-4710 
         369         1238           43          110           26           96 
TCGA-B0-4718 TCGA-B0-4813 TCGA-B0-4819 TCGA-B0-5097 TCGA-B0-5108 TCGA-B0-5110 
         616           18          183          665          911         1092 
TCGA-B0-5113 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
         359          657          535           59          493          554 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 
         652         1132          449         2408         3431         1487 
TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 
        3076         1420         1727         1835         2583         2741 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 
        1605         1203         3668         2414         3117         1459 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 
        2931         2722         1865         2963          992         1092 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 
          51          374          648          952          358          315 
TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 
         417          656          507          291          175            7 
TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5844 TCGA-B8-4146 
          38           16          141          166            7          511 
TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 
         826          838          762          750          523          777 
TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 
         788          700          636          722           36          822 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 
          26          737          522          505          194          434 
TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H 
        1046          435          830          519           53          256 
TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4162 
         150           66          110         3377         2881         3074 
TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4173 
        2839         3037           13         2718          701         1893 
TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 
        1670         2964         1625          845         1888         1133 
TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4338 TCGA-BP-4344 TCGA-BP-4347 TCGA-BP-4349 
         645          461         2859         1666         1367          372 
TCGA-BP-4351 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4765 
         970         2208         2372         2361          182         2184 
TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 
        1462          400         1876         1885         1843          411 
TCGA-BP-4777 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4795 TCGA-BP-4797 
        1731          354         1854         1489          620         1107 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 
        1124          204         1459          211         2660         2172 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 
        1935         1785         1834         1862         1871          205 
TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 
        1746         1794          433         1487         1502         1384 
TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4986 
        1433         1632          454         1014         1413          785 
TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 
        1124          118         1413          501          177         1308 
TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
        1371          932         1266          563         1177         1126 
TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 
         840         1140         1071          193         2412         2257 
TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
         293         2263         1495         1165         1291         1133 
TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 
        1132          693          406          822         1011          967 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 
         714          408          749         1018          603         1355 
TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4636 TCGA-CJ-4639 
        1063          951           29         1820         1924         2308 
TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
        1628         1793          646         2554         1498         2423 
TCGA-CJ-4872 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4878 TCGA-CJ-4882 TCGA-CJ-4884 
        1435         2283         2353         2186         1883         1759 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 
        2125         1952         1946         2085         1521          750 
TCGA-CJ-4894 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 
         841         1808         1528         1450         1520         1560 
TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-5671 
        1792         1496         1499         1531         1657         1943 
TCGA-CJ-5676 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 
        2575          552         1883         1889         2231         2038 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 
        1906         2548         2799         2489         2609         2017 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6088 TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4856 
        2378         2271         3222         3146          774           18 
TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 
        1787         1843         1928         2830         1868         1929 
TCGA-CZ-5453 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
          25         1712         1683         1732         1683         1430 
TCGA-CZ-5461 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5468 
         330          662         1740         1446          685           59 
TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
         946          386         2439         2067         1997          373 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 
         435          693         1905         1329         1398         1470 
TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-EU-5904 
         370          355         1130          723         1729          551 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-GK-A6C7 
         119          206          127           61 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               11                 3 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             2746              3668 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           1755.5            1210.0 
[1] "11.0 - 2746.0 (1755.5)" "3.0 - 3668.0 (1210.0)" 
[1] "hr=" "1.3"
D2V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  1Q GAIN MUTATED        17        8        17        8
  1Q GAIN WILD-TYPE     227       48       109       71
D2V3, multiclass
           clus
vv          1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  STAGE I                17               227
  STAGE II                8                48
  STAGE III              17               109
  STAGE IV                8                71
[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"
                   vv
clus                 T1  T2  T3  T4
  1Q GAIN MUTATED    19  10  21   0
  1Q GAIN WILD-TYPE 231  57 156  11
D2V4, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  T1              19               231
  T2              10                57
  T3              21               156
  T4               0                11
[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"
D2V5, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    24   3
  1Q GAIN WILD-TYPE 206  15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     24    3
  1Q GAIN WILD-TYPE  206   15
   clus
vv  1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  0              24               206
  1               3                15
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  1Q GAIN MUTATED    41   9   0
  1Q GAIN WILD-TYPE 376  69   9
D2V6, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  M0              41               376
  M1               9                69
  MX               0                 9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V7, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    16  34
  1Q GAIN WILD-TYPE 162 293
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     16   34
  1Q GAIN WILD-TYPE  162  293
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE              16               162
  MALE                34               293
[1] 2 2
[1] FALSE
D2V8, continuous
D2V9, continuous
[1] "Remove cluster labels:" "1Q GAIN MUTATED"       
clus
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                1                 7 
       TCGA-A3-A8CQ        TCGA-B2-A4SR        TCGA-B8-4621        TCGA-B8-5158 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-B8-5164        TCGA-B8-A54F        TCGA-B8-A54G 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1Q GAIN MUTATED       1                         3    46
  1Q GAIN WILD-TYPE     7                        30   411
D2V10, multiclass
                           clus
vv                          1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  ASIAN                                   1                 7
  BLACK OR AFRICAN AMERICAN               3                30
  WHITE                                  46               411
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V11, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED     3  32
  1Q GAIN WILD-TYPE  21 298
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      3   32
  1Q GAIN WILD-TYPE   21  298
                        clus
vv                       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                21
  NOT HISPANIC OR LATINO              32               298
[1] 2 2
[1] FALSE

Clustering(3) Variable = 2P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                 0   1
  2P GAIN MUTATED    53   6
  2P GAIN WILD-TYPE 285  20
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               59               305 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                6                20 
$`2P GAIN MUTATED`
TCGA-A3-3372 TCGA-A3-3382 TCGA-A3-A8CQ TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3444 
         735          574            3         2017          480         1471 
TCGA-AK-3450 TCGA-B0-4710 TCGA-B0-4813 TCGA-B0-5113 TCGA-B0-5702 TCGA-B4-5832 
        1779           96           18          359         1605            7 
TCGA-B4-5838 TCGA-B4-5843 TCGA-B8-4620 TCGA-B8-5159 TCGA-B8-5549 TCGA-B8-5550 
         166           11          777          722          194          434 
TCGA-B8-5551 TCGA-B8-A54I TCGA-BP-4162 TCGA-BP-4166 TCGA-BP-4174 TCGA-BP-4338 
          15          150         3074           13         1879         2859 
TCGA-BP-4347 TCGA-BP-4351 TCGA-BP-4756 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4775 
        1367          970          374         1462          400         1843 
TCGA-BP-4781 TCGA-BP-4804 TCGA-BP-4969 TCGA-BP-4989 TCGA-BP-5185 TCGA-BP-5200 
        2080         1459         1794          118         1132         1063 
TCGA-CJ-4876 TCGA-CJ-4893 TCGA-CJ-4897 TCGA-CJ-4901 TCGA-CJ-4903 TCGA-CJ-4907 
        1955          750         1808         1450         1560         1499 
TCGA-CJ-5671 TCGA-CJ-5676 TCGA-CJ-5682 TCGA-CJ-6032 TCGA-CW-5587 TCGA-CW-5588 
        1943         2575         1883         2548         2226         2017 
TCGA-CW-5591 TCGA-CZ-4854 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-5456 TCGA-CZ-5457 
        2271         1404         1943         1787         1712         1683 
TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5469 TCGA-CZ-5984 TCGA-EU-5905 
        1430          330          946         2067          119 

$`2P GAIN WILD-TYPE`
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 
        1120         1436           16          735         1493         1491 
TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 
        1130         1508         1478         1106         1186          751 
TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3347 
        1137         1485          665         1043          945         1610 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 
        1385          910         2688         1307         2504         1559 
TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 
         319          873         2270         2274         1621         1314 
TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 
        1070          630          567          861         1993          617 
TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 
        3343         2566         2223         1853         2192         2087 
TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3451 
        2044         1745         1423         1280         1217         1481 
TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
        1397          874         1143         1168          951          853 
TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4699 TCGA-B0-4706 TCGA-B0-4718 
         369         1238           43          110           26          616 
TCGA-B0-4819 TCGA-B0-5097 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5115 TCGA-B0-5116 
         183          665          911         1092          797          657 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
         535           59          493          554          652         1132 
TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 
         449         2408         3431         1487         3076         1420 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5703 
        1727         1835         2583         2741         1732         1203 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
        3668         2414         3117         1459         2931         2722 
TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
        1865         2963          992         1092           51          374 
TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 
         648          952          358          315          417          656 
TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
         507          291          175           38           16          141 
TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
           7          511          826          838          762          750 
TCGA-B8-4619 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5162 TCGA-B8-5163 
         523          788          700          636           36          822 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5552 TCGA-B8-5553 
          26          737          522          505         1046          435 
TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54J TCGA-B8-A7U6 
         830          519           53          256           66          110 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4167 
        3377         2881         2746         2839         3037         2718 
TCGA-BP-4169 TCGA-BP-4173 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 
         701         1893         1955         1670         2964         1625 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4344 
         845         1888         1133          645          461         1666 
TCGA-BP-4349 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4765 
         372         2208         2372         2361          182         2184 
TCGA-BP-4769 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4782 TCGA-BP-4784 
        1876         1885          411         1731          354         1854 
TCGA-BP-4789 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4807 
        1489          620         1107         1124          204          211 
TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 
        2660         2172         1935         1785         1834         1862 
TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
        1871          205         1746          433         1487         1502 
TCGA-BP-4973 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4982 TCGA-BP-4983 
        1384         1433         1632          454         1014         1413 
TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 
         785         1124         1413          501          177         1308 
TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
        1371          932         1266          563         1177         1126 
TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 
         840         1140         1071          193         2412         2257 
TCGA-BP-5175 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 
         932          293         2263         1495         1165         1291 
TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 
        1133          693          406          822         1011          967 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 
         714          408          749         1018          603         1355 
TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4639 
         951           29         1820         1416         1924         2308 
TCGA-CJ-4640 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
        1998         1628         1793          646         2554         1498 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4878 
        2423         1435         2259         2283         2353         2186 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4889 
        2014         1883         1759         2125         1952         1946 
TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4894 TCGA-CJ-4899 TCGA-CJ-4902 TCGA-CJ-4904 
        2085         1521          841         1528         1520         1792 
TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-5675 TCGA-CJ-5681 
        1496         1531         1657         1373         2430          552 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6031 TCGA-CW-5581 
        1889         2231         2038         1855         1906         2799 
TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5589 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 
        2489         2609         2378         3222         2552         3146 
TCGA-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 
         774           18         1843         1928         2830         1868 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5463 
        1929         1789           25         1732         1683          662 
TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5470 TCGA-CZ-5982 
        1740         1446          685           59          386         2439 
TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 
        1997          373          435          693         1905         1329 
TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 
        1398         1470          370          355         1130          723 
TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5906 TCGA-EU-5907 TCGA-GK-A6C7 
        1729          551          206          127           61 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                3                 7 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             3074              3668 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             1430              1266 
[1] "3.0 - 3074.0 (1430.0)" "7.0 - 3668.0 (1266.0)"
[1] "hr=" "1.7"
D3V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  2P GAIN MUTATED        32        9        26        8
  2P GAIN WILD-TYPE     212       47       100       71
D3V3, multiclass
           clus
vv          2P GAIN MUTATED 2P GAIN WILD-TYPE
  STAGE I                32               212
  STAGE II                9                47
  STAGE III              26               100
  STAGE IV                8                71
[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"
                   vv
clus                 T1  T2  T3  T4
  2P GAIN MUTATED    33   9  31   2
  2P GAIN WILD-TYPE 217  58 146   9
D3V4, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  T1              33               217
  T2               9                58
  T3              31               146
  T4               2                 9
[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"
D3V5, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    35   3
  2P GAIN WILD-TYPE 195  15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     35    3
  2P GAIN WILD-TYPE  195   15
   clus
vv  2P GAIN MUTATED 2P GAIN WILD-TYPE
  0              35               195
  1               3                15
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  2P GAIN MUTATED    65   8   2
  2P GAIN WILD-TYPE 352  70   7
D3V6, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  M0              65               352
  M1               8                70
  MX               2                 7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V7, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    27  48
  2P GAIN WILD-TYPE 151 279
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     27   48
  2P GAIN WILD-TYPE  151  279
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE              27               151
  MALE                48               279
[1] 2 2
[1] FALSE
D3V8, continuous
D3V9, continuous
[1] "Remove cluster labels:" "2P GAIN MUTATED"       
clus
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                1                 7 
       TCGA-B2-A4SR        TCGA-B8-4621        TCGA-B8-5158        TCGA-B8-5164 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-B8-A54F        TCGA-B8-A54G        TCGA-G6-A5PC 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2P GAIN MUTATED       1                         3    71
  2P GAIN WILD-TYPE     7                        30   386
D3V10, multiclass
                           clus
vv                          2P GAIN MUTATED 2P GAIN WILD-TYPE
  ASIAN                                   1                 7
  BLACK OR AFRICAN AMERICAN               3                30
  WHITE                                  71               386
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V11, binary
                   cls
clus                  0   1
  2P GAIN MUTATED     4  43
  2P GAIN WILD-TYPE  20 287
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      4   43
  2P GAIN WILD-TYPE   20  287
                        clus
vv                       2P GAIN MUTATED 2P GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                20
  NOT HISPANIC OR LATINO              43               287
[1] 2 2
[1] FALSE

Clustering(4) Variable = 2Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                 0   1
  2Q GAIN MUTATED    54   5
  2Q GAIN WILD-TYPE 284  21
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               59               305 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                5                21 
$`2Q GAIN MUTATED`
TCGA-A3-3372 TCGA-A3-3382 TCGA-A3-A8CQ TCGA-AK-3429 TCGA-AK-3444 TCGA-AK-3450 
         735          574            3         2017         1471         1779 
TCGA-B0-4710 TCGA-B0-4813 TCGA-B0-5113 TCGA-B0-5702 TCGA-B4-5832 TCGA-B4-5838 
          96           18          359         1605            7          166 
TCGA-B4-5843 TCGA-B8-4620 TCGA-B8-5159 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 
          11          777          722          194          434           15 
TCGA-B8-A54I TCGA-BP-4162 TCGA-BP-4166 TCGA-BP-4174 TCGA-BP-4338 TCGA-BP-4347 
         150         3074           13         1879         2859         1367 
TCGA-BP-4351 TCGA-BP-4756 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4775 TCGA-BP-4781 
         970          374         1462          400         1843         2080 
TCGA-BP-4804 TCGA-BP-4969 TCGA-BP-4989 TCGA-BP-5001 TCGA-BP-5174 TCGA-BP-5185 
        1459         1794          118         1177         2257         1132 
TCGA-BP-5200 TCGA-CJ-4876 TCGA-CJ-4893 TCGA-CJ-4897 TCGA-CJ-4901 TCGA-CJ-4903 
        1063         1955          750         1808         1450         1560 
TCGA-CJ-4907 TCGA-CJ-5671 TCGA-CJ-5676 TCGA-CJ-5682 TCGA-CJ-6032 TCGA-CW-5587 
        1499         1943         2575         1883         2548         2226 
TCGA-CW-5588 TCGA-CW-5591 TCGA-CZ-4854 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-5456 
        2017         2271         1404         1943         1787         1712 
TCGA-CZ-5457 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5469 TCGA-EU-5905 
        1683         1430          330          946          119 

$`2Q GAIN WILD-TYPE`
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 
        1120         1436           16          735         1493         1491 
TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 
        1130         1508         1478         1106         1186          751 
TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3347 
        1137         1485          665         1043          945         1610 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 
        1385          910         2688         1307         2504         1559 
TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 
         319          873         2270         2274         1621         1314 
TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 
        1070          630          567          861         1993          617 
TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 
        3343         2566         2223          480         1853         2192 
TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3447 
        2087         2044         1745         1423         1280         1217 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
        1481         1397          874         1143         1168          951 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4699 TCGA-B0-4706 
         853          369         1238           43          110           26 
TCGA-B0-4718 TCGA-B0-4819 TCGA-B0-5097 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5115 
         616          183          665          911         1092          797 
TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
         657          535           59          493          554          652 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 
        1132          449         2408         3431         1487         3076 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 
        1420         1727         1835         2583         2741         1732 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
        1203         3668         2414         3117         1459         2931 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
        2722         1865         2963          992         1092           51 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 
         374          648          952          358          315          417 
TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5835 
         656          507          291          175           38           16 
TCGA-B4-5836 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
         141            7          511          826          838          762 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5162 
         750          523          788          700          636           36 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5552 
         822           26          737          522          505         1046 
TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54J 
         435          830          519           53          256           66 
TCGA-B8-A7U6 TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4163 TCGA-BP-4165 
         110         3377         2881         2746         2839         3037 
TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4173 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 
        2718          701         1893         1955         1670         2964 
TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 
        1625          845         1888         1133          645          461 
TCGA-BP-4344 TCGA-BP-4349 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 
        1666          372         2208         2372         2361          182 
TCGA-BP-4765 TCGA-BP-4769 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4782 
        2184         1876         1885          411         1731          354 
TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4801 TCGA-BP-4803 
        1854         1489          620         1107         1124          204 
TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
         211         2660         2172         1935         1785         1834 
TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 
        1862         1871          205         1746          433         1487 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4982 
        1502         1384         1433         1632          454         1014 
TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 
        1413          785         1124         1413          501          177 
TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5004 
        1308         1371          932         1266          563         1126 
TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5175 
         840         1140         1071          193         2412          932 
TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
         293         2263         1495         1165         1291         1133 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 
         693          406          822         1011          967          714 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5201 
         408          749         1018          603         1355          951 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4639 TCGA-CJ-4640 
          29         1820         1416         1924         2308         1998 
TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
        1628         1793          646         2554         1498         2423 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4878 TCGA-CJ-4881 
        1435         2259         2283         2353         2186         2014 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4889 TCGA-CJ-4890 
        1883         1759         2125         1952         1946         2085 
TCGA-CJ-4892 TCGA-CJ-4894 TCGA-CJ-4899 TCGA-CJ-4902 TCGA-CJ-4904 TCGA-CJ-4905 
        1521          841         1528         1520         1792         1496 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-5675 TCGA-CJ-5681 TCGA-CJ-5683 
        1531         1657         1373         2430          552         1889 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6031 TCGA-CW-5581 TCGA-CW-5583 
        2231         2038         1855         1906         2799         2489 
TCGA-CW-5585 TCGA-CW-5589 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CZ-4853 
        2609         2378         3222         2552         3146          774 
TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 
          18         1843         1928         2830         1868         1929 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5463 TCGA-CZ-5464 
        1789           25         1732         1683          662         1740 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 
        1446          685           59          386         2439         2067 
TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 
        1997          373          435          693         1905         1329 
TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 
        1398         1470          370          355         1130          723 
TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5906 TCGA-EU-5907 TCGA-GK-A6C7 
        1729          551          206          127           61 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                3                 7 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             3074              3668 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             1430              1266 
[1] "3.0 - 3074.0 (1430.0)" "7.0 - 3668.0 (1266.0)"
[1] "hr=" "1.3"
D4V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  2Q GAIN MUTATED        34        9        25        9
  2Q GAIN WILD-TYPE     210       47       101       70
D4V3, multiclass
           clus
vv          2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  STAGE I                34               210
  STAGE II                9                47
  STAGE III              25               101
  STAGE IV                9                70
[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"
                   vv
clus                 T1  T2  T3  T4
  2Q GAIN MUTATED    35   9  31   2
  2Q GAIN WILD-TYPE 215  58 146   9
D4V4, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  T1              35               215
  T2               9                58
  T3              31               146
  T4               2                 9
[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"
D4V5, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    36   2
  2Q GAIN WILD-TYPE 194  16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     36    2
  2Q GAIN WILD-TYPE  194   16
   clus
vv  2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  0              36               194
  1               2                16
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  2Q GAIN MUTATED    66   9   2
  2Q GAIN WILD-TYPE 351  69   7
D4V6, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  M0              66               351
  M1               9                69
  MX               2                 7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V7, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    31  46
  2Q GAIN WILD-TYPE 147 281
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     31   46
  2Q GAIN WILD-TYPE  147  281
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE              31               147
  MALE                46               281
[1] 2 2
[1] FALSE
D4V8, continuous
D4V9, continuous
[1] "Remove cluster labels:" "2Q GAIN MUTATED"       
clus
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                1                 7 
       TCGA-B2-A4SR        TCGA-B8-4621        TCGA-B8-5158        TCGA-B8-5164 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-B8-A54F        TCGA-B8-A54G        TCGA-G6-A5PC 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2Q GAIN MUTATED       1                         3    73
  2Q GAIN WILD-TYPE     7                        30   384
D4V10, multiclass
                           clus
vv                          2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  ASIAN                                   1                 7
  BLACK OR AFRICAN AMERICAN               3                30
  WHITE                                  73               384
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V11, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED     5  44
  2Q GAIN WILD-TYPE  19 286
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      5   44
  2Q GAIN WILD-TYPE   19  286
                        clus
vv                       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   5                19
  NOT HISPANIC OR LATINO              44               286
[1] 2 2
[1] FALSE

Clustering(5) Variable = 3P GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                 0   1
  3P GAIN MUTATED    10   2
  3P GAIN WILD-TYPE 328  24
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               12               352 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                2                24 
$`3P GAIN MUTATED`
TCGA-A3-3374 TCGA-AK-3440 TCGA-AK-3453 TCGA-B0-4699 TCGA-B4-5835 TCGA-BP-4969 
        1314         1745         1397          110           16         1794 
TCGA-BP-4994 TCGA-BP-5175 TCGA-BP-5198 TCGA-CJ-4897 TCGA-CZ-5456 TCGA-CZ-5469 
        1308          932          603         1808         1712          946 

$`3P GAIN WILD-TYPE`
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 
        1120         1436           16          735         1493         1491 
TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 
        1130         1508         1478         1106         1186          751 
TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3347 
        1137         1485          665         1043          945         1610 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 
        1385          910         2688         1307         2504         1559 
TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 
         319          873         2270         2274          735         1621 
TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 
        1070          630          567          574          861         1993 
TCGA-A3-3387 TCGA-A3-A8CQ TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
         617            3         3343         2566         2223         2017 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3443 
         480         1853         2192         2087         2044         1423 
TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 
        1471         1280         1217         1779         1481          874 
TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 
        1143         1168          951          853          369         1238 
TCGA-AS-3778 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4718 TCGA-B0-4813 TCGA-B0-4819 
          43           26           96          616           18          183 
TCGA-B0-5097 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 
         665          911         1092          359          797          657 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
         535           59          493          554          652         1132 
TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 
         449         2408         3431         1487         3076         1420 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
        1727         1835         2583         2741         1732         1605 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
        1203         3668         2414         3117         1459         2931 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
        2722         1865         2963          992         1092           51 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 
         374          648          952          358          315          417 
TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 
         656          507          291          175            7           38 
TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 
         141          166           11            7          511          826 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 
         838          762          750          523          777          788 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 
         700          636          722           36          822           26 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 
         737          522          505          194          434           15 
TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H 
        1046          435          830          519           53          256 
TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4161 
         150           66          110         3377         2881         2746 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 
        3074         2839         3037           13         2718          701 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 
        1893         1879         1955         1670         2964         1625 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4338 
         845         1888         1133          645          461         2859 
TCGA-BP-4344 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4756 TCGA-BP-4758 
        1666         1367          372          970          374         2208 
TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 
        2372         2361          182         2184         1462          400 
TCGA-BP-4769 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 
        1876         1885         1843          411         1731         2080 
TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4801 
         354         1854         1489          620         1107         1124 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 
         204         1459          211         2660         2172         1935 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 
        1785         1834         1862         1871          205         1746 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4975 TCGA-BP-4976 
         433         1487         1502         1384         1433         1632 
TCGA-BP-4977 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4989 
         454         1014         1413          785         1124          118 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 
        1413          501          177         1371          932         1266 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 
         563         1177         1126          840         1140         1071 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5181 
         193         2412         2257          293         2263         1495 
TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 
        1165         1291         1133         1132          693          406 
TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
         822         1011          967          714          408          749 
TCGA-BP-5196 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 
        1018         1355         1063          951           29         1820 
TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4642 TCGA-CJ-4643 
        1416         1924         2308         1998         1628         1793 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 
         646         2554         1498         2423         1435         2259 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 
        2283         2353         1955         2186         2014         1883 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 
        1759         2125         1952         1946         2085         1521 
TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4899 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 
         750          841         1528         1450         1520         1560 
TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4916 
        1792         1496         1499         1531         1657         1373 
TCGA-CJ-5671 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
        1943         2430         2575          552         1883         1889 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CW-5581 
        2231         2038         1855         1906         2548         2799 
TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 
        2489         2609         2226         2017         2378         2271 
TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 
        3222         2552         3146          774         1404           18 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 
        1943         1787         1843         1928         2830         1868 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 
        1929         1789           25         1683         1732         1683 
TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 
        1430          330          662         1740         1446          685 
TCGA-CZ-5468 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
          59          386         2439         2067         1997          373 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 
         435          693         1905         1329         1398         1470 
TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-EU-5904 
         370          355         1130          723         1729          551 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-GK-A6C7 
         119          206          127           61 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               16                 3 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             1808              3668 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
           1311.0            1285.5 
[1] "16.0 - 1808.0 (1311.0)" "3.0 - 3668.0 (1285.5)" 
[1] "hr=" "2.7"
D5V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  3P GAIN MUTATED         6        3         4        6
  3P GAIN WILD-TYPE     238       53       122       73
D5V3, multiclass
           clus
vv          3P GAIN MUTATED 3P GAIN WILD-TYPE
  STAGE I                 6               238
  STAGE II                3                53
  STAGE III               4               122
  STAGE IV                6                73
[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"
                   vv
clus                 T1  T2  T3  T4
  3P GAIN MUTATED     6   3   9   1
  3P GAIN WILD-TYPE 244  64 168  10
D5V4, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  T1               6               244
  T2               3                64
  T3               9               168
  T4               1                10
[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"
D5V5, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     9   3
  3P GAIN WILD-TYPE 221  15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      9    3
  3P GAIN WILD-TYPE  221   15
   clus
vv  3P GAIN MUTATED 3P GAIN WILD-TYPE
  0               9               221
  1               3                15
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  3P GAIN MUTATED    13   6   0
  3P GAIN WILD-TYPE 404  72   9
D5V6, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  M0              13               404
  M1               6                72
  MX               0                 9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V7, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     9  10
  3P GAIN WILD-TYPE 169 317
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      9   10
  3P GAIN WILD-TYPE  169  317
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE               9               169
  MALE                10               317
[1] 2 2
[1] FALSE
D5V8, continuous
D5V9, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3P GAIN MUTATED       0                         1    18
  3P GAIN WILD-TYPE     8                        32   439
D5V10, multiclass
                           clus
vv                          3P GAIN MUTATED 3P GAIN WILD-TYPE
  ASIAN                                   0                 8
  BLACK OR AFRICAN AMERICAN               1                32
  WHITE                                  18               439
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V11, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     1  13
  3P GAIN WILD-TYPE  23 317
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      1   13
  3P GAIN WILD-TYPE   23  317
                        clus
vv                       3P GAIN MUTATED 3P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                23
  NOT HISPANIC OR LATINO              13               317
[1] 2 2
[1] FALSE

Clustering(6) Variable = 3Q GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                 0   1
  3Q GAIN MUTATED    36   4
  3Q GAIN WILD-TYPE 302  22
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               40               324 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                4                22 
$`3Q GAIN MUTATED`
TCGA-A3-3325 TCGA-A3-3374 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3453 
         751         1314         2087         2044         1745         1397 
TCGA-B0-4699 TCGA-B0-5097 TCGA-B0-5116 TCGA-B0-5696 TCGA-B0-5710 TCGA-B4-5835 
         110          665          657         1727         1459           16 
TCGA-B4-5838 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-5549 TCGA-B8-5551 TCGA-BP-4163 
         166          777          788          194           15         2839 
TCGA-BP-4167 TCGA-BP-4329 TCGA-BP-4338 TCGA-BP-4761 TCGA-BP-4960 TCGA-BP-4969 
        2718          845         2859          182         2172         1794 
TCGA-BP-4994 TCGA-BP-5169 TCGA-BP-5175 TCGA-BP-5198 TCGA-CJ-4640 TCGA-CJ-4871 
        1308          193          932          603         1998         2423 
TCGA-CJ-4881 TCGA-CJ-4897 TCGA-CJ-4901 TCGA-CW-5591 TCGA-CZ-4858 TCGA-CZ-5456 
        2014         1808         1450         2271         1943         1712 
TCGA-CZ-5460 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5469 
        1430         1740         1446          946 

$`3Q GAIN WILD-TYPE`
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 
        1120         1436           16          735         1493         1491 
TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3326 
        1130         1508         1478         1106         1186         1137 
TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3347 TCGA-A3-3349 
        1485          665         1043          945         1610         1385 
TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 
         910         2688         1307         2504         1559          319 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 
         873         2270         2274          735         1621         1070 
TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 
         630          567          574          861         1993          617 
TCGA-A3-A8CQ TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 
           3         3343         2566         2223         2017          480 
TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 
        1853         2192         1423         1471         1280         1217 
TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
        1779         1481          874         1143         1168          951 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4706 TCGA-B0-4710 
         853          369         1238           43           26           96 
TCGA-B0-4718 TCGA-B0-4813 TCGA-B0-4819 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 
         616           18          183          911         1092          359 
TCGA-B0-5115 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
         797          535           59          493          554          652 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 
        1132          449         2408         3431         1487         3076 
TCGA-B0-5695 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
        1420         1835         2583         2741         1732         1605 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5711 TCGA-B0-5712 
        1203         3668         2414         3117         2931         2722 
TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
        1865         2963          992         1092           51          374 
TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 
         648          952          358          315          417          656 
TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5836 
         507          291          175            7           38          141 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
          11            7          511          826          838          762 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 
         750          523          700          636          722           36 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5550 
         822           26          737          522          505          434 
TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H 
        1046          435          830          519           53          256 
TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4161 
         150           66          110         3377         2881         2746 
TCGA-BP-4162 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4169 TCGA-BP-4173 TCGA-BP-4174 
        3074         3037           13          701         1893         1879 
TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4330 TCGA-BP-4332 
        1955         1670         2964         1625         1888         1133 
TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4344 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 
         645          461         1666         1367          372          970 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4765 TCGA-BP-4766 
         374         2208         2372         2361         2184         1462 
TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 
         400         1876         1885         1843          411         1731 
TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4795 TCGA-BP-4797 
        2080          354         1854         1489          620         1107 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4961 
        1124          204         1459          211         2660         1935 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 
        1785         1834         1862         1871          205         1746 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4975 TCGA-BP-4976 
         433         1487         1502         1384         1433         1632 
TCGA-BP-4977 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4989 
         454         1014         1413          785         1124          118 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 
        1413          501          177         1371          932         1266 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 
         563         1177         1126          840         1140         1071 
TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 
        2412         2257          293         2263         1495         1165 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 
        1291         1133         1132          693          406          822 
TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
        1011          967          714          408          749         1018 
TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 
        1355         1063          951           29         1820         1416 
TCGA-CJ-4636 TCGA-CJ-4639 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 
        1924         2308         1628         1793          646         2554 
TCGA-CJ-4870 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 
        1498         1435         2259         2283         2353         1955 
TCGA-CJ-4878 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4889 
        2186         1883         1759         2125         1952         1946 
TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4899 TCGA-CJ-4902 
        2085         1521          750          841         1528         1520 
TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 
        1560         1792         1496         1499         1531         1657 
TCGA-CJ-4916 TCGA-CJ-5671 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5681 TCGA-CJ-5682 
        1373         1943         2430         2575          552         1883 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6031 TCGA-CJ-6032 
        1889         2231         2038         1855         1906         2548 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 
        2799         2489         2609         2226         2017         2378 
TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 
        3222         2552         3146          774         1404           18 
TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 
        1787         1843         1928         2830         1868         1929 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5461 
        1789           25         1683         1732         1683          330 
TCGA-CZ-5463 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 
         662          685           59          386         2439         2067 
TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 
        1997          373          435          693         1905         1329 
TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 
        1398         1470          370          355         1130          723 
TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-GK-A6C7 
        1729          551          119          206          127           61 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               15                 3 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             2859              3668 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
           1438.0            1227.5 
[1] "15.0 - 2859.0 (1438.0)" "3.0 - 3668.0 (1227.5)" 
[1] "hr=" "1.4"
D6V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  3Q GAIN MUTATED        17        5        21       17
  3Q GAIN WILD-TYPE     227       51       105       62
D6V3, multiclass
           clus
vv          3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  STAGE I                17               227
  STAGE II                5                51
  STAGE III              21               105
  STAGE IV               17                62
[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"
                   vv
clus                 T1  T2  T3  T4
  3Q GAIN MUTATED    17   6  33   4
  3Q GAIN WILD-TYPE 233  61 144   7
D6V4, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  T1              17               233
  T2               6                61
  T3              33               144
  T4               4                 7
[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"
D6V5, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    30   7
  3Q GAIN WILD-TYPE 200  11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     30    7
  3Q GAIN WILD-TYPE  200   11
   clus
vv  3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  0              30               200
  1               7                11
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  3Q GAIN MUTATED    43  17   0
  3Q GAIN WILD-TYPE 374  61   9
D6V6, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  M0              43               374
  M1              17                61
  MX               0                 9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V7, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    20  40
  3Q GAIN WILD-TYPE 158 287
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     20   40
  3Q GAIN WILD-TYPE  158  287
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE              20               158
  MALE                40               287
[1] 2 2
[1] FALSE
D6V8, continuous
D6V9, continuous
[1] "Remove cluster labels:" "3Q GAIN MUTATED"       
clus
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                1                 7 
       TCGA-A3-A8CQ        TCGA-B2-A4SR        TCGA-B8-5158        TCGA-B8-5164 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-B8-A54F        TCGA-B8-A54G        TCGA-G6-A5PC 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3Q GAIN MUTATED       0                         3    56
  3Q GAIN WILD-TYPE     8                        30   401
D6V10, multiclass
                           clus
vv                          3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  ASIAN                                   0                 8
  BLACK OR AFRICAN AMERICAN               3                30
  WHITE                                  56               401
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V11, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED     3  39
  3Q GAIN WILD-TYPE  21 291
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      3   39
  3Q GAIN WILD-TYPE   21  291
                        clus
vv                       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                21
  NOT HISPANIC OR LATINO              39               291
[1] 2 2
[1] FALSE

Clustering(7) Variable = 4P GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                 0   1
  4P GAIN MUTATED     7   2
  4P GAIN WILD-TYPE 331  24
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                9               355 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                2                24 
$`4P GAIN MUTATED`
TCGA-A3-3374 TCGA-AK-3430 TCGA-AK-3433 TCGA-AK-3440 TCGA-B0-4813 TCGA-BP-4166 
        1314          480         2192         1745           18           13 
TCGA-BP-4977 TCGA-BP-4989 TCGA-BP-4994 
         454          118         1308 

$`4P GAIN WILD-TYPE`
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 
        1120         1436           16          735         1493         1491 
TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 
        1130         1508         1478         1106         1186          751 
TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3347 
        1137         1485          665         1043          945         1610 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 
        1385          910         2688         1307         2504         1559 
TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 
         319          873         2270         2274          735         1621 
TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 
        1070          630          567          574          861         1993 
TCGA-A3-3387 TCGA-A3-A8CQ TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
         617            3         3343         2566         2223         2017 
TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 
        1853         2087         2044         1423         1471         1280 
TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3456 
        1217         1779         1481         1397          874         1143 
TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 
        1168          951          853          369         1238           43 
TCGA-B0-4699 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4718 TCGA-B0-4819 TCGA-B0-5097 
         110           26           96          616          183          665 
TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 
         911         1092          359          797          657          535 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
          59          493          554          652         1132          449 
TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5696 
        2408         3431         1487         3076         1420         1727 
TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
        1835         2583         2741         1732         1605         1203 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
        3668         2414         3117         1459         2931         2722 
TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
        1865         2963          992         1092           51          374 
TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 
         648          952          358          315          417          656 
TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 
         507          291          175            7           38           16 
TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 
         141          166           11            7          511          826 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 
         838          762          750          523          777          788 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 
         700          636          722           36          822           26 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 
         737          522          505          194          434           15 
TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H 
        1046          435          830          519           53          256 
TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4161 
         150           66          110         3377         2881         2746 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4173 
        3074         2839         3037         2718          701         1893 
TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 
        1879         1955         1670         2964         1625          845 
TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4338 TCGA-BP-4344 
        1888         1133          645          461         2859         1666 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 
        1367          372          970          374         2208         2372 
TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 
        2361          182         2184         1462          400         1876 
TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 
        1885         1843          411         1731         2080          354 
TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4801 TCGA-BP-4803 
        1854         1489          620         1107         1124          204 
TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
        1459          211         2660         2172         1935         1785 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 
        1834         1862         1871          205         1746         1794 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4975 TCGA-BP-4976 
         433         1487         1502         1384         1433         1632 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4991 TCGA-BP-4992 
        1014         1413          785         1124         1413          501 
TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 
         177         1371          932         1266          563         1177 
TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5169 TCGA-BP-5170 
        1126          840         1140         1071          193         2412 
TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 
        2257          932          293         2263         1495         1165 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 
        1291         1133         1132          693          406          822 
TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
        1011          967          714          408          749         1018 
TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 
         603         1355         1063          951           29         1820 
TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4642 TCGA-CJ-4643 
        1416         1924         2308         1998         1628         1793 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 
         646         2554         1498         2423         1435         2259 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 
        2283         2353         1955         2186         2014         1883 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 
        1759         2125         1952         1946         2085         1521 
TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4901 TCGA-CJ-4902 
         750          841         1808         1528         1450         1520 
TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 
        1560         1792         1496         1499         1531         1657 
TCGA-CJ-4916 TCGA-CJ-5671 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5681 TCGA-CJ-5682 
        1373         1943         2430         2575          552         1883 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6031 TCGA-CJ-6032 
        1889         2231         2038         1855         1906         2548 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 
        2799         2489         2609         2226         2017         2378 
TCGA-CW-5591 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4854 
        2271         3222         2552         3146          774         1404 
TCGA-CZ-4856 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 
          18         1943         1787         1843         1928         2830 
TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5456 TCGA-CZ-5457 
        1868         1929         1789           25         1712         1683 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5463 TCGA-CZ-5464 
        1732         1683         1430          330          662         1740 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 
        1446          685           59          946          386         2439 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
        2067         1997          373          435          693         1905 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 
        1329         1398         1470          370          355         1130 
TCGA-DV-5574 TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
         723         1729          551          119          206          127 
TCGA-GK-A6C7 
          61 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               13                 3 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
             2192              3668 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
              480              1307 
[1] "13.0 - 2192.0 (480.0)" "3.0 - 3668.0 (1307.0)"
[1] "hr=" "4.9"
D7V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  4P GAIN MUTATED         4        2         5        2
  4P GAIN WILD-TYPE     240       54       121       77
D7V3, multiclass
           clus
vv          4P GAIN MUTATED 4P GAIN WILD-TYPE
  STAGE I                 4               240
  STAGE II                2                54
  STAGE III               5               121
  STAGE IV                2                77
[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"
                   vv
clus                 T1  T2  T3  T4
  4P GAIN MUTATED     4   2   6   1
  4P GAIN WILD-TYPE 246  65 171  10
D7V4, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  T1               4               246
  T2               2                65
  T3               6               171
  T4               1                10
[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"
D7V5, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     8   1
  4P GAIN WILD-TYPE 222  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      8    1
  4P GAIN WILD-TYPE  222   17
   clus
vv  4P GAIN MUTATED 4P GAIN WILD-TYPE
  0               8               222
  1               1                17
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  4P GAIN MUTATED    11   2   0
  4P GAIN WILD-TYPE 406  76   9
D7V6, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  M0              11               406
  M1               2                76
  MX               0                 9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V7, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     3  10
  4P GAIN WILD-TYPE 175 317
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      3   10
  4P GAIN WILD-TYPE  175  317
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE               3               175
  MALE                10               317
[1] 2 2
[1] FALSE
D7V8, continuous
[1] "Remove cluster labels:" "4P GAIN MUTATED"       
clus
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                1                36 
       TCGA-A3-A8CQ        TCGA-AK-3426        TCGA-B0-4838        TCGA-B2-5639 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B4-5377        TCGA-B4-5378        TCGA-B4-5832        TCGA-B4-5834 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B4-5835        TCGA-B4-5836        TCGA-B4-5838        TCGA-B4-5843 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B4-5844        TCGA-CZ-4854        TCGA-CZ-4856        TCGA-CZ-4858 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CZ-4860        TCGA-CZ-4861        TCGA-CZ-4862        TCGA-CZ-5456 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CZ-5457        TCGA-CZ-5465        TCGA-CZ-5469        TCGA-CZ-5982 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DV-5565        TCGA-DV-5566        TCGA-DV-5567        TCGA-DV-5568 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DV-5569        TCGA-DV-5573        TCGA-DV-5574        TCGA-DV-5575 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DV-5576        TCGA-EU-5904        TCGA-EU-5905        TCGA-EU-5907 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
D7V9, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4P GAIN MUTATED       0                         1    12
  4P GAIN WILD-TYPE     8                        32   445
D7V10, multiclass
                           clus
vv                          4P GAIN MUTATED 4P GAIN WILD-TYPE
  ASIAN                                   0                 8
  BLACK OR AFRICAN AMERICAN               1                32
  WHITE                                  12               445
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V11, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     0   8
  4P GAIN WILD-TYPE  24 322
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      0    8
  4P GAIN WILD-TYPE   24  322
                        clus
vv                       4P GAIN MUTATED 4P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                24
  NOT HISPANIC OR LATINO               8               322
[1] 2 2
[1] FALSE

Clustering(8) Variable = 4Q GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                 0   1
  4Q GAIN MUTATED     8   2
  4Q GAIN WILD-TYPE 330  24
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               10               354 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                2                24 
$`4Q GAIN MUTATED`
TCGA-A3-3374 TCGA-AK-3430 TCGA-AK-3433 TCGA-AK-3440 TCGA-B0-4813 TCGA-BP-4166 
        1314          480         2192         1745           18           13 
TCGA-BP-4977 TCGA-BP-4989 TCGA-BP-4994 TCGA-BP-5177 
         454          118         1308          293 

$`4Q GAIN WILD-TYPE`
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 
        1120         1436           16          735         1493         1491 
TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 
        1130         1508         1478         1106         1186          751 
TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3347 
        1137         1485          665         1043          945         1610 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 
        1385          910         2688         1307         2504         1559 
TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 
         319          873         2270         2274          735         1621 
TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 
        1070          630          567          574          861         1993 
TCGA-A3-3387 TCGA-A3-A8CQ TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
         617            3         3343         2566         2223         2017 
TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 
        1853         2087         2044         1423         1471         1280 
TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3456 
        1217         1779         1481         1397          874         1143 
TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 
        1168          951          853          369         1238           43 
TCGA-B0-4699 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4718 TCGA-B0-4819 TCGA-B0-5097 
         110           26           96          616          183          665 
TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 
         911         1092          359          797          657          535 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
          59          493          554          652         1132          449 
TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5696 
        2408         3431         1487         3076         1420         1727 
TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
        1835         2583         2741         1732         1605         1203 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
        3668         2414         3117         1459         2931         2722 
TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
        1865         2963          992         1092           51          374 
TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 
         648          952          358          315          417          656 
TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 
         507          291          175            7           38           16 
TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 
         141          166           11            7          511          826 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 
         838          762          750          523          777          788 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 
         700          636          722           36          822           26 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 
         737          522          505          194          434           15 
TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H 
        1046          435          830          519           53          256 
TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4161 
         150           66          110         3377         2881         2746 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4173 
        3074         2839         3037         2718          701         1893 
TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 
        1879         1955         1670         2964         1625          845 
TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4338 TCGA-BP-4344 
        1888         1133          645          461         2859         1666 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 
        1367          372          970          374         2208         2372 
TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 
        2361          182         2184         1462          400         1876 
TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 
        1885         1843          411         1731         2080          354 
TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4801 TCGA-BP-4803 
        1854         1489          620         1107         1124          204 
TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
        1459          211         2660         2172         1935         1785 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 
        1834         1862         1871          205         1746         1794 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4975 TCGA-BP-4976 
         433         1487         1502         1384         1433         1632 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4991 TCGA-BP-4992 
        1014         1413          785         1124         1413          501 
TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 
         177         1371          932         1266          563         1177 
TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5169 TCGA-BP-5170 
        1126          840         1140         1071          193         2412 
TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 
        2257          932         2263         1495         1165         1291 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 
        1133         1132          693          406          822         1011 
TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 
         967          714          408          749         1018          603 
TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 
        1355         1063          951           29         1820         1416 
TCGA-CJ-4636 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 
        1924         2308         1998         1628         1793          646 
TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 
        2554         1498         2423         1435         2259         2283 
TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 
        2353         1955         2186         2014         1883         1759 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 
        2125         1952         1946         2085         1521          750 
TCGA-CJ-4894 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 
         841         1808         1528         1450         1520         1560 
TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4916 
        1792         1496         1499         1531         1657         1373 
TCGA-CJ-5671 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
        1943         2430         2575          552         1883         1889 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CW-5581 
        2231         2038         1855         1906         2548         2799 
TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 
        2489         2609         2226         2017         2378         2271 
TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 
        3222         2552         3146          774         1404           18 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 
        1943         1787         1843         1928         2830         1868 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 
        1929         1789           25         1712         1683         1732 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 
        1683         1430          330          662         1740         1446 
TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 
         685           59          946          386         2439         2067 
TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 
        1997          373          435          693         1905         1329 
TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 
        1398         1470          370          355         1130          723 
TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-GK-A6C7 
        1729          551          119          206          127           61 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               13                 3 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
             2192              3668 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
              467              1318 
[1] "13.0 - 2192.0 (467.0)" "3.0 - 3668.0 (1318.0)"
[1] "hr=" "4.8"
D8V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  4Q GAIN MUTATED         5        2         5        1
  4Q GAIN WILD-TYPE     239       54       121       78
D8V3, multiclass
           clus
vv          4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  STAGE I                 5               239
  STAGE II                2                54
  STAGE III               5               121
  STAGE IV                1                78
[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"
                   vv
clus                 T1  T2  T3  T4
  4Q GAIN MUTATED     5   2   6   0
  4Q GAIN WILD-TYPE 245  65 171  11
D8V4, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  T1               5               245
  T2               2                65
  T3               6               171
  T4               0                11
[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"
D8V5, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     7   1
  4Q GAIN WILD-TYPE 223  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      7    1
  4Q GAIN WILD-TYPE  223   17
   clus
vv  4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  0               7               223
  1               1                17
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  4Q GAIN MUTATED    12   1   0
  4Q GAIN WILD-TYPE 405  77   9
D8V6, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  M0              12               405
  M1               1                77
  MX               0                 9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V7, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     4   9
  4Q GAIN WILD-TYPE 174 318
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      4    9
  4Q GAIN WILD-TYPE  174  318
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE               4               174
  MALE                 9               318
[1] 2 2
[1] FALSE
D8V8, continuous
[1] "Remove cluster labels:" "4Q GAIN MUTATED"       
clus
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                1                36 
       TCGA-A3-A8CQ        TCGA-AK-3426        TCGA-B0-4838        TCGA-B2-5639 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B4-5377        TCGA-B4-5378        TCGA-B4-5832        TCGA-B4-5834 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B4-5835        TCGA-B4-5836        TCGA-B4-5838        TCGA-B4-5843 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B4-5844        TCGA-CZ-4854        TCGA-CZ-4856        TCGA-CZ-4858 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CZ-4860        TCGA-CZ-4861        TCGA-CZ-4862        TCGA-CZ-5456 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CZ-5457        TCGA-CZ-5465        TCGA-CZ-5469        TCGA-CZ-5982 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DV-5565        TCGA-DV-5566        TCGA-DV-5567        TCGA-DV-5568 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DV-5569        TCGA-DV-5573        TCGA-DV-5574        TCGA-DV-5575 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DV-5576        TCGA-EU-5904        TCGA-EU-5905        TCGA-EU-5907 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
D8V9, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4Q GAIN MUTATED       0                         1    12
  4Q GAIN WILD-TYPE     8                        32   445
D8V10, multiclass
                           clus
vv                          4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  ASIAN                                   0                 8
  BLACK OR AFRICAN AMERICAN               1                32
  WHITE                                  12               445
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V11, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     0   7
  4Q GAIN WILD-TYPE  24 323
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      0    7
  4Q GAIN WILD-TYPE   24  323
                        clus
vv                       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                24
  NOT HISPANIC OR LATINO               7               323
[1] 2 2
[1] FALSE

Clustering(9) Variable = 5P GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                 0   1
  5P GAIN MUTATED   133   7
  5P GAIN WILD-TYPE 205  19
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              140               224 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                7                19 
$`5P GAIN MUTATED`
TCGA-A3-3316 TCGA-A3-3322 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3331 TCGA-A3-3336 
        1493         1478         1186          751         1485         1043 
TCGA-A3-3347 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3372 TCGA-A3-3374 TCGA-A3-3382 
        1610         2688         1307          735         1314          574 
TCGA-A3-3385 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3445 
        1993         2017          480         2044         1745         1280 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3460 TCGA-AK-3461 TCGA-B0-4710 TCGA-B0-4819 
        1481         1397          951          853           96          183 
TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5121 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5701 
         359          797          554         1727         1835         1732 
TCGA-B0-5702 TCGA-B0-5705 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3924 TCGA-B2-4102 
        1605         3668         2722         1865         1092          952 
TCGA-B2-5635 TCGA-B4-5838 TCGA-B8-4620 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5549 
         315          166          777          722          822          194 
TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-A54H TCGA-B8-A54I TCGA-BP-4158 TCGA-BP-4160 
         434           15          256          150         3377         2881 
TCGA-BP-4162 TCGA-BP-4166 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4338 
        3074           13         1879         1955         1670         2859 
TCGA-BP-4344 TCGA-BP-4347 TCGA-BP-4351 TCGA-BP-4761 TCGA-BP-4768 TCGA-BP-4781 
        1666         1367          970          182          400         2080 
TCGA-BP-4797 TCGA-BP-4804 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4964 TCGA-BP-4965 
        1107         1459         1935         1785         1862         1871 
TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4971 TCGA-BP-4976 TCGA-BP-4983 
         205         1746         1794         1487         1632         1413 
TCGA-BP-4986 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4999 
         785          118         1413          501         1308         1266 
TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5170 TCGA-BP-5175 TCGA-BP-5177 TCGA-BP-5185 
        1126         1140         2412          932          293         1132 
TCGA-BP-5187 TCGA-BP-5191 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4635 
         406          967         1063          951           29         1416 
TCGA-CJ-4636 TCGA-CJ-4639 TCGA-CJ-4869 TCGA-CJ-4871 TCGA-CJ-4873 TCGA-CJ-4875 
        1924         2308         2554         2423         2259         2353 
TCGA-CJ-4881 TCGA-CJ-4885 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4897 TCGA-CJ-4899 
        2014         2125         2085         1521         1808         1528 
TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4907 TCGA-CJ-4912 TCGA-CJ-5671 TCGA-CJ-5675 
        1560         1792         1499         1657         1943         2430 
TCGA-CJ-5676 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 
        2575         1883         1889         2231         2038         1855 
TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5591 TCGA-CZ-4853 TCGA-CZ-4854 
        2609         2226         2017         2271          774         1404 
TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5456 
        1928         2830         1868         1929         1789         1712 
TCGA-CZ-5457 TCGA-CZ-5461 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5468 
        1683          330          662         1740          685           59 
TCGA-CZ-5470 TCGA-CZ-5984 TCGA-CZ-5986 TCGA-DV-5573 TCGA-DV-5574 TCGA-EU-5905 
         386         2067          373         1130          723          119 
TCGA-EU-5907 TCGA-GK-A6C7 
         127           61 

$`5P GAIN WILD-TYPE`
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3319 
        1120         1436           16          735         1491         1130 
TCGA-A3-3320 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3335 TCGA-A3-3343 TCGA-A3-3349 
        1508         1106         1137          665          945         1385 
TCGA-A3-3351 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 
         910         2504         1559          319          873         2270 
TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3383 
        2274         1621         1070          630          567          861 
TCGA-A3-3387 TCGA-A3-A8CQ TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3431 
         617            3         3343         2566         2223         1853 
TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3447 TCGA-AK-3450 
        2192         2087         1423         1471         1217         1779 
TCGA-AK-3454 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 
         874         1143         1168          369         1238           43 
TCGA-B0-4699 TCGA-B0-4706 TCGA-B0-4718 TCGA-B0-4813 TCGA-B0-5097 TCGA-B0-5108 
         110           26          616           18          665          911 
TCGA-B0-5110 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5399 
        1092          657          535           59          493          652 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 
        1132          449         2408         3431         1487         3076 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5703 TCGA-B0-5706 TCGA-B0-5709 
        1420         2583         2741         1203         2414         3117 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-4098 TCGA-B2-4099 
        1459         2931         2963          992           51          374 
TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 
         648          358          417          656          507          291 
TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5843 
         175            7           38           16          141           11 
TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
           7          511          826          838          762          750 
TCGA-B8-4619 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5162 TCGA-B8-5164 
         523          788          700          636           36           26 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D 
         737          522          505         1046          435          830 
TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4161 TCGA-BP-4163 
         519           53           66          110         2746         2839 
TCGA-BP-4165 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4173 TCGA-BP-4325 TCGA-BP-4326 
        3037         2718          701         1893         2964         1625 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4349 
         845         1888         1133          645          461          372 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4765 TCGA-BP-4766 
         374         2208         2372         2361         2184         1462 
TCGA-BP-4769 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4782 
        1876         1885         1843          411         1731          354 
TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4795 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4807 
        1854         1489          620         1124          204          211 
TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4963 TCGA-BP-4970 TCGA-BP-4972 TCGA-BP-4973 
        2660         2172         1834          433         1502         1384 
TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4982 TCGA-BP-4987 TCGA-BP-4993 TCGA-BP-4995 
        1433          454         1014         1124          177         1371 
TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5006 TCGA-BP-5008 TCGA-BP-5169 
         932          563         1177          840         1071          193 
TCGA-BP-5174 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
        2257         2263         1495         1165         1291         1133 
TCGA-BP-5186 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
         693          822         1011          714          408          749 
TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-CJ-4634 TCGA-CJ-4640 TCGA-CJ-4642 
        1018          603         1355         1820         1998         1628 
TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4870 TCGA-CJ-4872 TCGA-CJ-4874 TCGA-CJ-4876 
        1793          646         1498         1435         2283         1955 
TCGA-CJ-4878 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4886 TCGA-CJ-4889 TCGA-CJ-4893 
        2186         1883         1759         1952         1946          750 
TCGA-CJ-4894 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4916 
         841         1450         1520         1496         1531         1373 
TCGA-CJ-5681 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5589 
         552         1906         2548         2799         2489         2378 
TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CZ-4856 TCGA-CZ-4858 TCGA-CZ-4859 
        3222         2552         3146           18         1943         1787 
TCGA-CZ-4862 TCGA-CZ-5453 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5465 
        1843           25         1732         1683         1430         1446 
TCGA-CZ-5469 TCGA-CZ-5982 TCGA-CZ-5985 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
         946         2439         1997          435          693         1905 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5575 
        1329         1398         1470          370          355         1729 
TCGA-EU-5904 TCGA-EU-5906 
         551          206 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               13                 3 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             3668              3431 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             1483              1131 
[1] "13.0 - 3668.0 (1483.0)" "3.0 - 3431.0 (1131.0)" 
[1] "hr=" "1.9"
D9V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  5P GAIN MUTATED        80       21        57       29
  5P GAIN WILD-TYPE     164       35        69       50
D9V3, multiclass
           clus
vv          5P GAIN MUTATED 5P GAIN WILD-TYPE
  STAGE I                80               164
  STAGE II               21                35
  STAGE III              57                69
  STAGE IV               29                50
[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"
                   vv
clus                 T1  T2  T3  T4
  5P GAIN MUTATED    82  26  75   4
  5P GAIN WILD-TYPE 168  41 102   7
D9V4, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  T1              82               168
  T2              26                41
  T3              75               102
  T4               4                 7
[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"
D9V5, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    88   8
  5P GAIN WILD-TYPE 142  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     88    8
  5P GAIN WILD-TYPE  142   10
   clus
vv  5P GAIN MUTATED 5P GAIN WILD-TYPE
  0              88               142
  1               8                10
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  5P GAIN MUTATED   155  29   3
  5P GAIN WILD-TYPE 262  49   6
D9V6, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  M0             155               262
  M1              29                49
  MX               3                 6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V7, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    54 133
  5P GAIN WILD-TYPE 124 194
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     54  133
  5P GAIN WILD-TYPE  124  194
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE              54               124
  MALE               133               194
[1] 2 2
[1] FALSE
D9V8, continuous
D9V9, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5P GAIN MUTATED       3                         6   176
  5P GAIN WILD-TYPE     5                        27   281
D9V10, multiclass
                           clus
vv                          5P GAIN MUTATED 5P GAIN WILD-TYPE
  ASIAN                                   3                 5
  BLACK OR AFRICAN AMERICAN               6                27
  WHITE                                 176               281
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V11, binary
                   cls
clus                  0   1
  5P GAIN MUTATED     9 120
  5P GAIN WILD-TYPE  15 210
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      9  120
  5P GAIN WILD-TYPE   15  210
                        clus
vv                       5P GAIN MUTATED 5P GAIN WILD-TYPE
  HISPANIC OR LATINO                   9                15
  NOT HISPANIC OR LATINO             120               210
[1] 2 2
[1] FALSE

Clustering(10) Variable = 5Q GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                 0   1
  5Q GAIN MUTATED   142   7
  5Q GAIN WILD-TYPE 196  19
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
              149               215 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                7                19 
$`5Q GAIN MUTATED`
TCGA-A3-3316 TCGA-A3-3322 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3331 TCGA-A3-3336 
        1493         1478         1186          751         1485         1043 
TCGA-A3-3347 TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3372 
        1610          910         2688         1307         2504          735 
TCGA-A3-3374 TCGA-A3-3382 TCGA-A3-3385 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3436 
        1314          574         1993         2017          480         2044 
TCGA-AK-3440 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3460 
        1745         1471         1280         1481         1397          951 
TCGA-AK-3461 TCGA-B0-4710 TCGA-B0-4819 TCGA-B0-5108 TCGA-B0-5113 TCGA-B0-5115 
         853           96          183          911          359          797 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5701 TCGA-B0-5702 
         493          554         1727         1835         1732         1605 
TCGA-B0-5705 TCGA-B0-5710 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3924 TCGA-B2-4102 
        3668         1459         2722         1865         1092          952 
TCGA-B2-5635 TCGA-B4-5838 TCGA-B8-4146 TCGA-B8-4620 TCGA-B8-5159 TCGA-B8-5163 
         315          166          511          777          722          822 
TCGA-B8-5165 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-A54H TCGA-B8-A54I 
         737          194          434           15          256          150 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4162 TCGA-BP-4166 TCGA-BP-4174 TCGA-BP-4176 
        3377         2881         3074           13         1879         1955 
TCGA-BP-4177 TCGA-BP-4338 TCGA-BP-4344 TCGA-BP-4347 TCGA-BP-4351 TCGA-BP-4768 
        1670         2859         1666         1367          970          400 
TCGA-BP-4781 TCGA-BP-4797 TCGA-BP-4804 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4964 
        2080         1107         1459         1935         1785         1862 
TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4971 TCGA-BP-4976 
        1871          205         1746         1794         1487         1632 
TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 
        1413          785          118         1413          501         1308 
TCGA-BP-4999 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5170 TCGA-BP-5175 TCGA-BP-5177 
        1266         1126         1140         2412          932          293 
TCGA-BP-5185 TCGA-BP-5187 TCGA-BP-5191 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 
        1132          406          967         1063          951           29 
TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4639 TCGA-CJ-4869 TCGA-CJ-4871 TCGA-CJ-4873 
        1416         1924         2308         2554         2423         2259 
TCGA-CJ-4875 TCGA-CJ-4885 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4897 TCGA-CJ-4899 
        2353         2125         2085         1521         1808         1528 
TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-5671 
        1560         1792         1499         1531         1657         1943 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 
        2430         2575         1883         1889         2231         2038 
TCGA-CJ-6027 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 
        1855         2609         2226         2017         2378         2271 
TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 
         774         1404         1928         2830         1868         1929 
TCGA-CZ-5452 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5461 TCGA-CZ-5463 
        1789         1712         1683         1732          330          662 
TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5470 TCGA-CZ-5984 TCGA-CZ-5986 
        1740          685           59          386         2067          373 
TCGA-DV-5573 TCGA-DV-5574 TCGA-EU-5905 TCGA-EU-5907 TCGA-GK-A6C7 
        1130          723          119          127           61 

$`5Q GAIN WILD-TYPE`
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3319 
        1120         1436           16          735         1491         1130 
TCGA-A3-3320 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3335 TCGA-A3-3343 TCGA-A3-3349 
        1508         1106         1137          665          945         1385 
TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 
        1559          319          873         2270         2274         1621 
TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3387 TCGA-A3-A8CQ 
        1070          630          567          861          617            3 
TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 
        3343         2566         2223         1853         2192         2087 
TCGA-AK-3443 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3456 TCGA-AK-3458 
        1423         1217         1779          874         1143         1168 
TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4699 TCGA-B0-4706 TCGA-B0-4718 
         369         1238           43          110           26          616 
TCGA-B0-4813 TCGA-B0-5097 TCGA-B0-5110 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 
          18          665         1092          657          535           59 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 
         652         1132          449         2408         3431         1487 
TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5703 TCGA-B0-5706 
        3076         1420         2583         2741         1203         2414 
TCGA-B0-5709 TCGA-B0-5711 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-4098 TCGA-B2-4099 
        3117         2931         2963          992           51          374 
TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 
         648          358          417          656          507          291 
TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5843 
         175            7           38           16          141           11 
TCGA-B4-5844 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 
           7          826          838          762          750          523 
TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5162 TCGA-B8-5164 TCGA-B8-5545 
         788          700          636           36           26          522 
TCGA-B8-5546 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G 
         505         1046          435          830          519           53 
TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4161 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4167 
          66          110         2746         2839         3037         2718 
TCGA-BP-4169 TCGA-BP-4173 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 
         701         1893         2964         1625          845         1888 
TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4349 TCGA-BP-4756 TCGA-BP-4758 
        1133          645          461          372          374         2208 
TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 
        2372         2361          182         2184         1462         1876 
TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4782 TCGA-BP-4784 
        1885         1843          411         1731          354         1854 
TCGA-BP-4789 TCGA-BP-4795 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4807 TCGA-BP-4959 
        1489          620         1124          204          211         2660 
TCGA-BP-4960 TCGA-BP-4963 TCGA-BP-4970 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4975 
        2172         1834          433         1502         1384         1433 
TCGA-BP-4977 TCGA-BP-4982 TCGA-BP-4987 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 
         454         1014         1124          177         1371          932 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5006 TCGA-BP-5008 TCGA-BP-5169 TCGA-BP-5174 
         563         1177          840         1071          193         2257 
TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 
        2263         1495         1165         1291         1133          693 
TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
         822         1011          714          408          749         1018 
TCGA-BP-5198 TCGA-BP-5199 TCGA-CJ-4634 TCGA-CJ-4640 TCGA-CJ-4642 TCGA-CJ-4643 
         603         1355         1820         1998         1628         1793 
TCGA-CJ-4868 TCGA-CJ-4870 TCGA-CJ-4872 TCGA-CJ-4874 TCGA-CJ-4876 TCGA-CJ-4878 
         646         1498         1435         2283         1955         2186 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4886 TCGA-CJ-4889 TCGA-CJ-4893 
        2014         1883         1759         1952         1946          750 
TCGA-CJ-4894 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4905 TCGA-CJ-4916 TCGA-CJ-5681 
         841         1450         1520         1496         1373          552 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-6088 TCGA-CW-6090 
        1906         2548         2799         2489         3222         2552 
TCGA-CW-6093 TCGA-CZ-4856 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-5453 
        3146           18         1943         1787         1843           25 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5465 TCGA-CZ-5469 TCGA-CZ-5982 TCGA-CZ-5985 
        1683         1430         1446          946         2439         1997 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 
         435          693         1905         1329         1398         1470 
TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5906 
         370          355         1729          551          206 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               13                 3 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             3668              3431 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             1478              1130 
[1] "13.0 - 3668.0 (1478.0)" "3.0 - 3431.0 (1130.0)" 
[1] "hr=" "2.1"
D10V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  5Q GAIN MUTATED        90       22        58       30
  5Q GAIN WILD-TYPE     154       34        68       49
D10V3, multiclass
           clus
vv          5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  STAGE I                90               154
  STAGE II               22                34
  STAGE III              58                68
  STAGE IV               30                49
[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"
                   vv
clus                 T1  T2  T3  T4
  5Q GAIN MUTATED    92  27  78   3
  5Q GAIN WILD-TYPE 158  40  99   8
D10V4, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  T1              92               158
  T2              27                40
  T3              78                99
  T4               3                 8
[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"
D10V5, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    97   7
  5Q GAIN WILD-TYPE 133  11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     97    7
  5Q GAIN WILD-TYPE  133   11
   clus
vv  5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  0              97               133
  1               7                11
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  5Q GAIN MUTATED   166  31   3
  5Q GAIN WILD-TYPE 251  47   6
D10V6, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  M0             166               251
  M1              31                47
  MX               3                 6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V7, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    59 141
  5Q GAIN WILD-TYPE 119 186
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     59  141
  5Q GAIN WILD-TYPE  119  186
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE              59               119
  MALE               141               186
[1] 2 2
[1] FALSE
D10V8, continuous
D10V9, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5Q GAIN MUTATED       3                         6   189
  5Q GAIN WILD-TYPE     5                        27   268
D10V10, multiclass
                           clus
vv                          5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  ASIAN                                   3                 5
  BLACK OR AFRICAN AMERICAN               6                27
  WHITE                                 189               268
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V11, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    10 131
  5Q GAIN WILD-TYPE  14 199
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     10  131
  5Q GAIN WILD-TYPE   14  199
                        clus
vv                       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  HISPANIC OR LATINO                  10                14
  NOT HISPANIC OR LATINO             131               199
[1] 2 2
[1] FALSE

Clustering(11) Variable = 6P GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                 0   1
  6P GAIN MUTATED     7   1
  6P GAIN WILD-TYPE 331  25
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                8               356 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                1                25 
$`6P GAIN MUTATED`
TCGA-A3-3313 TCGA-B0-5113 TCGA-B8-5549 TCGA-BP-4781 TCGA-BP-5177 TCGA-CJ-4885 
         735          359          194         2080          293         2125 
TCGA-CZ-5457 TCGA-CZ-5460 
        1683         1430 

$`6P GAIN WILD-TYPE`
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 
        1120         1436           16         1493         1491         1130 
TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 
        1508         1478         1106         1186          751         1137 
TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3347 TCGA-A3-3349 
        1485          665         1043          945         1610         1385 
TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 
         910         2688         1307         2504         1559          319 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 
         873         2270         2274          735         1621         1314 
TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 
        1070          630          567          574          861         1993 
TCGA-A3-3387 TCGA-A3-A8CQ TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
         617            3         3343         2566         2223         2017 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
         480         1853         2192         2087         2044         1745 
TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 
        1423         1471         1280         1217         1779         1481 
TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
        1397          874         1143         1168          951          853 
TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4699 TCGA-B0-4706 TCGA-B0-4710 
         369         1238           43          110           26           96 
TCGA-B0-4718 TCGA-B0-4813 TCGA-B0-4819 TCGA-B0-5097 TCGA-B0-5108 TCGA-B0-5110 
         616           18          183          665          911         1092 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
         797          657          535           59          493          554 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 
         652         1132          449         2408         3431         1487 
TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 
        3076         1420         1727         1835         2583         2741 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 
        1732         1605         1203         3668         2414         3117 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 
        1459         2931         2722         1865         2963          992 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 
        1092           51          374          648          952          358 
TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 
         315          417          656          507          291          175 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 
           7           38           16          141          166           11 
TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
           7          511          826          838          762          750 
TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 
         523          777          788          700          636          722 
TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
          36          822           26          737          522          505 
TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54F 
         434           15         1046          435          830          519 
TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4158 
          53          256          150           66          110         3377 
TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 
        2881         2746         3074         2839         3037           13 
TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 
        2718          701         1893         1879         1955         1670 
TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 
        2964         1625          845         1888         1133          645 
TCGA-BP-4335 TCGA-BP-4338 TCGA-BP-4344 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 
         461         2859         1666         1367          372          970 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4765 
         374         2208         2372         2361          182         2184 
TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 
        1462          400         1876         1885         1843          411 
TCGA-BP-4777 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4795 TCGA-BP-4797 
        1731          354         1854         1489          620         1107 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 
        1124          204         1459          211         2660         2172 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 
        1935         1785         1834         1862         1871          205 
TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 
        1746         1794          433         1487         1502         1384 
TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4986 
        1433         1632          454         1014         1413          785 
TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 
        1124          118         1413          501          177         1308 
TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
        1371          932         1266          563         1177         1126 
TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 
         840         1140         1071          193         2412         2257 
TCGA-BP-5175 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
         932         2263         1495         1165         1291         1133 
TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 
        1132          693          406          822         1011          967 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 
         714          408          749         1018          603         1355 
TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 
        1063          951           29         1820         1416         1924 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 
        2308         1998         1628         1793          646         2554 
TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 
        1498         2423         1435         2259         2283         2353 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4886 
        1955         2186         2014         1883         1759         1952 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4897 
        1946         2085         1521          750          841         1808 
TCGA-CJ-4899 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 
        1528         1450         1520         1560         1792         1496 
TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-5671 TCGA-CJ-5675 
        1499         1531         1657         1373         1943         2430 
TCGA-CJ-5676 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 
        2575          552         1883         1889         2231         2038 
TCGA-CJ-6027 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 
        1855         1906         2548         2799         2489         2609 
TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6088 TCGA-CW-6090 
        2226         2017         2378         2271         3222         2552 
TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4858 TCGA-CZ-4859 
        3146          774         1404           18         1943         1787 
TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 
        1843         1928         2830         1868         1929         1789 
TCGA-CZ-5453 TCGA-CZ-5456 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5461 TCGA-CZ-5463 
          25         1712         1732         1683          330          662 
TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 
        1740         1446          685           59          946          386 
TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 
        2439         2067         1997          373          435          693 
TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 
        1905         1329         1398         1470          370          355 
TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 
        1130          723         1729          551          119          206 
TCGA-EU-5907 TCGA-GK-A6C7 
         127           61 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              194                 3 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             2125              3668 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           1082.5            1299.0 
[1] "194.0 - 2125.0 (1082.5)" "3.0 - 3668.0 (1299.0)"  
[1] "hr=" "2"  
D11V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  6P GAIN MUTATED         4        0         5        2
  6P GAIN WILD-TYPE     240       56       121       77
D11V3, multiclass
           clus
vv          6P GAIN MUTATED 6P GAIN WILD-TYPE
  STAGE I                 4               240
  STAGE II                0                56
  STAGE III               5               121
  STAGE IV                2                77
[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"
                   vv
clus                 T1  T2  T3  T4
  6P GAIN MUTATED     4   0   7   0
  6P GAIN WILD-TYPE 246  67 170  11
D11V4, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  T1               4               246
  T2               0                67
  T3               7               170
  T4               0                11
[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"
D11V5, binary
                   cls
clus                  0   1
  6P GAIN MUTATED     6   0
  6P GAIN WILD-TYPE 224  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      6    0
  6P GAIN WILD-TYPE  224   18
   clus
vv  6P GAIN MUTATED 6P GAIN WILD-TYPE
  0               6               224
  1               0                18
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  6P GAIN MUTATED     9   2   0
  6P GAIN WILD-TYPE 408  76   9
D11V6, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  M0               9               408
  M1               2                76
  MX               0                 9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V7, binary
                   cls
clus                  0   1
  6P GAIN MUTATED     2   9
  6P GAIN WILD-TYPE 176 318
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      2    9
  6P GAIN WILD-TYPE  176  318
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE               2               176
  MALE                 9               318
[1] 2 2
[1] FALSE
D11V8, continuous
[1] "Remove cluster labels:" "6P GAIN MUTATED"       
clus
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                1                36 
       TCGA-A3-A8CQ        TCGA-AK-3426        TCGA-AK-3430        TCGA-B0-4838 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B2-5639        TCGA-B4-5377        TCGA-B4-5378        TCGA-B4-5832 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B4-5834        TCGA-B4-5835        TCGA-B4-5836        TCGA-B4-5838 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B4-5843        TCGA-B4-5844        TCGA-CZ-4854        TCGA-CZ-4856 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CZ-4858        TCGA-CZ-4860        TCGA-CZ-4861        TCGA-CZ-4862 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CZ-5456        TCGA-CZ-5465        TCGA-CZ-5469        TCGA-CZ-5982 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DV-5565        TCGA-DV-5566        TCGA-DV-5567        TCGA-DV-5568 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DV-5569        TCGA-DV-5573        TCGA-DV-5574        TCGA-DV-5575 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DV-5576        TCGA-EU-5904        TCGA-EU-5905        TCGA-EU-5907 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
D11V9, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6P GAIN MUTATED       0                         1    10
  6P GAIN WILD-TYPE     8                        32   447
D11V10, multiclass
                           clus
vv                          6P GAIN MUTATED 6P GAIN WILD-TYPE
  ASIAN                                   0                 8
  BLACK OR AFRICAN AMERICAN               1                32
  WHITE                                  10               447
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V11, binary
                   cls
clus                  0   1
  6P GAIN MUTATED     0   6
  6P GAIN WILD-TYPE  24 324
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      0    6
  6P GAIN WILD-TYPE   24  324
                        clus
vv                       6P GAIN MUTATED 6P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                24
  NOT HISPANIC OR LATINO               6               324
[1] 2 2
[1] FALSE

Clustering(12) Variable = 6Q GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                 0   1
  6Q GAIN MUTATED     5   1
  6Q GAIN WILD-TYPE 333  25
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                6               358 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                1                25 
$`6Q GAIN MUTATED`
TCGA-A3-3313 TCGA-B0-5113 TCGA-B8-5549 TCGA-BP-4781 TCGA-CJ-4885 TCGA-CZ-5457 
         735          359          194         2080         2125         1683 

$`6Q GAIN WILD-TYPE`
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 
        1120         1436           16         1493         1491         1130 
TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 
        1508         1478         1106         1186          751         1137 
TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3347 TCGA-A3-3349 
        1485          665         1043          945         1610         1385 
TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 
         910         2688         1307         2504         1559          319 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 
         873         2270         2274          735         1621         1314 
TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 
        1070          630          567          574          861         1993 
TCGA-A3-3387 TCGA-A3-A8CQ TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
         617            3         3343         2566         2223         2017 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
         480         1853         2192         2087         2044         1745 
TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 
        1423         1471         1280         1217         1779         1481 
TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
        1397          874         1143         1168          951          853 
TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4699 TCGA-B0-4706 TCGA-B0-4710 
         369         1238           43          110           26           96 
TCGA-B0-4718 TCGA-B0-4813 TCGA-B0-4819 TCGA-B0-5097 TCGA-B0-5108 TCGA-B0-5110 
         616           18          183          665          911         1092 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
         797          657          535           59          493          554 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 
         652         1132          449         2408         3431         1487 
TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 
        3076         1420         1727         1835         2583         2741 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 
        1732         1605         1203         3668         2414         3117 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 
        1459         2931         2722         1865         2963          992 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 
        1092           51          374          648          952          358 
TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 
         315          417          656          507          291          175 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 
           7           38           16          141          166           11 
TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
           7          511          826          838          762          750 
TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 
         523          777          788          700          636          722 
TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
          36          822           26          737          522          505 
TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54F 
         434           15         1046          435          830          519 
TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4158 
          53          256          150           66          110         3377 
TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 
        2881         2746         3074         2839         3037           13 
TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 
        2718          701         1893         1879         1955         1670 
TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 
        2964         1625          845         1888         1133          645 
TCGA-BP-4335 TCGA-BP-4338 TCGA-BP-4344 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 
         461         2859         1666         1367          372          970 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4765 
         374         2208         2372         2361          182         2184 
TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 
        1462          400         1876         1885         1843          411 
TCGA-BP-4777 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4795 TCGA-BP-4797 
        1731          354         1854         1489          620         1107 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 
        1124          204         1459          211         2660         2172 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 
        1935         1785         1834         1862         1871          205 
TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 
        1746         1794          433         1487         1502         1384 
TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4986 
        1433         1632          454         1014         1413          785 
TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 
        1124          118         1413          501          177         1308 
TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
        1371          932         1266          563         1177         1126 
TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 
         840         1140         1071          193         2412         2257 
TCGA-BP-5175 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 
         932          293         2263         1495         1165         1291 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 
        1133         1132          693          406          822         1011 
TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 
         967          714          408          749         1018          603 
TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 
        1355         1063          951           29         1820         1416 
TCGA-CJ-4636 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 
        1924         2308         1998         1628         1793          646 
TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 
        2554         1498         2423         1435         2259         2283 
TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 
        2353         1955         2186         2014         1883         1759 
TCGA-CJ-4886 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 
        1952         1946         2085         1521          750          841 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 
        1808         1528         1450         1520         1560         1792 
TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-5671 
        1496         1499         1531         1657         1373         1943 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
        2430         2575          552         1883         1889         2231 
TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CW-5581 TCGA-CW-5583 
        2038         1855         1906         2548         2799         2489 
TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6088 
        2609         2226         2017         2378         2271         3222 
TCGA-CW-6090 TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4858 
        2552         3146          774         1404           18         1943 
TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 
        1787         1843         1928         2830         1868         1929 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5456 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
        1789           25         1712         1732         1683         1430 
TCGA-CZ-5461 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5468 
         330          662         1740         1446          685           59 
TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
         946          386         2439         2067         1997          373 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 
         435          693         1905         1329         1398         1470 
TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-EU-5904 
         370          355         1130          723         1729          551 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-GK-A6C7 
         119          206          127           61 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
              194                 3 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
             2125              3668 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
             1209              1299 
[1] "194.0 - 2125.0 (1209.0)" "3.0 - 3668.0 (1299.0)"  
[1] "hr=" "2.5"
D12V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  6Q GAIN MUTATED         3        0         5        1
  6Q GAIN WILD-TYPE     241       56       121       78
D12V3, multiclass
           clus
vv          6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  STAGE I                 3               241
  STAGE II                0                56
  STAGE III               5               121
  STAGE IV                1                78
[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"
                   vv
clus                 T1  T2  T3  T4
  6Q GAIN MUTATED     3   0   6   0
  6Q GAIN WILD-TYPE 247  67 171  11
D12V4, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  T1               3               247
  T2               0                67
  T3               6               171
  T4               0                11
[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"
D12V5, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     6   0
  6Q GAIN WILD-TYPE 224  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      6    0
  6Q GAIN WILD-TYPE  224   18
   clus
vv  6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  0               6               224
  1               0                18
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  6Q GAIN MUTATED     8   1   0
  6Q GAIN WILD-TYPE 409  77   9
D12V6, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  M0               8               409
  M1               1                77
  MX               0                 9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V7, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     1   8
  6Q GAIN WILD-TYPE 177 319
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      1    8
  6Q GAIN WILD-TYPE  177  319
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE               1               177
  MALE                 8               319
[1] 2 2
[1] FALSE
D12V8, continuous
[1] "Remove cluster labels:" "6Q GAIN MUTATED"       
clus
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                1                36 
       TCGA-A3-A8CQ        TCGA-AK-3426        TCGA-AK-3430        TCGA-B0-4838 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B2-5639        TCGA-B4-5377        TCGA-B4-5378        TCGA-B4-5832 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B4-5834        TCGA-B4-5835        TCGA-B4-5836        TCGA-B4-5838 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B4-5843        TCGA-B4-5844        TCGA-CZ-4854        TCGA-CZ-4856 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CZ-4858        TCGA-CZ-4860        TCGA-CZ-4861        TCGA-CZ-4862 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CZ-5456        TCGA-CZ-5465        TCGA-CZ-5469        TCGA-CZ-5982 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DV-5565        TCGA-DV-5566        TCGA-DV-5567        TCGA-DV-5568 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DV-5569        TCGA-DV-5573        TCGA-DV-5574        TCGA-DV-5575 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DV-5576        TCGA-EU-5904        TCGA-EU-5905        TCGA-EU-5907 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
D12V9, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6Q GAIN MUTATED       0                         1     8
  6Q GAIN WILD-TYPE     8                        32   449
D12V10, multiclass
                           clus
vv                          6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  ASIAN                                   0                 8
  BLACK OR AFRICAN AMERICAN               1                32
  WHITE                                   8               449
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V11, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     0   5
  6Q GAIN WILD-TYPE  24 325
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      0    5
  6Q GAIN WILD-TYPE   24  325
                        clus
vv                       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                24
  NOT HISPANIC OR LATINO               5               325
[1] 2 2
[1] FALSE

Clustering(13) Variable = 7P GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                 0   1
  7P GAIN MUTATED   111   9
  7P GAIN WILD-TYPE 227  17
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              120               244 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                9                17 
$`7P GAIN MUTATED`
TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3324 TCGA-A3-3325 
         735         1493         1491         1478         1186          751 
TCGA-A3-3336 TCGA-A3-3347 TCGA-A3-3358 TCGA-A3-3363 TCGA-A3-3372 TCGA-A3-3374 
        1043         1610         1307          319          735         1314 
TCGA-A3-3382 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A8CQ TCGA-AK-3425 TCGA-AK-3427 
         574         1993          617            3         3343         2566 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3433 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3444 
        2017          480         2192         2044         1745         1471 
TCGA-AK-3453 TCGA-B0-4710 TCGA-B0-5113 TCGA-B0-5116 TCGA-B0-5698 TCGA-B0-5701 
        1397           96          359          657         2583         1732 
TCGA-B0-5703 TCGA-B0-5713 TCGA-B2-3924 TCGA-B2-5633 TCGA-B4-5832 TCGA-B4-5835 
        1203         1865         1092          358            7           16 
TCGA-B4-5838 TCGA-B4-5843 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 
         166           11          523          777          788          700 
TCGA-B8-5550 TCGA-B8-A54I TCGA-BP-4158 TCGA-BP-4162 TCGA-BP-4166 TCGA-BP-4167 
         434          150         3377         3074           13         2718 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4325 TCGA-BP-4332 TCGA-BP-4335 
        1893         1879         1955         2964         1133          461 
TCGA-BP-4338 TCGA-BP-4351 TCGA-BP-4759 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4775 
        2859          970         2372         1462          400         1843 
TCGA-BP-4781 TCGA-BP-4797 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4962 
        2080         1107          204         1459         2172         1785 
TCGA-BP-4963 TCGA-BP-4967 TCGA-BP-4969 TCGA-BP-4971 TCGA-BP-4973 TCGA-BP-4977 
        1834          205         1794         1487         1384          454 
TCGA-BP-4983 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 
        1413         1124          118          501         1308          932 
TCGA-BP-5001 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5177 TCGA-BP-5198 TCGA-BP-5200 
        1177          193         2412          293          603         1063 
TCGA-BP-5201 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 
         951         1416         1924         2423         1435         2259 
TCGA-CJ-4875 TCGA-CJ-4885 TCGA-CJ-4889 TCGA-CJ-4897 TCGA-CJ-4901 TCGA-CJ-4903 
        2353         2125         1946         1808         1450         1560 
TCGA-CJ-4907 TCGA-CJ-4912 TCGA-CJ-5671 TCGA-CJ-5682 TCGA-CJ-5684 TCGA-CW-5588 
        1499         1657         1943         1883         2231         2017 
TCGA-CW-5591 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4858 TCGA-CZ-4866 TCGA-CZ-5453 
        2271         3146         1404         1943         1868           25 
TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5464 TCGA-CZ-5466 
        1712         1683         1430          330         1740          685 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5984 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5574 
          59          946         2067         1905         1329          723 

$`7P GAIN WILD-TYPE`
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3323 
        1120         1436           16         1130         1508         1106 
TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3343 TCGA-A3-3349 TCGA-A3-3351 
        1137         1485          665          945         1385          910 
TCGA-A3-3357 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 
        2688         2504         1559          873         2270         2274 
TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3383 TCGA-AK-3428 
        1621         1070          630          567          861         2223 
TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 
        1853         2087         1423         1280         1217         1779 
TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
        1481          874         1143         1168          951          853 
TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4699 TCGA-B0-4706 TCGA-B0-4718 
         369         1238           43          110           26          616 
TCGA-B0-4813 TCGA-B0-4819 TCGA-B0-5097 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5115 
          18          183          665          911         1092          797 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
         535           59          493          554          652         1132 
TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 
         449         2408         3431         1487         3076         1420 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5702 TCGA-B0-5705 TCGA-B0-5706 
        1727         1835         2741         1605         3668         2414 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5812 TCGA-B2-3923 
        3117         1459         2931         2722         2963          992 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5635 TCGA-B2-5639 
          51          374          648          952          315          417 
TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5836 
         656          507          291          175           38          141 
TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
           7          511          826          838          762          750 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
         636          722           36          822           26          737 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
         522          505          194           15         1046          435 
TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54J TCGA-B8-A7U6 
         830          519           53          256           66          110 
TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4169 TCGA-BP-4177 
        2881         2746         2839         3037          701         1670 
TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4334 TCGA-BP-4344 TCGA-BP-4347 
        1625          845         1888          645         1666         1367 
TCGA-BP-4349 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4765 
         372          374         2208         2361          182         2184 
TCGA-BP-4769 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4782 TCGA-BP-4784 
        1876         1885          411         1731          354         1854 
TCGA-BP-4789 TCGA-BP-4795 TCGA-BP-4801 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4961 
        1489          620         1124          211         2660         1935 
TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4972 TCGA-BP-4975 
        1862         1871         1746          433         1502         1433 
TCGA-BP-4976 TCGA-BP-4982 TCGA-BP-4986 TCGA-BP-4991 TCGA-BP-4993 TCGA-BP-4995 
        1632         1014          785         1413          177         1371 
TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 
        1266          563         1126          840         1140         1071 
TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 
        2257          932         2263         1495         1165         1291 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 
        1133         1132          693          406          822         1011 
TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5199 
         967          714          408          749         1018         1355 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4642 TCGA-CJ-4643 
          29         1820         2308         1998         1628         1793 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4874 TCGA-CJ-4876 TCGA-CJ-4878 
         646         2554         1498         2283         1955         2186 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4886 TCGA-CJ-4890 TCGA-CJ-4892 
        2014         1883         1759         1952         2085         1521 
TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4899 TCGA-CJ-4902 TCGA-CJ-4904 TCGA-CJ-4905 
         750          841         1528         1520         1792         1496 
TCGA-CJ-4908 TCGA-CJ-4916 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5681 TCGA-CJ-5683 
        1531         1373         2430         2575          552         1889 
TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CW-5581 TCGA-CW-5583 
        2038         1855         1906         2548         2799         2489 
TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-6088 TCGA-CW-6090 TCGA-CZ-4853 
        2609         2226         2378         3222         2552          774 
TCGA-CZ-4856 TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-5451 
          18         1787         1843         1928         2830         1929 
TCGA-CZ-5452 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5470 
        1789         1732         1683          662         1446          386 
TCGA-CZ-5982 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-DV-5566 
        2439         1997          373          435          693         1398 
TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5575 TCGA-EU-5904 
        1470          370          355         1130         1729          551 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-GK-A6C7 
         119          206          127           61 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                3                 7 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             3377              3668 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           1423.0            1138.5 
[1] "3.0 - 3377.0 (1423.0)" "7.0 - 3668.0 (1138.5)"
[1] "hr=" "1"  
D13V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  7P GAIN MUTATED        69       18        46       34
  7P GAIN WILD-TYPE     175       38        80       45
D13V3, multiclass
           clus
vv          7P GAIN MUTATED 7P GAIN WILD-TYPE
  STAGE I                69               175
  STAGE II               18                38
  STAGE III              46                80
  STAGE IV               34                45
[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"
                   vv
clus                 T1  T2  T3  T4
  7P GAIN MUTATED    71  23  69   4
  7P GAIN WILD-TYPE 179  44 108   7
D13V4, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  T1              71               179
  T2              23                44
  T3              69               108
  T4               4                 7
[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"
D13V5, binary
                   cls
clus                  0   1
  7P GAIN MUTATED    80   8
  7P GAIN WILD-TYPE 150  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     80    8
  7P GAIN WILD-TYPE  150   10
   clus
vv  7P GAIN MUTATED 7P GAIN WILD-TYPE
  0              80               150
  1               8                10
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  7P GAIN MUTATED   130  35   2
  7P GAIN WILD-TYPE 287  43   7
D13V6, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  M0             130               287
  M1              35                43
  MX               2                 7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V7, binary
                   cls
clus                  0   1
  7P GAIN MUTATED    44 123
  7P GAIN WILD-TYPE 134 204
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     44  123
  7P GAIN WILD-TYPE  134  204
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE              44               134
  MALE               123               204
[1] 2 2
[1] FALSE
D13V8, continuous
D13V9, continuous
[1] "Remove cluster labels:" "7P GAIN MUTATED"       
clus
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                2                 6 
       TCGA-B2-A4SR        TCGA-B8-5158        TCGA-B8-5164        TCGA-B8-A54F 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-B8-A54G        TCGA-G6-A5PC 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7P GAIN MUTATED       4                         6   155
  7P GAIN WILD-TYPE     4                        27   302
D13V10, multiclass
                           clus
vv                          7P GAIN MUTATED 7P GAIN WILD-TYPE
  ASIAN                                   4                 4
  BLACK OR AFRICAN AMERICAN               6                27
  WHITE                                 155               302
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V11, binary
                   cls
clus                  0   1
  7P GAIN MUTATED     5 101
  7P GAIN WILD-TYPE  19 229
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      5  101
  7P GAIN WILD-TYPE   19  229
                        clus
vv                       7P GAIN MUTATED 7P GAIN WILD-TYPE
  HISPANIC OR LATINO                   5                19
  NOT HISPANIC OR LATINO             101               229
[1] 2 2
[1] FALSE

Clustering(14) Variable = 7Q GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                 0   1
  7Q GAIN MUTATED   108  11
  7Q GAIN WILD-TYPE 230  15
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              119               245 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               11                15 
$`7Q GAIN MUTATED`
TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3324 TCGA-A3-3325 
         735         1493         1491         1478         1186          751 
TCGA-A3-3336 TCGA-A3-3347 TCGA-A3-3358 TCGA-A3-3363 TCGA-A3-3372 TCGA-A3-3374 
        1043         1610         1307          319          735         1314 
TCGA-A3-3382 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A8CQ TCGA-AK-3425 TCGA-AK-3427 
         574         1993          617            3         3343         2566 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3433 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3444 
        2017          480         2192         2044         1745         1471 
TCGA-AK-3453 TCGA-B0-4710 TCGA-B0-4819 TCGA-B0-5113 TCGA-B0-5116 TCGA-B0-5698 
        1397           96          183          359          657         2583 
TCGA-B0-5701 TCGA-B0-5703 TCGA-B0-5713 TCGA-B2-3924 TCGA-B2-5639 TCGA-B4-5832 
        1732         1203         1865         1092          417            7 
TCGA-B4-5835 TCGA-B4-5838 TCGA-B4-5843 TCGA-B8-4146 TCGA-B8-4619 TCGA-B8-4620 
          16          166           11          511          523          777 
TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5550 TCGA-B8-A54I TCGA-BP-4158 TCGA-BP-4162 
         788          700          434          150         3377         3074 
TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4325 
          13         2718         1893         1879         1955         2964 
TCGA-BP-4332 TCGA-BP-4335 TCGA-BP-4338 TCGA-BP-4351 TCGA-BP-4759 TCGA-BP-4766 
        1133          461         2859          970         2372         1462 
TCGA-BP-4768 TCGA-BP-4775 TCGA-BP-4781 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4960 
         400         1843         2080          204         1459         2172 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4967 TCGA-BP-4969 TCGA-BP-4971 TCGA-BP-4973 
        1785         1834          205         1794         1487         1384 
TCGA-BP-4977 TCGA-BP-4983 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4992 TCGA-BP-4994 
         454         1413         1124          118          501         1308 
TCGA-BP-4998 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5177 TCGA-BP-5198 TCGA-BP-5200 
         932          193         2412          293          603         1063 
TCGA-BP-5201 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 
         951         1416         1924         2423         1435         2259 
TCGA-CJ-4875 TCGA-CJ-4885 TCGA-CJ-4889 TCGA-CJ-4897 TCGA-CJ-4901 TCGA-CJ-4903 
        2353         2125         1946         1808         1450         1560 
TCGA-CJ-4907 TCGA-CJ-5671 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CW-5588 
        1499         1943         1883         1889         2231         2017 
TCGA-CW-5591 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4858 TCGA-CZ-4866 TCGA-CZ-5456 
        2271         3146         1404         1943         1868         1712 
TCGA-CZ-5457 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5468 
        1683         1430          330         1740          685           59 
TCGA-CZ-5469 TCGA-CZ-5984 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5574 
         946         2067         1905         1329          723 

$`7Q GAIN WILD-TYPE`
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3323 
        1120         1436           16         1130         1508         1106 
TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3343 TCGA-A3-3349 TCGA-A3-3351 
        1137         1485          665          945         1385          910 
TCGA-A3-3357 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 
        2688         2504         1559          873         2270         2274 
TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3383 TCGA-AK-3428 
        1621         1070          630          567          861         2223 
TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 
        1853         2087         1423         1280         1217         1779 
TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
        1481          874         1143         1168          951          853 
TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4699 TCGA-B0-4706 TCGA-B0-4718 
         369         1238           43          110           26          616 
TCGA-B0-4813 TCGA-B0-5097 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5115 TCGA-B0-5117 
          18          665          911         1092          797          535 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
          59          493          554          652         1132          449 
TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5696 
        2408         3431         1487         3076         1420         1727 
TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5702 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 
        1835         2741         1605         3668         2414         3117 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-4098 
        1459         2931         2722         2963          992           51 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 
         374          648          952          358          315          656 
TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5836 TCGA-B4-5844 
         507          291          175           38          141            7 
TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-5158 TCGA-B8-5159 
         826          838          762          750          636          722 
TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
          36          822           26          737          522          505 
TCGA-B8-5549 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54F 
         194           15         1046          435          830          519 
TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4160 TCGA-BP-4161 
          53          256           66          110         2881         2746 
TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4169 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 
        2839         3037          701         1670         1625          845 
TCGA-BP-4330 TCGA-BP-4334 TCGA-BP-4344 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4756 
        1888          645         1666         1367          372          374 
TCGA-BP-4758 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4765 TCGA-BP-4769 TCGA-BP-4774 
        2208         2361          182         2184         1876         1885 
TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4795 
         411         1731          354         1854         1489          620 
TCGA-BP-4797 TCGA-BP-4801 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4961 TCGA-BP-4964 
        1107         1124          211         2660         1935         1862 
TCGA-BP-4965 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4972 TCGA-BP-4975 TCGA-BP-4976 
        1871         1746          433         1502         1433         1632 
TCGA-BP-4982 TCGA-BP-4986 TCGA-BP-4991 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 
        1014          785         1413          177         1371         1266 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 
         563         1177         1126          840         1140         1071 
TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 
        2257          932         2263         1495         1165         1291 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 
        1133         1132          693          406          822         1011 
TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5199 
         967          714          408          749         1018         1355 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4642 TCGA-CJ-4643 
          29         1820         2308         1998         1628         1793 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4874 TCGA-CJ-4876 TCGA-CJ-4878 
         646         2554         1498         2283         1955         2186 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4886 TCGA-CJ-4890 TCGA-CJ-4892 
        2014         1883         1759         1952         2085         1521 
TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4899 TCGA-CJ-4902 TCGA-CJ-4904 TCGA-CJ-4905 
         750          841         1528         1520         1792         1496 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5681 
        1531         1657         1373         2430         2575          552 
TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CW-5581 TCGA-CW-5583 
        2038         1855         1906         2548         2799         2489 
TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-6088 TCGA-CW-6090 TCGA-CZ-4853 
        2609         2226         2378         3222         2552          774 
TCGA-CZ-4856 TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-5451 
          18         1787         1843         1928         2830         1929 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5463 TCGA-CZ-5465 
        1789           25         1732         1683          662         1446 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 
         386         2439         1997          373          435          693 
TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5575 
        1398         1470          370          355         1130         1729 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-GK-A6C7 
         551          119          206          127           61 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                3                 7 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             3377              3668 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             1430              1140 
[1] "3.0 - 3377.0 (1430.0)" "7.0 - 3668.0 (1140.0)"
[1] "hr=" "1.4"
D14V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  7Q GAIN MUTATED        69       16        46       37
  7Q GAIN WILD-TYPE     175       40        80       42
D14V3, multiclass
           clus
vv          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  STAGE I                69               175
  STAGE II               16                40
  STAGE III              46                80
  STAGE IV               37                42
[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"
                   vv
clus                 T1  T2  T3  T4
  7Q GAIN MUTATED    71  21  72   4
  7Q GAIN WILD-TYPE 179  46 105   7
D14V4, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  T1              71               179
  T2              21                46
  T3              72               105
  T4               4                 7
[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"
D14V5, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED    78   8
  7Q GAIN WILD-TYPE 152  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     78    8
  7Q GAIN WILD-TYPE  152   10
   clus
vv  7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  0              78               152
  1               8                10
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  7Q GAIN MUTATED   128  38   2
  7Q GAIN WILD-TYPE 289  40   7
D14V6, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  M0             128               289
  M1              38                40
  MX               2                 7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V7, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED    46 122
  7Q GAIN WILD-TYPE 132 205
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     46  122
  7Q GAIN WILD-TYPE  132  205
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE              46               132
  MALE               122               205
[1] 2 2
[1] FALSE
D14V8, continuous
D14V9, continuous
[1] "Remove cluster labels:" "7Q GAIN MUTATED"       
clus
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                2                 6 
       TCGA-B2-A4SR        TCGA-B8-5158        TCGA-B8-5164        TCGA-B8-A54F 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-B8-A54G        TCGA-G6-A5PC 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7Q GAIN MUTATED       4                         6   156
  7Q GAIN WILD-TYPE     4                        27   301
D14V10, multiclass
                           clus
vv                          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  ASIAN                                   4                 4
  BLACK OR AFRICAN AMERICAN               6                27
  WHITE                                 156               301
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V11, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED     4 104
  7Q GAIN WILD-TYPE  20 226
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      4  104
  7Q GAIN WILD-TYPE   20  226
                        clus
vv                       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                20
  NOT HISPANIC OR LATINO             104               226
[1] 2 2
[1] FALSE

Clustering(15) Variable = 8P GAIN MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                 0   1
  8P GAIN MUTATED    18   4
  8P GAIN WILD-TYPE 320  22
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               22               342 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                4                22 
$`8P GAIN MUTATED`
TCGA-A3-3313 TCGA-A3-3316 TCGA-AK-3433 TCGA-AK-3445 TCGA-B0-5097 TCGA-B4-5832 
         735         1493         2192         1280          665            7 
TCGA-BP-4768 TCGA-BP-4983 TCGA-BP-5000 TCGA-BP-5185 TCGA-BP-5191 TCGA-CJ-4871 
         400         1413          563         1132          967         2423 
TCGA-CJ-4901 TCGA-CW-5588 TCGA-CW-5591 TCGA-CZ-4858 TCGA-CZ-4866 TCGA-CZ-5456 
        1450         2017         2271         1943         1868         1712 
TCGA-CZ-5464 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5987 
        1740          946          386          435 

$`8P GAIN WILD-TYPE`
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 
        1120         1436           16         1491         1130         1508 
TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 
        1478         1106         1186          751         1137         1485 
TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 
         665         1043          945         1610         1385          910 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
        2688         1307         2504         1559          319          873 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 
        2270         2274          735         1621         1314         1070 
TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 
         630          567          574          861         1993          617 
TCGA-A3-A8CQ TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 
           3         3343         2566         2223         2017          480 
TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 
        1853         2087         2044         1745         1423         1471 
TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3456 
        1217         1779         1481         1397          874         1143 
TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 
        1168          951          853          369         1238           43 
TCGA-B0-4699 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4718 TCGA-B0-4813 TCGA-B0-4819 
         110           26           96          616           18          183 
TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 
         911         1092          359          797          657          535 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
          59          493          554          652         1132          449 
TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5696 
        2408         3431         1487         3076         1420         1727 
TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
        1835         2583         2741         1732         1605         1203 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
        3668         2414         3117         1459         2931         2722 
TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
        1865         2963          992         1092           51          374 
TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 
         648          952          358          315          417          656 
TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
         507          291          175           38           16          141 
TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
         166           11            7          511          826          838 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 
         762          750          523          777          788          700 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
         636          722           36          822           26          737 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
         522          505          194          434           15         1046 
TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I 
         435          830          519           53          256          150 
TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 
          66          110         3377         2881         2746         3074 
TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4173 
        2839         3037           13         2718          701         1893 
TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 
        1879         1955         1670         2964         1625          845 
TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4338 TCGA-BP-4344 
        1888         1133          645          461         2859         1666 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 
        1367          372          970          374         2208         2372 
TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4774 
        2361          182         2184         1462         1876         1885 
TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 
        1843          411         1731         2080          354         1854 
TCGA-BP-4789 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 
        1489          620         1107         1124          204         1459 
TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
         211         2660         2172         1935         1785         1834 
TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 
        1862         1871          205         1746         1794          433 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 
        1487         1502         1384         1433         1632          454 
TCGA-BP-4982 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
        1014          785         1124          118         1413          501 
TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5001 
         177         1308         1371          932         1266         1177 
TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5169 TCGA-BP-5170 
        1126          840         1140         1071          193         2412 
TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 
        2257          932          293         2263         1495         1165 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 
        1291         1133          693          406          822         1011 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 
         714          408          749         1018          603         1355 
TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 
        1063          951           29         1820         1416         1924 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 
        2308         1998         1628         1793          646         2554 
TCGA-CJ-4870 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 
        1498         1435         2259         2283         2353         1955 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 
        2186         2014         1883         1759         2125         1952 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4897 
        1946         2085         1521          750          841         1808 
TCGA-CJ-4899 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 
        1528         1520         1560         1792         1496         1499 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-5671 TCGA-CJ-5675 TCGA-CJ-5676 
        1531         1657         1373         1943         2430         2575 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 
         552         1883         1889         2231         2038         1855 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5587 
        1906         2548         2799         2489         2609         2226 
TCGA-CW-5589 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4854 
        2378         3222         2552         3146          774         1404 
TCGA-CZ-4856 TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-5451 
          18         1787         1843         1928         2830         1929 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
        1789           25         1683         1732         1683         1430 
TCGA-CZ-5461 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5982 
         330          662         1446          685           59         2439 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 
        2067         1997          373          693         1905         1329 
TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 
        1398         1470          370          355         1130          723 
TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-GK-A6C7 
        1729          551          119          206          127           61 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                7                 3 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             2423              3668 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           1346.5            1299.0 
[1] "7.0 - 2423.0 (1346.5)" "3.0 - 3668.0 (1299.0)"
[1] "hr=" "2.9"
D15V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  8P GAIN MUTATED         6        7         9        7
  8P GAIN WILD-TYPE     238       49       117       72
D15V3, multiclass
           clus
vv          8P GAIN MUTATED 8P GAIN WILD-TYPE
  STAGE I                 6               238
  STAGE II                7                49
  STAGE III               9               117
  STAGE IV                7                72
[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"
                   vv
clus                 T1  T2  T3  T4
  8P GAIN MUTATED     6   8  15   0
  8P GAIN WILD-TYPE 244  59 162  11
D15V4, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  T1               6               244
  T2               8                59
  T3              15               162
  T4               0                11
[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"
D15V5, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    12   1
  8P GAIN WILD-TYPE 218  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     12    1
  8P GAIN WILD-TYPE  218   17
   clus
vv  8P GAIN MUTATED 8P GAIN WILD-TYPE
  0              12               218
  1               1                17
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  8P GAIN MUTATED    22   7   0
  8P GAIN WILD-TYPE 395  71   9
D15V6, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  M0              22               395
  M1               7                71
  MX               0                 9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V7, binary
                   cls
clus                  0   1
  8P GAIN MUTATED     9  20
  8P GAIN WILD-TYPE 169 307
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      9   20
  8P GAIN WILD-TYPE  169  307
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE               9               169
  MALE                20               307
[1] 2 2
[1] FALSE
D15V8, continuous
D15V9, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8P GAIN MUTATED       1                         1    26
  8P GAIN WILD-TYPE     7                        32   431
D15V10, multiclass
                           clus
vv                          8P GAIN MUTATED 8P GAIN WILD-TYPE
  ASIAN                                   1                 7
  BLACK OR AFRICAN AMERICAN               1                32
  WHITE                                  26               431
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V11, binary
                   cls
clus                  0   1
  8P GAIN MUTATED     0  18
  8P GAIN WILD-TYPE  24 312
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      0   18
  8P GAIN WILD-TYPE   24  312
                        clus
vv                       8P GAIN MUTATED 8P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                24
  NOT HISPANIC OR LATINO              18               312
[1] 2 2
[1] FALSE

Clustering(16) Variable = 8Q GAIN MUTATION ANALYSIS
D16V1, survival
                   sevent
clus2                 0   1
  8Q GAIN MUTATED    38   6
  8Q GAIN WILD-TYPE 300  20
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               44               320 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                6                20 
$`8Q GAIN MUTATED`
TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3319 TCGA-A3-3325 TCGA-A3-3336 
          16          735         1493         1130          751         1043 
TCGA-AK-3425 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3445 TCGA-B0-5097 TCGA-B0-5108 
        3343         2192         2087         1280          665          911 
TCGA-B4-5832 TCGA-B8-5158 TCGA-B8-5163 TCGA-B8-5551 TCGA-B8-A54I TCGA-BP-4174 
           7          636          822           15          150         1879 
TCGA-BP-4338 TCGA-BP-4761 TCGA-BP-4768 TCGA-BP-4962 TCGA-BP-4983 TCGA-BP-5000 
        2859          182          400         1785         1413          563 
TCGA-BP-5169 TCGA-BP-5175 TCGA-BP-5185 TCGA-BP-5191 TCGA-CJ-4871 TCGA-CJ-4881 
         193          932         1132          967         2423         2014 
TCGA-CJ-4901 TCGA-CJ-4912 TCGA-CW-5588 TCGA-CW-5591 TCGA-CZ-4854 TCGA-CZ-4858 
        1450         1657         2017         2271         1404         1943 
TCGA-CZ-4866 TCGA-CZ-5456 TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5469 
        1868         1712         1740          685           59          946 
TCGA-CZ-5470 TCGA-CZ-5987 
         386          435 

$`8Q GAIN WILD-TYPE`
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3317 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 
        1120         1436         1491         1508         1478         1106 
TCGA-A3-3324 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3343 TCGA-A3-3347 
        1186         1137         1485          665          945         1610 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 
        1385          910         2688         1307         2504         1559 
TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 
         319          873         2270         2274          735         1621 
TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 
        1314         1070          630          567          574          861 
TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A8CQ TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
        1993          617            3         2566         2223         2017 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 
         480         1853         2044         1745         1423         1471 
TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3456 
        1217         1779         1481         1397          874         1143 
TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 
        1168          951          853          369         1238           43 
TCGA-B0-4699 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4718 TCGA-B0-4813 TCGA-B0-4819 
         110           26           96          616           18          183 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 
        1092          359          797          657          535           59 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 
         493          554          652         1132          449         2408 
TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 
        3431         1487         3076         1420         1727         1835 
TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 
        2583         2741         1732         1605         1203         3668 
TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
        2414         3117         1459         2931         2722         1865 
TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 
        2963          992         1092           51          374          648 
TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR 
         952          358          315          417          656          507 
TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
         291          175           38           16          141          166 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
          11            7          511          826          838          762 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5159 
         750          523          777          788          700          722 
TCGA-B8-5162 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 
          36           26          737          522          505          194 
TCGA-B8-5550 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G 
         434         1046          435          830          519           53 
TCGA-B8-A54H TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4161 
         256           66          110         3377         2881         2746 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 
        3074         2839         3037           13         2718          701 
TCGA-BP-4173 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 
        1893         1955         1670         2964         1625          845 
TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4344 TCGA-BP-4347 
        1888         1133          645          461         1666         1367 
TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 
         372          970          374         2208         2372         2361 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 
        2184         1462         1876         1885         1843          411 
TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4795 
        1731         2080          354         1854         1489          620 
TCGA-BP-4797 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 
        1107         1124          204         1459          211         2660 
TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 
        2172         1935         1834         1862         1871          205 
TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 
        1746         1794          433         1487         1502         1384 
TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4982 TCGA-BP-4986 TCGA-BP-4987 
        1433         1632          454         1014          785         1124 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 
         118         1413          501          177         1308         1371 
TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 
         932         1266         1177         1126          840         1140 
TCGA-BP-5008 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5181 
        1071         2412         2257          293         2263         1495 
TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 
        1165         1291         1133          693          406          822 
TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 
        1011          714          408          749         1018          603 
TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 
        1355         1063          951           29         1820         1416 
TCGA-CJ-4636 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 
        1924         2308         1998         1628         1793          646 
TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 
        2554         1498         1435         2259         2283         2353 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 
        1955         2186         1883         1759         2125         1952 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4897 
        1946         2085         1521          750          841         1808 
TCGA-CJ-4899 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 
        1528         1520         1560         1792         1496         1499 
TCGA-CJ-4908 TCGA-CJ-4916 TCGA-CJ-5671 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5681 
        1531         1373         1943         2430         2575          552 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6031 
        1883         1889         2231         2038         1855         1906 
TCGA-CJ-6032 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 
        2548         2799         2489         2609         2226         2378 
TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4859 
        3222         2552         3146          774           18         1787 
TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 
        1843         1928         2830         1929         1789           25 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5463 
        1683         1732         1683         1430          330          662 
TCGA-CZ-5465 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5988 
        1446         2439         2067         1997          373          693 
TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 
        1905         1329         1398         1470          370          355 
TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 
        1130          723         1729          551          119          206 
TCGA-EU-5907 TCGA-GK-A6C7 
         127           61 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                7                 3 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             3343              3668 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           1086.5            1321.5 
[1] "7.0 - 3343.0 (1086.5)" "3.0 - 3668.0 (1321.5)"
[1] "hr=" "2.3"
D16V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  8Q GAIN MUTATED        18       10        19       13
  8Q GAIN WILD-TYPE     226       46       107       66
D16V3, multiclass
           clus
vv          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  STAGE I                18               226
  STAGE II               10                46
  STAGE III              19               107
  STAGE IV               13                66
[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"
                   vv
clus                 T1  T2  T3  T4
  8Q GAIN MUTATED    19  11  29   1
  8Q GAIN WILD-TYPE 231  56 148  10
D16V4, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  T1              19               231
  T2              11                56
  T3              29               148
  T4               1                10
[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"
D16V5, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED    26   3
  8Q GAIN WILD-TYPE 204  15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     26    3
  8Q GAIN WILD-TYPE  204   15
   clus
vv  8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  0              26               204
  1               3                15
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  8Q GAIN MUTATED    45  14   1
  8Q GAIN WILD-TYPE 372  64   8
D16V6, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  M0              45               372
  M1              14                64
  MX               1                 8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V7, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED    16  44
  8Q GAIN WILD-TYPE 162 283
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     16   44
  8Q GAIN WILD-TYPE  162  283
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE              16               162
  MALE                44               283
[1] 2 2
[1] FALSE
D16V8, continuous
D16V9, continuous
[1] "Remove cluster labels:" "8Q GAIN MUTATED"       
clus
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                1                 7 
       TCGA-A3-A8CQ        TCGA-B2-A4SR        TCGA-B8-4621        TCGA-B8-5164 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-B8-A54F        TCGA-B8-A54G        TCGA-G6-A5PC 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8Q GAIN MUTATED       1                         3    54
  8Q GAIN WILD-TYPE     7                        30   403
D16V10, multiclass
                           clus
vv                          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  ASIAN                                   1                 7
  BLACK OR AFRICAN AMERICAN               3                30
  WHITE                                  54               403
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V11, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED     1  35
  8Q GAIN WILD-TYPE  23 295
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      1   35
  8Q GAIN WILD-TYPE   23  295
                        clus
vv                       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                23
  NOT HISPANIC OR LATINO              35               295
[1] 2 2
[1] FALSE

Clustering(17) Variable = 9P GAIN MUTATION ANALYSIS
D17V1, survival
                   sevent
clus2                 0   1
  9P GAIN MUTATED    10   0
  9P GAIN WILD-TYPE 328  26
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               10               354 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                0                26 
$`9P GAIN MUTATED`
TCGA-A3-3374 TCGA-AK-3429 TCGA-AK-3433 TCGA-AK-3440 TCGA-BP-4969 TCGA-BP-5181 
        1314         2017         2192         1745         1794         1495 
TCGA-CJ-4870 TCGA-CJ-4897 TCGA-CZ-4866 TCGA-CZ-5457 
        1498         1808         1868         1683 

$`9P GAIN WILD-TYPE`
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 
        1120         1436           16          735         1493         1491 
TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 
        1130         1508         1478         1106         1186          751 
TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3347 
        1137         1485          665         1043          945         1610 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 
        1385          910         2688         1307         2504         1559 
TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 
         319          873         2270         2274          735         1621 
TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 
        1070          630          567          574          861         1993 
TCGA-A3-3387 TCGA-A3-A8CQ TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3430 
         617            3         3343         2566         2223          480 
TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 
        1853         2087         2044         1423         1471         1280 
TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3456 
        1217         1779         1481         1397          874         1143 
TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 
        1168          951          853          369         1238           43 
TCGA-B0-4699 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4718 TCGA-B0-4813 TCGA-B0-4819 
         110           26           96          616           18          183 
TCGA-B0-5097 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 
         665          911         1092          359          797          657 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
         535           59          493          554          652         1132 
TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 
         449         2408         3431         1487         3076         1420 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
        1727         1835         2583         2741         1732         1605 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
        1203         3668         2414         3117         1459         2931 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
        2722         1865         2963          992         1092           51 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 
         374          648          952          358          315          417 
TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 
         656          507          291          175            7           38 
TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 
          16          141          166           11            7          511 
TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 
         826          838          762          750          523          777 
TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 
         788          700          636          722           36          822 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 
          26          737          522          505          194          434 
TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G 
          15         1046          435          830          519           53 
TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4158 TCGA-BP-4160 
         256          150           66          110         3377         2881 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 
        2746         3074         2839         3037           13         2718 
TCGA-BP-4169 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 
         701         1893         1879         1955         1670         2964 
TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 
        1625          845         1888         1133          645          461 
TCGA-BP-4338 TCGA-BP-4344 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4756 
        2859         1666         1367          372          970          374 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4765 TCGA-BP-4766 
        2208         2372         2361          182         2184         1462 
TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 
         400         1876         1885         1843          411         1731 
TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4795 TCGA-BP-4797 
        2080          354         1854         1489          620         1107 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 
        1124          204         1459          211         2660         2172 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 
        1935         1785         1834         1862         1871          205 
TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4975 
        1746          433         1487         1502         1384         1433 
TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4987 
        1632          454         1014         1413          785         1124 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 
         118         1413          501          177         1308         1371 
TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 
         932         1266          563         1177         1126          840 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5175 
        1140         1071          193         2412         2257          932 
TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 
         293         2263         1165         1291         1133         1132 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 
         693          406          822         1011          967          714 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 
         408          749         1018          603         1355         1063 
TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4639 
         951           29         1820         1416         1924         2308 
TCGA-CJ-4640 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4871 
        1998         1628         1793          646         2554         2423 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
        1435         2259         2283         2353         1955         2186 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4889 
        2014         1883         1759         2125         1952         1946 
TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4899 TCGA-CJ-4901 
        2085         1521          750          841         1528         1450 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 
        1520         1560         1792         1496         1499         1531 
TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-5671 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5681 
        1657         1373         1943         2430         2575          552 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6031 
        1883         1889         2231         2038         1855         1906 
TCGA-CJ-6032 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 
        2548         2799         2489         2609         2226         2017 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CZ-4853 
        2378         2271         3222         2552         3146          774 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-4863 
        1404           18         1943         1787         1843         1928 
TCGA-CZ-4864 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5456 TCGA-CZ-5458 
        2830         1929         1789           25         1712         1732 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 
        1683         1430          330          662         1740         1446 
TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 
         685           59          946          386         2439         2067 
TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 
        1997          373          435          693         1905         1329 
TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 
        1398         1470          370          355         1130          723 
TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-GK-A6C7 
        1729          551          119          206          127           61 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
             1314                 3 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
             2192              3668 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           1769.5            1210.0 
[1] "1314.0 - 2192.0 (1769.5)" "3.0 - 3668.0 (1210.0)"   
[1] "hr="     "2.6e+07"
D17V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  9P GAIN MUTATED         6        2         3        2
  9P GAIN WILD-TYPE     238       54       123       77
D17V3, multiclass
           clus
vv          9P GAIN MUTATED 9P GAIN WILD-TYPE
  STAGE I                 6               238
  STAGE II                2                54
  STAGE III               3               123
  STAGE IV                2                77
[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"
                   vv
clus                 T1  T2  T3  T4
  9P GAIN MUTATED     6   2   3   2
  9P GAIN WILD-TYPE 244  65 174   9
D17V4, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  T1               6               244
  T2               2                65
  T3               3               174
  T4               2                 9
[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"
D17V5, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     5   0
  9P GAIN WILD-TYPE 225  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      5    0
  9P GAIN WILD-TYPE  225   18
   clus
vv  9P GAIN MUTATED 9P GAIN WILD-TYPE
  0               5               225
  1               0                18
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  9P GAIN MUTATED    13   0   0
  9P GAIN WILD-TYPE 404  78   9
D17V6, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  M0              13               404
  M1               0                78
  MX               0                 9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V7, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     9   4
  9P GAIN WILD-TYPE 169 323
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      9    4
  9P GAIN WILD-TYPE  169  323
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE               9               169
  MALE                 4               323
[1] 2 2
[1] FALSE
D17V8, continuous
[1] "Remove cluster labels:" "9P GAIN MUTATED"       
clus
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                1                36 
       TCGA-A3-A8CQ        TCGA-AK-3426        TCGA-AK-3430        TCGA-B0-4838 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-B2-5639        TCGA-B4-5377        TCGA-B4-5378        TCGA-B4-5832 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-B4-5834        TCGA-B4-5835        TCGA-B4-5836        TCGA-B4-5838 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-B4-5843        TCGA-B4-5844        TCGA-CZ-4854        TCGA-CZ-4856 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CZ-4858        TCGA-CZ-4860        TCGA-CZ-4861        TCGA-CZ-4862 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CZ-5456        TCGA-CZ-5465        TCGA-CZ-5469        TCGA-CZ-5982 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DV-5565        TCGA-DV-5566        TCGA-DV-5567        TCGA-DV-5568 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DV-5569        TCGA-DV-5573        TCGA-DV-5574        TCGA-DV-5575 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DV-5576        TCGA-EU-5904        TCGA-EU-5905        TCGA-EU-5907 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
D17V9, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9P GAIN MUTATED       0                         2    11
  9P GAIN WILD-TYPE     8                        31   446
D17V10, multiclass
                           clus
vv                          9P GAIN MUTATED 9P GAIN WILD-TYPE
  ASIAN                                   0                 8
  BLACK OR AFRICAN AMERICAN               2                31
  WHITE                                  11               446
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V11, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     1  10
  9P GAIN WILD-TYPE  23 320
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      1   10
  9P GAIN WILD-TYPE   23  320
                        clus
vv                       9P GAIN MUTATED 9P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                23
  NOT HISPANIC OR LATINO              10               320
[1] 2 2
[1] FALSE

Clustering(18) Variable = 9Q GAIN MUTATION ANALYSIS
D18V1, survival
                   sevent
clus2                 0   1
  9Q GAIN MUTATED     8   1
  9Q GAIN WILD-TYPE 330  25
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                9               355 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                1                25 
$`9Q GAIN MUTATED`
TCGA-A3-3374 TCGA-AK-3429 TCGA-AK-3433 TCGA-AK-3440 TCGA-BP-4969 TCGA-CJ-4897 
        1314         2017         2192         1745         1794         1808 
TCGA-CZ-4866 TCGA-CZ-5457 TCGA-CZ-5468 
        1868         1683           59 

$`9Q GAIN WILD-TYPE`
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 
        1120         1436           16          735         1493         1491 
TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 
        1130         1508         1478         1106         1186          751 
TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3347 
        1137         1485          665         1043          945         1610 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 
        1385          910         2688         1307         2504         1559 
TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 
         319          873         2270         2274          735         1621 
TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 
        1070          630          567          574          861         1993 
TCGA-A3-3387 TCGA-A3-A8CQ TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3430 
         617            3         3343         2566         2223          480 
TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 
        1853         2087         2044         1423         1471         1280 
TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3456 
        1217         1779         1481         1397          874         1143 
TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 
        1168          951          853          369         1238           43 
TCGA-B0-4699 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4718 TCGA-B0-4813 TCGA-B0-4819 
         110           26           96          616           18          183 
TCGA-B0-5097 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 
         665          911         1092          359          797          657 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
         535           59          493          554          652         1132 
TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 
         449         2408         3431         1487         3076         1420 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
        1727         1835         2583         2741         1732         1605 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
        1203         3668         2414         3117         1459         2931 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
        2722         1865         2963          992         1092           51 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 
         374          648          952          358          315          417 
TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 
         656          507          291          175            7           38 
TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 
          16          141          166           11            7          511 
TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 
         826          838          762          750          523          777 
TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 
         788          700          636          722           36          822 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 
          26          737          522          505          194          434 
TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G 
          15         1046          435          830          519           53 
TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4158 TCGA-BP-4160 
         256          150           66          110         3377         2881 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 
        2746         3074         2839         3037           13         2718 
TCGA-BP-4169 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 
         701         1893         1879         1955         1670         2964 
TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 
        1625          845         1888         1133          645          461 
TCGA-BP-4338 TCGA-BP-4344 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4756 
        2859         1666         1367          372          970          374 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4765 TCGA-BP-4766 
        2208         2372         2361          182         2184         1462 
TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 
         400         1876         1885         1843          411         1731 
TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4795 TCGA-BP-4797 
        2080          354         1854         1489          620         1107 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 
        1124          204         1459          211         2660         2172 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 
        1935         1785         1834         1862         1871          205 
TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4975 
        1746          433         1487         1502         1384         1433 
TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4987 
        1632          454         1014         1413          785         1124 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 
         118         1413          501          177         1308         1371 
TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 
         932         1266          563         1177         1126          840 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5175 
        1140         1071          193         2412         2257          932 
TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
         293         2263         1495         1165         1291         1133 
TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 
        1132          693          406          822         1011          967 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 
         714          408          749         1018          603         1355 
TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 
        1063          951           29         1820         1416         1924 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 
        2308         1998         1628         1793          646         2554 
TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 
        1498         2423         1435         2259         2283         2353 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
        1955         2186         2014         1883         1759         2125 
TCGA-CJ-4886 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 
        1952         1946         2085         1521          750          841 
TCGA-CJ-4899 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 
        1528         1450         1520         1560         1792         1496 
TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-5671 TCGA-CJ-5675 
        1499         1531         1657         1373         1943         2430 
TCGA-CJ-5676 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 
        2575          552         1883         1889         2231         2038 
TCGA-CJ-6027 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 
        1855         1906         2548         2799         2489         2609 
TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6088 TCGA-CW-6090 
        2226         2017         2378         2271         3222         2552 
TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4858 TCGA-CZ-4859 
        3146          774         1404           18         1943         1787 
TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 
        1843         1928         2830         1929         1789           25 
TCGA-CZ-5456 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5463 
        1712         1732         1683         1430          330          662 
TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 
        1740         1446          685          946          386         2439 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
        2067         1997          373          435          693         1905 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 
        1329         1398         1470          370          355         1130 
TCGA-DV-5574 TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
         723         1729          551          119          206          127 
TCGA-GK-A6C7 
          61 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               59                 3 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
             2192              3668 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
             1794              1238 
[1] "59.0 - 2192.0 (1794.0)" "3.0 - 3668.0 (1238.0)" 
[1] "hr=" "1.3"
D18V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  9Q GAIN MUTATED         4        2         2        4
  9Q GAIN WILD-TYPE     240       54       124       75
D18V3, multiclass
           clus
vv          9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  STAGE I                 4               240
  STAGE II                2                54
  STAGE III               2               124
  STAGE IV                4                75
[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"
                   vv
clus                 T1  T2  T3  T4
  9Q GAIN MUTATED     4   2   3   3
  9Q GAIN WILD-TYPE 246  65 174   8
D18V4, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  T1               4               246
  T2               2                65
  T3               3               174
  T4               3                 8
[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"
D18V5, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     5   0
  9Q GAIN WILD-TYPE 225  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      5    0
  9Q GAIN WILD-TYPE  225   18
   clus
vv  9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  0               5               225
  1               0                18
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  9Q GAIN MUTATED    10   2   0
  9Q GAIN WILD-TYPE 407  76   9
D18V6, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  M0              10               407
  M1               2                76
  MX               0                 9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V7, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     7   5
  9Q GAIN WILD-TYPE 171 322
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      7    5
  9Q GAIN WILD-TYPE  171  322
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE               7               171
  MALE                 5               322
[1] 2 2
[1] FALSE
D18V8, continuous
[1] "Remove cluster labels:" "9Q GAIN MUTATED"       
clus
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                1                36 
       TCGA-A3-A8CQ        TCGA-AK-3426        TCGA-AK-3430        TCGA-B0-4838 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-B2-5639        TCGA-B4-5377        TCGA-B4-5378        TCGA-B4-5832 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-B4-5834        TCGA-B4-5835        TCGA-B4-5836        TCGA-B4-5838 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-B4-5843        TCGA-B4-5844        TCGA-CZ-4854        TCGA-CZ-4856 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CZ-4858        TCGA-CZ-4860        TCGA-CZ-4861        TCGA-CZ-4862 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CZ-5456        TCGA-CZ-5465        TCGA-CZ-5469        TCGA-CZ-5982 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DV-5565        TCGA-DV-5566        TCGA-DV-5567        TCGA-DV-5568 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DV-5569        TCGA-DV-5573        TCGA-DV-5574        TCGA-DV-5575 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DV-5576        TCGA-EU-5904        TCGA-EU-5905        TCGA-EU-5907 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
D18V9, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9Q GAIN MUTATED       0                         1    11
  9Q GAIN WILD-TYPE     8                        32   446
D18V10, multiclass
                           clus
vv                          9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  ASIAN                                   0                 8
  BLACK OR AFRICAN AMERICAN               1                32
  WHITE                                  11               446
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V11, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     1  10
  9Q GAIN WILD-TYPE  23 320
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      1   10
  9Q GAIN WILD-TYPE   23  320
                        clus
vv                       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                23
  NOT HISPANIC OR LATINO              10               320
[1] 2 2
[1] FALSE

Clustering(19) Variable = 10P GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                  0   1
  10P GAIN MUTATED    11   2
  10P GAIN WILD-TYPE 327  24
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                13                351 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 2                 24 
$`10P GAIN MUTATED`
TCGA-A3-3316 TCGA-AK-3453 TCGA-B4-5832 TCGA-B4-5838 TCGA-BP-4338 TCGA-BP-4768 
        1493         1397            7          166         2859          400 
TCGA-BP-4781 TCGA-BP-5175 TCGA-CW-5588 TCGA-CZ-4858 TCGA-CZ-4866 TCGA-CZ-5468 
        2080          932         2017         1943         1868           59 
TCGA-EU-5905 
         119 

$`10P GAIN WILD-TYPE`
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3319 
        1120         1436           16          735         1491         1130 
TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 
        1508         1478         1106         1186          751         1137 
TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3347 TCGA-A3-3349 
        1485          665         1043          945         1610         1385 
TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 
         910         2688         1307         2504         1559          319 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 
         873         2270         2274          735         1621         1314 
TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 
        1070          630          567          574          861         1993 
TCGA-A3-3387 TCGA-A3-A8CQ TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
         617            3         3343         2566         2223         2017 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
         480         1853         2192         2087         2044         1745 
TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 
        1423         1471         1280         1217         1779         1481 
TCGA-AK-3454 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 
         874         1143         1168          951          853          369 
TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4699 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4718 
        1238           43          110           26           96          616 
TCGA-B0-4813 TCGA-B0-4819 TCGA-B0-5097 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 
          18          183          665          911         1092          359 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
         797          657          535           59          493          554 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 
         652         1132          449         2408         3431         1487 
TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 
        3076         1420         1727         1835         2583         2741 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 
        1732         1605         1203         3668         2414         3117 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 
        1459         2931         2722         1865         2963          992 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 
        1092           51          374          648          952          358 
TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 
         315          417          656          507          291          175 
TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 
          38           16          141           11            7          511 
TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 
         826          838          762          750          523          777 
TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 
         788          700          636          722           36          822 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 
          26          737          522          505          194          434 
TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G 
          15         1046          435          830          519           53 
TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4158 TCGA-BP-4160 
         256          150           66          110         3377         2881 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 
        2746         3074         2839         3037           13         2718 
TCGA-BP-4169 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 
         701         1893         1879         1955         1670         2964 
TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 
        1625          845         1888         1133          645          461 
TCGA-BP-4344 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4756 TCGA-BP-4758 
        1666         1367          372          970          374         2208 
TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 
        2372         2361          182         2184         1462         1876 
TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4782 TCGA-BP-4784 
        1885         1843          411         1731          354         1854 
TCGA-BP-4789 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 
        1489          620         1107         1124          204         1459 
TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
         211         2660         2172         1935         1785         1834 
TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 
        1862         1871          205         1746         1794          433 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 
        1487         1502         1384         1433         1632          454 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 
        1014         1413          785         1124          118         1413 
TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 
         501          177         1308         1371          932         1266 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 
         563         1177         1126          840         1140         1071 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5181 
         193         2412         2257          293         2263         1495 
TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 
        1165         1291         1133         1132          693          406 
TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
         822         1011          967          714          408          749 
TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 
        1018          603         1355         1063          951           29 
TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4642 
        1820         1416         1924         2308         1998         1628 
TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 
        1793          646         2554         1498         2423         1435 
TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 
        2259         2283         2353         1955         2186         2014 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4889 TCGA-CJ-4890 
        1883         1759         2125         1952         1946         2085 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4901 
        1521          750          841         1808         1528         1450 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 
        1520         1560         1792         1496         1499         1531 
TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-5671 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5681 
        1657         1373         1943         2430         2575          552 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6031 
        1883         1889         2231         2038         1855         1906 
TCGA-CJ-6032 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 
        2548         2799         2489         2609         2226         2378 
TCGA-CW-5591 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4854 
        2271         3222         2552         3146          774         1404 
TCGA-CZ-4856 TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-5451 
          18         1787         1843         1928         2830         1929 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 
        1789           25         1712         1683         1732         1683 
TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 
        1430          330          662         1740         1446          685 
TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
         946          386         2439         2067         1997          373 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 
         435          693         1905         1329         1398         1470 
TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-EU-5904 
         370          355         1130          723         1729          551 
TCGA-EU-5906 TCGA-EU-5907 TCGA-GK-A6C7 
         206          127           61 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 7                  3 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
              2859               3668 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
              1397               1291 
[1] "7.0 - 2859.0 (1397.0)" "3.0 - 3668.0 (1291.0)"
[1] "hr=" "2.4"
D19V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  10P GAIN MUTATED         7        4         3        3
  10P GAIN WILD-TYPE     237       52       123       76
D19V3, multiclass
           clus
vv          10P GAIN MUTATED 10P GAIN WILD-TYPE
  STAGE I                  7                237
  STAGE II                 4                 52
  STAGE III                3                123
  STAGE IV                 3                 76
[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"
                    vv
clus                  T1  T2  T3  T4
  10P GAIN MUTATED     7   5   4   1
  10P GAIN WILD-TYPE 243  62 173  10
D19V4, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  T1                7                243
  T2                5                 62
  T3                4                173
  T4                1                 10
[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"
D19V5, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     6   2
  10P GAIN WILD-TYPE 224  16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      6    2
  10P GAIN WILD-TYPE  224   16
   clus
vv  10P GAIN MUTATED 10P GAIN WILD-TYPE
  0                6                224
  1                2                 16
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  10P GAIN MUTATED    14   3   0
  10P GAIN WILD-TYPE 403  75   9
D19V6, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  M0               14                403
  M1                3                 75
  MX                0                  9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V7, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     5  12
  10P GAIN WILD-TYPE 173 315
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      5   12
  10P GAIN WILD-TYPE  173  315
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE                5                173
  MALE                 12                315
[1] 2 2
[1] FALSE
D19V8, continuous
D19V9, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10P GAIN MUTATED       0                         0    17
  10P GAIN WILD-TYPE     8                        33   440
D19V10, multiclass
                           clus
vv                          10P GAIN MUTATED 10P GAIN WILD-TYPE
  ASIAN                                    0                  8
  BLACK OR AFRICAN AMERICAN                0                 33
  WHITE                                   17                440
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V11, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     0  10
  10P GAIN WILD-TYPE  24 320
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      0   10
  10P GAIN WILD-TYPE   24  320
                        clus
vv                       10P GAIN MUTATED 10P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 24
  NOT HISPANIC OR LATINO               10                320
[1] 2 2
[1] FALSE

Clustering(20) Variable = 10Q GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                  0   1
  10Q GAIN MUTATED     8   2
  10Q GAIN WILD-TYPE 330  24
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                10                354 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 2                 24 
$`10Q GAIN MUTATED`
TCGA-AK-3453 TCGA-B4-5832 TCGA-BP-4768 TCGA-BP-4781 TCGA-BP-5175 TCGA-CW-5588 
        1397            7          400         2080          932         2017 
TCGA-CZ-4858 TCGA-CZ-4866 TCGA-CZ-5468 TCGA-EU-5905 
        1943         1868           59          119 

$`10Q GAIN WILD-TYPE`
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 
        1120         1436           16          735         1493         1491 
TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 
        1130         1508         1478         1106         1186          751 
TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3347 
        1137         1485          665         1043          945         1610 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 
        1385          910         2688         1307         2504         1559 
TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 
         319          873         2270         2274          735         1621 
TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 
        1314         1070          630          567          574          861 
TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A8CQ TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 
        1993          617            3         3343         2566         2223 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 
        2017          480         1853         2192         2087         2044 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 
        1745         1423         1471         1280         1217         1779 
TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
        1481          874         1143         1168          951          853 
TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4699 TCGA-B0-4706 TCGA-B0-4710 
         369         1238           43          110           26           96 
TCGA-B0-4718 TCGA-B0-4813 TCGA-B0-4819 TCGA-B0-5097 TCGA-B0-5108 TCGA-B0-5110 
         616           18          183          665          911         1092 
TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 
         359          797          657          535           59          493 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 
         554          652         1132          449         2408         3431 
TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 
        1487         3076         1420         1727         1835         2583 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
        2741         1732         1605         1203         3668         2414 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 
        3117         1459         2931         2722         1865         2963 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 
         992         1092           51          374          648          952 
TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 
         358          315          417          656          507          291 
TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 
         175           38           16          141          166           11 
TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
           7          511          826          838          762          750 
TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 
         523          777          788          700          636          722 
TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
          36          822           26          737          522          505 
TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D 
         194          434           15         1046          435          830 
TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 
         519           53          256          150           66          110 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 
        3377         2881         2746         3074         2839         3037 
TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 
          13         2718          701         1893         1879         1955 
TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 
        1670         2964         1625          845         1888         1133 
TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4338 TCGA-BP-4344 TCGA-BP-4347 TCGA-BP-4349 
         645          461         2859         1666         1367          372 
TCGA-BP-4351 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 
         970          374         2208         2372         2361          182 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 
        2184         1462         1876         1885         1843          411 
TCGA-BP-4777 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4795 TCGA-BP-4797 
        1731          354         1854         1489          620         1107 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 
        1124          204         1459          211         2660         2172 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 
        1935         1785         1834         1862         1871          205 
TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 
        1746         1794          433         1487         1502         1384 
TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4986 
        1433         1632          454         1014         1413          785 
TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 
        1124          118         1413          501          177         1308 
TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
        1371          932         1266          563         1177         1126 
TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 
         840         1140         1071          193         2412         2257 
TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
         293         2263         1495         1165         1291         1133 
TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 
        1132          693          406          822         1011          967 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 
         714          408          749         1018          603         1355 
TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 
        1063          951           29         1820         1416         1924 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 
        2308         1998         1628         1793          646         2554 
TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 
        1498         2423         1435         2259         2283         2353 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
        1955         2186         2014         1883         1759         2125 
TCGA-CJ-4886 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 
        1952         1946         2085         1521          750          841 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 
        1808         1528         1450         1520         1560         1792 
TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-5671 
        1496         1499         1531         1657         1373         1943 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
        2430         2575          552         1883         1889         2231 
TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CW-5581 TCGA-CW-5583 
        2038         1855         1906         2548         2799         2489 
TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6088 TCGA-CW-6090 
        2609         2226         2378         2271         3222         2552 
TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4859 TCGA-CZ-4862 
        3146          774         1404           18         1787         1843 
TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5456 
        1928         2830         1929         1789           25         1712 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5463 
        1683         1732         1683         1430          330          662 
TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 
        1740         1446          685          946          386         2439 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
        2067         1997          373          435          693         1905 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 
        1329         1398         1470          370          355         1130 
TCGA-DV-5574 TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5906 TCGA-EU-5907 TCGA-GK-A6C7 
         723         1729          551          206          127           61 

  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 7                  3 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
              2080               3668 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
            1164.5             1299.0 
[1] "7.0 - 2080.0 (1164.5)" "3.0 - 3668.0 (1299.0)"
[1] "hr=" "3.5"
D20V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  10Q GAIN MUTATED         6        2         2        2
  10Q GAIN WILD-TYPE     238       54       124       77
D20V3, multiclass
           clus
vv          10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  STAGE I                  6                238
  STAGE II                 2                 54
  STAGE III                2                124
  STAGE IV                 2                 77
[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"
                    vv
clus                  T1  T2  T3  T4
  10Q GAIN MUTATED     6   2   4   0
  10Q GAIN WILD-TYPE 244  65 173  11
D20V4, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  T1                6                244
  T2                2                 65
  T3                4                173
  T4                0                 11
[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"
D20V5, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     3   1
  10Q GAIN WILD-TYPE 227  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      3    1
  10Q GAIN WILD-TYPE  227   17
   clus
vv  10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  0                3                227
  1                1                 17
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  10Q GAIN MUTATED    10   2   0
  10Q GAIN WILD-TYPE 407  76   9
D20V6, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  M0               10                407
  M1                2                 76
  MX                0                  9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V7, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     6   6
  10Q GAIN WILD-TYPE 172 321
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      6    6
  10Q GAIN WILD-TYPE  172  321
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  FEMALE                6                172
  MALE                  6                321
[1] 2 2
[1] FALSE
D20V8, continuous
D20V9, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10Q GAIN MUTATED       0                         0    12
  10Q GAIN WILD-TYPE     8                        33   445
D20V10, multiclass
                           clus
vv                          10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  ASIAN                                    0                  8
  BLACK OR AFRICAN AMERICAN                0                 33
  WHITE                                   12                445
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V11, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     0   8
  10Q GAIN WILD-TYPE  24 322
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      0    8
  10Q GAIN WILD-TYPE   24  322
                        clus
vv                       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 24
  NOT HISPANIC OR LATINO                8                322
[1] 2 2
[1] FALSE

Clustering(21) Variable = 11P GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                  0   1
  11P GAIN MUTATED    22   3
  11P GAIN WILD-TYPE 316  23
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                25                339 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 3                 23 
$`11P GAIN MUTATED`
TCGA-A3-3313 TCGA-A3-3372 TCGA-AK-3433 TCGA-AK-3440 TCGA-AK-3453 TCGA-B0-4710 
         735          735         2192         1745         1397           96 
TCGA-B0-5113 TCGA-B4-5832 TCGA-B8-4620 TCGA-B8-A54I TCGA-BP-4167 TCGA-BP-4351 
         359            7          777          150         2718          970 
TCGA-BP-4994 TCGA-BP-5185 TCGA-BP-5200 TCGA-CJ-4635 TCGA-CJ-4871 TCGA-CJ-4885 
        1308         1132         1063         1416         2423         2125 
TCGA-CJ-4907 TCGA-CJ-5682 TCGA-CZ-4858 TCGA-CZ-4866 TCGA-CZ-5460 TCGA-CZ-5468 
        1499         1883         1943         1868         1430           59 
TCGA-EU-5905 
         119 

$`11P GAIN WILD-TYPE`
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 
        1120         1436           16         1493         1491         1130 
TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 
        1508         1478         1106         1186          751         1137 
TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3347 TCGA-A3-3349 
        1485          665         1043          945         1610         1385 
TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 
         910         2688         1307         2504         1559          319 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 
         873         2270         2274         1621         1314         1070 
TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 
         630          567          574          861         1993          617 
TCGA-A3-A8CQ TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 
           3         3343         2566         2223         2017          480 
TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 
        1853         2087         2044         1423         1471         1280 
TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3456 TCGA-AK-3458 
        1217         1779         1481          874         1143         1168 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4699 
         951          853          369         1238           43          110 
TCGA-B0-4706 TCGA-B0-4718 TCGA-B0-4813 TCGA-B0-4819 TCGA-B0-5097 TCGA-B0-5108 
          26          616           18          183          665          911 
TCGA-B0-5110 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 
        1092          797          657          535           59          493 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 
         554          652         1132          449         2408         3431 
TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 
        1487         3076         1420         1727         1835         2583 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
        2741         1732         1605         1203         3668         2414 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 
        3117         1459         2931         2722         1865         2963 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 
         992         1092           51          374          648          952 
TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 
         358          315          417          656          507          291 
TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 
         175           38           16          141          166           11 
TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
           7          511          826          838          762          750 
TCGA-B8-4619 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 
         523          788          700          636          722           36 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 
         822           26          737          522          505          194 
TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54F 
         434           15         1046          435          830          519 
TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4158 TCGA-BP-4160 
          53          256           66          110         3377         2881 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4169 
        2746         3074         2839         3037           13          701 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 
        1893         1879         1955         1670         2964         1625 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4338 
         845         1888         1133          645          461         2859 
TCGA-BP-4344 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 
        1666         1367          372          374         2208         2372 
TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 
        2361          182         2184         1462          400         1876 
TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 
        1885         1843          411         1731         2080          354 
TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4801 TCGA-BP-4803 
        1854         1489          620         1107         1124          204 
TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
        1459          211         2660         2172         1935         1785 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 
        1834         1862         1871          205         1746         1794 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4975 TCGA-BP-4976 
         433         1487         1502         1384         1433         1632 
TCGA-BP-4977 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4989 
         454         1014         1413          785         1124          118 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 
        1413          501          177         1371          932         1266 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 
         563         1177         1126          840         1140         1071 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5177 TCGA-BP-5180 
         193         2412         2257          932          293         2263 
TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5187 
        1495         1165         1291         1133          693          406 
TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
         822         1011          967          714          408          749 
TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 
        1018          603         1355          951           29         1820 
TCGA-CJ-4636 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 
        1924         2308         1998         1628         1793          646 
TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 
        2554         1498         1435         2259         2283         2353 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4886 
        1955         2186         2014         1883         1759         1952 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4897 
        1946         2085         1521          750          841         1808 
TCGA-CJ-4899 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 
        1528         1450         1520         1560         1792         1496 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-5671 TCGA-CJ-5675 TCGA-CJ-5676 
        1531         1657         1373         1943         2430         2575 
TCGA-CJ-5681 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6031 
         552         1889         2231         2038         1855         1906 
TCGA-CJ-6032 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 
        2548         2799         2489         2609         2226         2017 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CZ-4853 
        2378         2271         3222         2552         3146          774 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 
        1404           18         1787         1843         1928         2830 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 
        1929         1789           25         1712         1683         1732 
TCGA-CZ-5459 TCGA-CZ-5461 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 
        1683          330          662         1740         1446          685 
TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
         946          386         2439         2067         1997          373 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 
         435          693         1905         1329         1398         1470 
TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-EU-5904 
         370          355         1130          723         1729          551 
TCGA-EU-5906 TCGA-EU-5907 TCGA-GK-A6C7 
         206          127           61 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 7                  3 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              2718               3668 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              1308               1291 
[1] "7.0 - 2718.0 (1308.0)" "3.0 - 3668.0 (1291.0)"
[1] "hr=" "1.9"
D21V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  11P GAIN MUTATED         8        4        11        8
  11P GAIN WILD-TYPE     236       52       115       71
D21V3, multiclass
           clus
vv          11P GAIN MUTATED 11P GAIN WILD-TYPE
  STAGE I                  8                236
  STAGE II                 4                 52
  STAGE III               11                115
  STAGE IV                 8                 71
[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"
                    vv
clus                  T1  T2  T3  T4
  11P GAIN MUTATED     8   4  18   1
  11P GAIN WILD-TYPE 242  63 159  10
D21V4, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  T1                8                242
  T2                4                 63
  T3               18                159
  T4                1                 10
[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"
D21V5, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    10   0
  11P GAIN WILD-TYPE 220  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     10    0
  11P GAIN WILD-TYPE  220   18
   clus
vv  11P GAIN MUTATED 11P GAIN WILD-TYPE
  0               10                220
  1                0                 18
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  11P GAIN MUTATED    22   8   1
  11P GAIN WILD-TYPE 395  70   8
D21V6, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  M0               22                395
  M1                8                 70
  MX                1                  8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V7, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    10  21
  11P GAIN WILD-TYPE 168 306
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     10   21
  11P GAIN WILD-TYPE  168  306
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE               10                168
  MALE                 21                306
[1] 2 2
[1] FALSE
D21V8, continuous
D21V9, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11P GAIN MUTATED       0                         2    29
  11P GAIN WILD-TYPE     8                        31   428
D21V10, multiclass
                           clus
vv                          11P GAIN MUTATED 11P GAIN WILD-TYPE
  ASIAN                                    0                  8
  BLACK OR AFRICAN AMERICAN                2                 31
  WHITE                                   29                428
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V11, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     1  19
  11P GAIN WILD-TYPE  23 311
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      1   19
  11P GAIN WILD-TYPE   23  311
                        clus
vv                       11P GAIN MUTATED 11P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 23
  NOT HISPANIC OR LATINO               19                311
[1] 2 2
[1] FALSE

Clustering(22) Variable = 11Q GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                  0   1
  11Q GAIN MUTATED    22   2
  11Q GAIN WILD-TYPE 316  24
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                24                340 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 2                 24 
$`11Q GAIN MUTATED`
TCGA-A3-3313 TCGA-A3-3372 TCGA-AK-3433 TCGA-AK-3440 TCGA-AK-3453 TCGA-B0-4710 
         735          735         2192         1745         1397           96 
TCGA-B0-5113 TCGA-B2-4099 TCGA-B8-4620 TCGA-B8-A54I TCGA-BP-4167 TCGA-BP-4351 
         359          374          777          150         2718          970 
TCGA-BP-4994 TCGA-BP-5185 TCGA-BP-5200 TCGA-CJ-4635 TCGA-CJ-4871 TCGA-CJ-4885 
        1308         1132         1063         1416         2423         2125 
TCGA-CJ-4907 TCGA-CJ-5682 TCGA-CZ-4858 TCGA-CZ-4866 TCGA-CZ-5460 TCGA-EU-5905 
        1499         1883         1943         1868         1430          119 

$`11Q GAIN WILD-TYPE`
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 
        1120         1436           16         1493         1491         1130 
TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 
        1508         1478         1106         1186          751         1137 
TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3347 TCGA-A3-3349 
        1485          665         1043          945         1610         1385 
TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 
         910         2688         1307         2504         1559          319 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 
         873         2270         2274         1621         1314         1070 
TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 
         630          567          574          861         1993          617 
TCGA-A3-A8CQ TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 
           3         3343         2566         2223         2017          480 
TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 
        1853         2087         2044         1423         1471         1280 
TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3456 TCGA-AK-3458 
        1217         1779         1481          874         1143         1168 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4699 
         951          853          369         1238           43          110 
TCGA-B0-4706 TCGA-B0-4718 TCGA-B0-4813 TCGA-B0-4819 TCGA-B0-5097 TCGA-B0-5108 
          26          616           18          183          665          911 
TCGA-B0-5110 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 
        1092          797          657          535           59          493 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 
         554          652         1132          449         2408         3431 
TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 
        1487         3076         1420         1727         1835         2583 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
        2741         1732         1605         1203         3668         2414 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 
        3117         1459         2931         2722         1865         2963 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 
         992         1092           51          648          952          358 
TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 
         315          417          656          507          291          175 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 
           7           38           16          141          166           11 
TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
           7          511          826          838          762          750 
TCGA-B8-4619 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 
         523          788          700          636          722           36 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 
         822           26          737          522          505          194 
TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54F 
         434           15         1046          435          830          519 
TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4158 TCGA-BP-4160 
          53          256           66          110         3377         2881 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4169 
        2746         3074         2839         3037           13          701 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 
        1893         1879         1955         1670         2964         1625 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4338 
         845         1888         1133          645          461         2859 
TCGA-BP-4344 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 
        1666         1367          372          374         2208         2372 
TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 
        2361          182         2184         1462          400         1876 
TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 
        1885         1843          411         1731         2080          354 
TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4801 TCGA-BP-4803 
        1854         1489          620         1107         1124          204 
TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
        1459          211         2660         2172         1935         1785 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 
        1834         1862         1871          205         1746         1794 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4975 TCGA-BP-4976 
         433         1487         1502         1384         1433         1632 
TCGA-BP-4977 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4989 
         454         1014         1413          785         1124          118 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 
        1413          501          177         1371          932         1266 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 
         563         1177         1126          840         1140         1071 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5177 TCGA-BP-5180 
         193         2412         2257          932          293         2263 
TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5187 
        1495         1165         1291         1133          693          406 
TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
         822         1011          967          714          408          749 
TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 
        1018          603         1355          951           29         1820 
TCGA-CJ-4636 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 
        1924         2308         1998         1628         1793          646 
TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 
        2554         1498         1435         2259         2283         2353 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4886 
        1955         2186         2014         1883         1759         1952 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4897 
        1946         2085         1521          750          841         1808 
TCGA-CJ-4899 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 
        1528         1450         1520         1560         1792         1496 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-5671 TCGA-CJ-5675 TCGA-CJ-5676 
        1531         1657         1373         1943         2430         2575 
TCGA-CJ-5681 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6031 
         552         1889         2231         2038         1855         1906 
TCGA-CJ-6032 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 
        2548         2799         2489         2609         2226         2017 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CZ-4853 
        2378         2271         3222         2552         3146          774 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 
        1404           18         1787         1843         1928         2830 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 
        1929         1789           25         1712         1683         1732 
TCGA-CZ-5459 TCGA-CZ-5461 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 
        1683          330          662         1740         1446          685 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
          59          946          386         2439         2067         1997 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
         373          435          693         1905         1329         1398 
TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 
        1470          370          355         1130          723         1729 
TCGA-EU-5904 TCGA-EU-5906 TCGA-EU-5907 TCGA-GK-A6C7 
         551          206          127           61 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                96                  3 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              2718               3668 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            1352.5             1285.5 
[1] "96.0 - 2718.0 (1352.5)" "3.0 - 3668.0 (1285.5)" 
[1] "hr=" "1.2"
D22V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  11Q GAIN MUTATED         9        4        10        6
  11Q GAIN WILD-TYPE     235       52       116       73
D22V3, multiclass
           clus
vv          11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  STAGE I                  9                235
  STAGE II                 4                 52
  STAGE III               10                116
  STAGE IV                 6                 73
[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"
                    vv
clus                  T1  T2  T3  T4
  11Q GAIN MUTATED     9   4  16   0
  11Q GAIN WILD-TYPE 241  63 161  11
D22V4, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  T1                9                241
  T2                4                 63
  T3               16                161
  T4                0                 11
[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"
D22V5, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     9   0
  11Q GAIN WILD-TYPE 221  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      9    0
  11Q GAIN WILD-TYPE  221   18
   clus
vv  11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  0                9                221
  1                0                 18
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  11Q GAIN MUTATED    22   6   1
  11Q GAIN WILD-TYPE 395  72   8
D22V6, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  M0               22                395
  M1                6                 72
  MX                1                  8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V7, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    10  19
  11Q GAIN WILD-TYPE 168 308
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     10   19
  11Q GAIN WILD-TYPE  168  308
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE               10                168
  MALE                 19                308
[1] 2 2
[1] FALSE
D22V8, continuous
[1] "Remove cluster labels:" "11Q GAIN MUTATED"      
clus
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 2                 35 
        TCGA-A3-A8CQ         TCGA-AK-3426         TCGA-AK-3430 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-B0-4838         TCGA-B2-5639         TCGA-B4-5377 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-B4-5378         TCGA-B4-5832         TCGA-B4-5834 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-B4-5835         TCGA-B4-5836         TCGA-B4-5838 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-B4-5843         TCGA-B4-5844         TCGA-CZ-4854 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CZ-4856         TCGA-CZ-4860         TCGA-CZ-4861 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CZ-4862         TCGA-CZ-5456         TCGA-CZ-5457 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CZ-5465         TCGA-CZ-5469         TCGA-CZ-5982 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DV-5565         TCGA-DV-5566         TCGA-DV-5567 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DV-5568         TCGA-DV-5569         TCGA-DV-5573 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DV-5574         TCGA-DV-5575         TCGA-DV-5576 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EU-5904         TCGA-EU-5907 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
D22V9, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11Q GAIN MUTATED       0                         2    27
  11Q GAIN WILD-TYPE     8                        31   430
D22V10, multiclass
                           clus
vv                          11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  ASIAN                                    0                  8
  BLACK OR AFRICAN AMERICAN                2                 31
  WHITE                                   27                430
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V11, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     1  18
  11Q GAIN WILD-TYPE  23 312
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      1   18
  11Q GAIN WILD-TYPE   23  312
                        clus
vv                       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 23
  NOT HISPANIC OR LATINO               18                312
[1] 2 2
[1] FALSE

Clustering(23) Variable = 12P GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                  0   1
  12P GAIN MUTATED    70   9
  12P GAIN WILD-TYPE 268  17
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                79                285 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 9                 17 
$`12P GAIN MUTATED`
TCGA-A3-3319 TCGA-A3-3325 TCGA-A3-3347 TCGA-A3-3358 TCGA-A3-3372 TCGA-A3-3374 
        1130          751         1610         1307          735         1314 
TCGA-A3-3382 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3430 TCGA-AK-3433 TCGA-AK-3436 
         574          617         3343          480         2192         2044 
TCGA-AK-3440 TCGA-AK-3453 TCGA-B0-4699 TCGA-B0-4710 TCGA-B0-4819 TCGA-B0-5113 
        1745         1397          110           96          183          359 
TCGA-B0-5116 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5713 TCGA-B4-5832 TCGA-B4-5838 
         657         1727         1835         1865            7          166 
TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5163 TCGA-B8-5551 TCGA-B8-A54F TCGA-B8-A54I 
         788          700          822           15          519          150 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4167 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4338 
        3074         2839         2718         1879         1955         2859 
TCGA-BP-4351 TCGA-BP-4761 TCGA-BP-4768 TCGA-BP-4782 TCGA-BP-4803 TCGA-BP-4804 
         970          182          400          354          204         1459 
TCGA-BP-4960 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4977 TCGA-BP-4983 TCGA-BP-4992 
        2172         1834         1862          454         1413          501 
TCGA-BP-4994 TCGA-BP-5175 TCGA-BP-5185 TCGA-BP-5191 TCGA-BP-5194 TCGA-BP-5200 
        1308          932         1132          967          408         1063 
TCGA-CJ-4636 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4884 TCGA-CJ-4903 TCGA-CJ-4907 
        1924         1435         2259         1759         1560         1499 
TCGA-CJ-4912 TCGA-CJ-5671 TCGA-CJ-5676 TCGA-CJ-5682 TCGA-CJ-5684 TCGA-CW-5588 
        1657         1943         2575         1883         2231         2017 
TCGA-CW-5591 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4866 TCGA-CZ-5456 TCGA-CZ-5461 
        2271         1404           18         1868         1712          330 
TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5984 TCGA-CZ-5987 
        1740          685           59          946         2067          435 
TCGA-EU-5905 
         119 

$`12P GAIN WILD-TYPE`
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 
        1120         1436           16          735         1493         1491 
TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3326 TCGA-A3-3331 
        1508         1478         1106         1186         1137         1485 
TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 
         665         1043          945         1385          910         2688 
TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 
        2504         1559          319          873         2270         2274 
TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 
        1621         1070          630          567          861         1993 
TCGA-A3-A8CQ TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3431 TCGA-AK-3434 
           3         2566         2223         2017         1853         2087 
TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 
        1423         1471         1280         1217         1779         1481 
TCGA-AK-3454 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 
         874         1143         1168          951          853          369 
TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4706 TCGA-B0-4718 TCGA-B0-4813 TCGA-B0-5097 
        1238           43           26          616           18          665 
TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5115 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 
         911         1092          797          535           59          493 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 
         554          652         1132          449         2408         3431 
TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 
        1487         3076         1420         2583         2741         1732 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 
        1605         1203         3668         2414         3117         1459 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
        2931         2722         2963          992         1092           51 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 
         374          648          952          358          315          417 
TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5835 
         656          507          291          175           38           16 
TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
         141           11            7          511          826          838 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-5158 TCGA-B8-5159 
         762          750          523          777          636          722 
TCGA-B8-5162 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 
          36           26          737          522          505          194 
TCGA-B8-5550 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54G TCGA-B8-A54H 
         434         1046          435          830           53          256 
TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4165 
          66          110         3377         2881         2746         3037 
TCGA-BP-4166 TCGA-BP-4169 TCGA-BP-4173 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 
          13          701         1893         1670         2964         1625 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4344 
         845         1888         1133          645          461         1666 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 
        1367          372          374         2208         2372         2361 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 
        2184         1462         1876         1885         1843          411 
TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4795 TCGA-BP-4797 
        1731         2080         1854         1489          620         1107 
TCGA-BP-4801 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4965 
        1124          211         2660         1935         1785         1871 
TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
         205         1746         1794          433         1487         1502 
TCGA-BP-4973 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4982 TCGA-BP-4986 TCGA-BP-4987 
        1384         1433         1632         1014          785         1124 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 
         118         1413          177         1371          932         1266 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 
         563         1177         1126          840         1140         1071 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5181 
         193         2412         2257          293         2263         1495 
TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 
        1165         1291         1133          693          406          822 
TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 
        1011          714          749         1018          603         1355 
TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4639 TCGA-CJ-4640 
         951           29         1820         1416         2308         1998 
TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
        1628         1793          646         2554         1498         2423 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 
        2283         2353         1955         2186         2014         1883 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 
        2125         1952         1946         2085         1521          750 
TCGA-CJ-4894 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4904 
         841         1808         1528         1450         1520         1792 
TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4916 TCGA-CJ-5675 TCGA-CJ-5681 TCGA-CJ-5683 
        1496         1531         1373         2430          552         1889 
TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CW-5581 TCGA-CW-5583 
        2038         1855         1906         2548         2799         2489 
TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 
        2609         2226         2378         3222         2552         3146 
TCGA-CZ-4853 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 
         774         1943         1787         1843         1928         2830 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 
        1929         1789           25         1683         1732         1683 
TCGA-CZ-5460 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5985 
        1430          662         1446          386         2439         1997 
TCGA-CZ-5986 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 
         373          693         1905         1329         1398         1470 
TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-EU-5904 
         370          355         1130          723         1729          551 
TCGA-EU-5906 TCGA-EU-5907 TCGA-GK-A6C7 
         206          127           61 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 7                  3 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              3343               3668 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              1308               1280 
[1] "7.0 - 3343.0 (1308.0)" "3.0 - 3668.0 (1280.0)"
[1] "hr=" "2"  
D23V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  12P GAIN MUTATED        43        9        39       28
  12P GAIN WILD-TYPE     201       47        87       51
D23V3, multiclass
           clus
vv          12P GAIN MUTATED 12P GAIN WILD-TYPE
  STAGE I                 43                201
  STAGE II                 9                 47
  STAGE III               39                 87
  STAGE IV                28                 51
[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"
                    vv
clus                  T1  T2  T3  T4
  12P GAIN MUTATED    45  13  57   4
  12P GAIN WILD-TYPE 205  54 120   7
D23V4, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  T1               45                205
  T2               13                 54
  T3               57                120
  T4                4                  7
[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"
D23V5, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    56   8
  12P GAIN WILD-TYPE 174  10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     56    8
  12P GAIN WILD-TYPE  174   10
   clus
vv  12P GAIN MUTATED 12P GAIN WILD-TYPE
  0               56                174
  1                8                 10
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  12P GAIN MUTATED    90  27   2
  12P GAIN WILD-TYPE 327  51   7
D23V6, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  M0               90                327
  M1               27                 51
  MX                2                  7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V7, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    39  80
  12P GAIN WILD-TYPE 139 247
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     39   80
  12P GAIN WILD-TYPE  139  247
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE               39                139
  MALE                 80                247
[1] 2 2
[1] FALSE
D23V8, continuous
D23V9, continuous
[1] "Remove cluster labels:" "12P GAIN MUTATED"      
clus
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 2                  6 
        TCGA-A3-A8CQ         TCGA-B2-A4SR         TCGA-B8-5158 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-B8-5164         TCGA-B8-A54G         TCGA-G6-A5PC 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12P GAIN MUTATED       2                         5   110
  12P GAIN WILD-TYPE     6                        28   347
D23V10, multiclass
                           clus
vv                          12P GAIN MUTATED 12P GAIN WILD-TYPE
  ASIAN                                    2                  6
  BLACK OR AFRICAN AMERICAN                5                 28
  WHITE                                  110                347
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V11, binary
                    cls
clus                   0   1
  12P GAIN MUTATED     3  80
  12P GAIN WILD-TYPE  21 250
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      3   80
  12P GAIN WILD-TYPE   21  250
                        clus
vv                       12P GAIN MUTATED 12P GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                 21
  NOT HISPANIC OR LATINO               80                250
[1] 2 2
[1] FALSE

Clustering(24) Variable = 12Q GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                  0   1
  12Q GAIN MUTATED    71   9
  12Q GAIN WILD-TYPE 267  17
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                80                284 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 9                 17 
$`12Q GAIN MUTATED`
TCGA-A3-3319 TCGA-A3-3325 TCGA-A3-3347 TCGA-A3-3358 TCGA-A3-3372 TCGA-A3-3374 
        1130          751         1610         1307          735         1314 
TCGA-A3-3382 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3430 TCGA-AK-3433 TCGA-AK-3436 
         574          617         3343          480         2192         2044 
TCGA-AK-3440 TCGA-AK-3453 TCGA-B0-4699 TCGA-B0-4710 TCGA-B0-4819 TCGA-B0-5113 
        1745         1397          110           96          183          359 
TCGA-B0-5116 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5713 TCGA-B4-5832 TCGA-B4-5838 
         657         1727         1835         1865            7          166 
TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5163 TCGA-B8-5551 TCGA-B8-A54F TCGA-B8-A54I 
         788          700          822           15          519          150 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4167 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4338 
        3074         2839         2718         1879         1955         2859 
TCGA-BP-4351 TCGA-BP-4761 TCGA-BP-4768 TCGA-BP-4782 TCGA-BP-4803 TCGA-BP-4804 
         970          182          400          354          204         1459 
TCGA-BP-4960 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4977 TCGA-BP-4983 TCGA-BP-4992 
        2172         1834         1862          454         1413          501 
TCGA-BP-4994 TCGA-BP-5175 TCGA-BP-5185 TCGA-BP-5191 TCGA-BP-5194 TCGA-BP-5200 
        1308          932         1132          967          408         1063 
TCGA-CJ-4636 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4881 TCGA-CJ-4884 TCGA-CJ-4903 
        1924         1435         2259         2014         1759         1560 
TCGA-CJ-4907 TCGA-CJ-4912 TCGA-CJ-5671 TCGA-CJ-5676 TCGA-CJ-5682 TCGA-CJ-5684 
        1499         1657         1943         2575         1883         2231 
TCGA-CW-5588 TCGA-CW-5591 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4866 TCGA-CZ-5456 
        2017         2271         1404           18         1868         1712 
TCGA-CZ-5461 TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5984 
         330         1740          685           59          946         2067 
TCGA-CZ-5987 TCGA-EU-5905 
         435          119 

$`12Q GAIN WILD-TYPE`
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 
        1120         1436           16          735         1493         1491 
TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3326 TCGA-A3-3331 
        1508         1478         1106         1186         1137         1485 
TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 
         665         1043          945         1385          910         2688 
TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 
        2504         1559          319          873         2270         2274 
TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 
        1621         1070          630          567          861         1993 
TCGA-A3-A8CQ TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3431 TCGA-AK-3434 
           3         2566         2223         2017         1853         2087 
TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 
        1423         1471         1280         1217         1779         1481 
TCGA-AK-3454 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 
         874         1143         1168          951          853          369 
TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4706 TCGA-B0-4718 TCGA-B0-4813 TCGA-B0-5097 
        1238           43           26          616           18          665 
TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5115 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 
         911         1092          797          535           59          493 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 
         554          652         1132          449         2408         3431 
TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 
        1487         3076         1420         2583         2741         1732 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 
        1605         1203         3668         2414         3117         1459 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
        2931         2722         2963          992         1092           51 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 
         374          648          952          358          315          417 
TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5835 
         656          507          291          175           38           16 
TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
         141           11            7          511          826          838 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-5158 TCGA-B8-5159 
         762          750          523          777          636          722 
TCGA-B8-5162 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 
          36           26          737          522          505          194 
TCGA-B8-5550 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54G TCGA-B8-A54H 
         434         1046          435          830           53          256 
TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4165 
          66          110         3377         2881         2746         3037 
TCGA-BP-4166 TCGA-BP-4169 TCGA-BP-4173 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 
          13          701         1893         1670         2964         1625 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4344 
         845         1888         1133          645          461         1666 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 
        1367          372          374         2208         2372         2361 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 
        2184         1462         1876         1885         1843          411 
TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4795 TCGA-BP-4797 
        1731         2080         1854         1489          620         1107 
TCGA-BP-4801 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4965 
        1124          211         2660         1935         1785         1871 
TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
         205         1746         1794          433         1487         1502 
TCGA-BP-4973 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4982 TCGA-BP-4986 TCGA-BP-4987 
        1384         1433         1632         1014          785         1124 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 
         118         1413          177         1371          932         1266 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 
         563         1177         1126          840         1140         1071 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5181 
         193         2412         2257          293         2263         1495 
TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 
        1165         1291         1133          693          406          822 
TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 
        1011          714          749         1018          603         1355 
TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4639 TCGA-CJ-4640 
         951           29         1820         1416         2308         1998 
TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
        1628         1793          646         2554         1498         2423 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4882 TCGA-CJ-4885 
        2283         2353         1955         2186         1883         2125 
TCGA-CJ-4886 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 
        1952         1946         2085         1521          750          841 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4904 TCGA-CJ-4905 
        1808         1528         1450         1520         1792         1496 
TCGA-CJ-4908 TCGA-CJ-4916 TCGA-CJ-5675 TCGA-CJ-5681 TCGA-CJ-5683 TCGA-CJ-5686 
        1531         1373         2430          552         1889         2038 
TCGA-CJ-6027 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 
        1855         1906         2548         2799         2489         2609 
TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CZ-4853 
        2226         2378         3222         2552         3146          774 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-5451 
        1943         1787         1843         1928         2830         1929 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
        1789           25         1683         1732         1683         1430 
TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5985 TCGA-CZ-5986 
         662         1446          386         2439         1997          373 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 
         693         1905         1329         1398         1470          370 
TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5906 
         355         1130          723         1729          551          206 
TCGA-EU-5907 TCGA-GK-A6C7 
         127           61 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 7                  3 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              3343               3668 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              1311               1273 
[1] "7.0 - 3343.0 (1311.0)" "3.0 - 3668.0 (1273.0)"
[1] "hr=" "1.9"
D24V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  12Q GAIN MUTATED        43        9        40       28
  12Q GAIN WILD-TYPE     201       47        86       51
D24V3, multiclass
           clus
vv          12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  STAGE I                 43                201
  STAGE II                 9                 47
  STAGE III               40                 86
  STAGE IV                28                 51
[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"
                    vv
clus                  T1  T2  T3  T4
  12Q GAIN MUTATED    45  13  58   4
  12Q GAIN WILD-TYPE 205  54 119   7
D24V4, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  T1               45                205
  T2               13                 54
  T3               58                119
  T4                4                  7
[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"
D24V5, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    56   8
  12Q GAIN WILD-TYPE 174  10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     56    8
  12Q GAIN WILD-TYPE  174   10
   clus
vv  12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  0               56                174
  1                8                 10
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  12Q GAIN MUTATED    91  27   2
  12Q GAIN WILD-TYPE 326  51   7
D24V6, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  M0               91                326
  M1               27                 51
  MX                2                  7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V7, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    39  81
  12Q GAIN WILD-TYPE 139 246
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     39   81
  12Q GAIN WILD-TYPE  139  246
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE               39                139
  MALE                 81                246
[1] 2 2
[1] FALSE
D24V8, continuous
D24V9, continuous
[1] "Remove cluster labels:" "12Q GAIN MUTATED"      
clus
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 2                  6 
        TCGA-A3-A8CQ         TCGA-B2-A4SR         TCGA-B8-5158 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-B8-5164         TCGA-B8-A54G         TCGA-G6-A5PC 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12Q GAIN MUTATED       2                         5   111
  12Q GAIN WILD-TYPE     6                        28   346
D24V10, multiclass
                           clus
vv                          12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  ASIAN                                    2                  6
  BLACK OR AFRICAN AMERICAN                5                 28
  WHITE                                  111                346
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V11, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED     3  81
  12Q GAIN WILD-TYPE  21 249
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      3   81
  12Q GAIN WILD-TYPE   21  249
                        clus
vv                       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                 21
  NOT HISPANIC OR LATINO               81                249
[1] 2 2
[1] FALSE

Clustering(25) Variable = 13Q GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                  0   1
  13Q GAIN MUTATED    18   3
  13Q GAIN WILD-TYPE 320  23
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                21                343 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 3                 23 
$`13Q GAIN MUTATED`
TCGA-A3-3325 TCGA-AK-3453 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-5690 TCGA-B2-5639 
         751         1397           26           96         2408          417 
TCGA-BP-4166 TCGA-BP-4332 TCGA-BP-4983 TCGA-BP-5198 TCGA-BP-5200 TCGA-CJ-4905 
          13         1133         1413          603         1063         1496 
TCGA-CJ-4907 TCGA-CJ-4912 TCGA-CJ-5671 TCGA-CJ-5676 TCGA-CJ-5682 TCGA-CZ-5460 
        1499         1657         1943         2575         1883         1430 
TCGA-CZ-5461 TCGA-CZ-5464 TCGA-DV-5574 
         330         1740          723 

$`13Q GAIN WILD-TYPE`
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 
        1120         1436           16          735         1493         1491 
TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3326 
        1130         1508         1478         1106         1186         1137 
TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3347 TCGA-A3-3349 
        1485          665         1043          945         1610         1385 
TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 
         910         2688         1307         2504         1559          319 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 
         873         2270         2274          735         1621         1314 
TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 
        1070          630          567          574          861         1993 
TCGA-A3-3387 TCGA-A3-A8CQ TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
         617            3         3343         2566         2223         2017 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
         480         1853         2192         2087         2044         1745 
TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 
        1423         1471         1280         1217         1779         1481 
TCGA-AK-3454 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 
         874         1143         1168          951          853          369 
TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4699 TCGA-B0-4718 TCGA-B0-4813 TCGA-B0-4819 
        1238           43          110          616           18          183 
TCGA-B0-5097 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 
         665          911         1092          359          797          657 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
         535           59          493          554          652         1132 
TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5696 
         449         3431         1487         3076         1420         1727 
TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
        1835         2583         2741         1732         1605         1203 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
        3668         2414         3117         1459         2931         2722 
TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
        1865         2963          992         1092           51          374 
TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 TCGA-B2-A4SR 
         648          952          358          315          656          507 
TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
         291          175            7           38           16          141 
TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
         166           11            7          511          826          838 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 
         762          750          523          777          788          700 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
         636          722           36          822           26          737 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
         522          505          194          434           15         1046 
TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I 
         435          830          519           53          256          150 
TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 
          66          110         3377         2881         2746         3074 
TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4173 TCGA-BP-4174 
        2839         3037         2718          701         1893         1879 
TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 
        1955         1670         2964         1625          845         1888 
TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4338 TCGA-BP-4344 TCGA-BP-4347 TCGA-BP-4349 
         645          461         2859         1666         1367          372 
TCGA-BP-4351 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 
         970          374         2208         2372         2361          182 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4774 TCGA-BP-4775 
        2184         1462          400         1876         1885         1843 
TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4789 
         411         1731         2080          354         1854         1489 
TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 
         620         1107         1124          204         1459          211 
TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 
        2660         2172         1935         1785         1834         1862 
TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 
        1871          205         1746         1794          433         1487 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4982 
        1502         1384         1433         1632          454         1014 
TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 
         785         1124          118         1413          501          177 
TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 
        1308         1371          932         1266          563         1177 
TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5169 TCGA-BP-5170 
        1126          840         1140         1071          193         2412 
TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 
        2257          932          293         2263         1495         1165 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 
        1291         1133         1132          693          406          822 
TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
        1011          967          714          408          749         1018 
TCGA-BP-5199 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 
        1355          951           29         1820         1416         1924 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 
        2308         1998         1628         1793          646         2554 
TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 
        1498         2423         1435         2259         2283         2353 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
        1955         2186         2014         1883         1759         2125 
TCGA-CJ-4886 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 
        1952         1946         2085         1521          750          841 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 
        1808         1528         1450         1520         1560         1792 
TCGA-CJ-4908 TCGA-CJ-4916 TCGA-CJ-5675 TCGA-CJ-5681 TCGA-CJ-5683 TCGA-CJ-5684 
        1531         1373         2430          552         1889         2231 
TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CW-5581 TCGA-CW-5583 
        2038         1855         1906         2548         2799         2489 
TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6088 
        2609         2226         2017         2378         2271         3222 
TCGA-CW-6090 TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4858 
        2552         3146          774         1404           18         1943 
TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 
        1787         1843         1928         2830         1868         1929 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 
        1789           25         1712         1683         1732         1683 
TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 
         662         1446          685           59          946          386 
TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 
        2439         2067         1997          373          435          693 
TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 
        1905         1329         1398         1470          370          355 
TCGA-DV-5573 TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
        1130         1729          551          119          206          127 
TCGA-GK-A6C7 
          61 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                13                  3 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              2575               3668 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              1397               1291 
[1] "13.0 - 2575.0 (1397.0)" "3.0 - 3668.0 (1291.0)" 
[1] "hr=" "2.4"
D25V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  13Q GAIN MUTATED         6        3         8        5
  13Q GAIN WILD-TYPE     238       53       118       74
D25V3, multiclass
           clus
vv          13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  STAGE I                  6                238
  STAGE II                 3                 53
  STAGE III                8                118
  STAGE IV                 5                 74
[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"
                    vv
clus                  T1  T2  T3  T4
  13Q GAIN MUTATED     7   3  12   0
  13Q GAIN WILD-TYPE 243  64 165  11
D25V4, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  T1                7                243
  T2                3                 64
  T3               12                165
  T4                0                 11
[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"
D25V5, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     4   0
  13Q GAIN WILD-TYPE 226  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      4    0
  13Q GAIN WILD-TYPE  226   18
   clus
vv  13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  0                4                226
  1                0                 18
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  13Q GAIN MUTATED    17   5   0
  13Q GAIN WILD-TYPE 400  73   9
D25V6, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  M0               17                400
  M1                5                 73
  MX                0                  9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V7, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     5  17
  13Q GAIN WILD-TYPE 173 310
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      5   17
  13Q GAIN WILD-TYPE  173  310
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE                5                173
  MALE                 17                310
[1] 2 2
[1] FALSE
D25V8, continuous
[1] "Remove cluster labels:" "13Q GAIN MUTATED"      
clus
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 2                 35 
        TCGA-A3-A8CQ         TCGA-AK-3426         TCGA-AK-3430 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-B0-4838         TCGA-B4-5377         TCGA-B4-5378 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-B4-5832         TCGA-B4-5834         TCGA-B4-5835 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-B4-5836         TCGA-B4-5838         TCGA-B4-5843 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-B4-5844         TCGA-CZ-4854         TCGA-CZ-4856 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CZ-4858         TCGA-CZ-4860         TCGA-CZ-4861 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CZ-4862         TCGA-CZ-5456         TCGA-CZ-5457 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CZ-5465         TCGA-CZ-5469         TCGA-CZ-5982 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DV-5565         TCGA-DV-5566         TCGA-DV-5567 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DV-5568         TCGA-DV-5569         TCGA-DV-5573 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DV-5575         TCGA-DV-5576         TCGA-EU-5904 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EU-5905         TCGA-EU-5907 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
D25V9, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  13Q GAIN MUTATED       1                         0    21
  13Q GAIN WILD-TYPE     7                        33   436
D25V10, multiclass
                           clus
vv                          13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  ASIAN                                    1                  7
  BLACK OR AFRICAN AMERICAN                0                 33
  WHITE                                   21                436
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V11, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     3  13
  13Q GAIN WILD-TYPE  21 317
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      3   13
  13Q GAIN WILD-TYPE   21  317
                        clus
vv                       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                 21
  NOT HISPANIC OR LATINO               13                317
[1] 2 2
[1] FALSE

Clustering(26) Variable = 14Q GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                  0   1
  14Q GAIN MUTATED     8   1
  14Q GAIN WILD-TYPE 330  25
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 9                355 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 1                 25 
$`14Q GAIN MUTATED`
TCGA-A3-3325 TCGA-A3-3374 TCGA-AK-3433 TCGA-AK-3440 TCGA-B0-4699 TCGA-BP-4351 
         751         1314         2192         1745          110          970 
TCGA-BP-4994 TCGA-CJ-4901 TCGA-CZ-5460 
        1308         1450         1430 

$`14Q GAIN WILD-TYPE`
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 
        1120         1436           16          735         1493         1491 
TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3326 
        1130         1508         1478         1106         1186         1137 
TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3347 TCGA-A3-3349 
        1485          665         1043          945         1610         1385 
TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 
         910         2688         1307         2504         1559          319 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 
         873         2270         2274          735         1621         1070 
TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 
         630          567          574          861         1993          617 
TCGA-A3-A8CQ TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 
           3         3343         2566         2223         2017          480 
TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 
        1853         2087         2044         1423         1471         1280 
TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3456 
        1217         1779         1481         1397          874         1143 
TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 
        1168          951          853          369         1238           43 
TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4718 TCGA-B0-4813 TCGA-B0-4819 TCGA-B0-5097 
          26           96          616           18          183          665 
TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 
         911         1092          359          797          657          535 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
          59          493          554          652         1132          449 
TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5696 
        2408         3431         1487         3076         1420         1727 
TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
        1835         2583         2741         1732         1605         1203 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
        3668         2414         3117         1459         2931         2722 
TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
        1865         2963          992         1092           51          374 
TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 
         648          952          358          315          417          656 
TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 
         507          291          175            7           38           16 
TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 
         141          166           11            7          511          826 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 
         838          762          750          523          777          788 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 
         700          636          722           36          822           26 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 
         737          522          505          194          434           15 
TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H 
        1046          435          830          519           53          256 
TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4161 
         150           66          110         3377         2881         2746 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 
        3074         2839         3037           13         2718          701 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 
        1893         1879         1955         1670         2964         1625 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4338 
         845         1888         1133          645          461         2859 
TCGA-BP-4344 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 
        1666         1367          372          374         2208         2372 
TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 
        2361          182         2184         1462          400         1876 
TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 
        1885         1843          411         1731         2080          354 
TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4801 TCGA-BP-4803 
        1854         1489          620         1107         1124          204 
TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
        1459          211         2660         2172         1935         1785 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 
        1834         1862         1871          205         1746         1794 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4975 TCGA-BP-4976 
         433         1487         1502         1384         1433         1632 
TCGA-BP-4977 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4989 
         454         1014         1413          785         1124          118 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 
        1413          501          177         1371          932         1266 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 
         563         1177         1126          840         1140         1071 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5177 TCGA-BP-5180 
         193         2412         2257          932          293         2263 
TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
        1495         1165         1291         1133         1132          693 
TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 
         406          822         1011          967          714          408 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 
         749         1018          603         1355         1063          951 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4639 TCGA-CJ-4640 
          29         1820         1416         1924         2308         1998 
TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
        1628         1793          646         2554         1498         2423 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
        1435         2259         2283         2353         1955         2186 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4889 
        2014         1883         1759         2125         1952         1946 
TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4897 TCGA-CJ-4899 
        2085         1521          750          841         1808         1528 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 
        1520         1560         1792         1496         1499         1531 
TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-5671 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5681 
        1657         1373         1943         2430         2575          552 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6031 
        1883         1889         2231         2038         1855         1906 
TCGA-CJ-6032 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 
        2548         2799         2489         2609         2226         2017 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CZ-4853 
        2378         2271         3222         2552         3146          774 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-4863 
        1404           18         1943         1787         1843         1928 
TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5456 
        2830         1868         1929         1789           25         1712 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5461 TCGA-CZ-5463 TCGA-CZ-5464 
        1683         1732         1683          330          662         1740 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 
        1446          685           59          946          386         2439 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
        2067         1997          373          435          693         1905 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 
        1329         1398         1470          370          355         1130 
TCGA-DV-5574 TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
         723         1729          551          119          206          127 
TCGA-GK-A6C7 
          61 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
               110                  3 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              2192               3668 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              1314               1280 
[1] "110.0 - 2192.0 (1314.0)" "3.0 - 3668.0 (1280.0)"  
[1] "hr=" "1.6"
D26V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  14Q GAIN MUTATED         5        2         4        5
  14Q GAIN WILD-TYPE     239       54       122       74
D26V3, multiclass
           clus
vv          14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  STAGE I                  5                239
  STAGE II                 2                 54
  STAGE III                4                122
  STAGE IV                 5                 74
[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"
                    vv
clus                  T1  T2  T3  T4
  14Q GAIN MUTATED     5   2   6   3
  14Q GAIN WILD-TYPE 245  65 171   8
D26V4, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  T1                5                245
  T2                2                 65
  T3                6                171
  T4                3                  8
[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"
D26V5, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     9   0
  14Q GAIN WILD-TYPE 221  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      9    0
  14Q GAIN WILD-TYPE  221   18
   clus
vv  14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  0                9                221
  1                0                 18
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  14Q GAIN MUTATED    12   4   0
  14Q GAIN WILD-TYPE 405  74   9
D26V6, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  M0               12                405
  M1                4                 74
  MX                0                  9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V7, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     5  11
  14Q GAIN WILD-TYPE 173 316
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      5   11
  14Q GAIN WILD-TYPE  173  316
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE                5                173
  MALE                 11                316
[1] 2 2
[1] FALSE
D26V8, continuous
D26V9, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  14Q GAIN MUTATED       0                         1    15
  14Q GAIN WILD-TYPE     8                        32   442
D26V10, multiclass
                           clus
vv                          14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  ASIAN                                    0                  8
  BLACK OR AFRICAN AMERICAN                1                 32
  WHITE                                   15                442
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V11, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     0  11
  14Q GAIN WILD-TYPE  24 319
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      0   11
  14Q GAIN WILD-TYPE   24  319
                        clus
vv                       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 24
  NOT HISPANIC OR LATINO               11                319
[1] 2 2
[1] FALSE

Clustering(27) Variable = 15Q GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                  0   1
  15Q GAIN MUTATED    20   1
  15Q GAIN WILD-TYPE 318  25
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                21                343 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 1                 25 
$`15Q GAIN MUTATED`
TCGA-A3-3325 TCGA-A3-3372 TCGA-A3-3374 TCGA-A3-3387 TCGA-AK-3430 TCGA-AK-3433 
         751          735         1314          617          480         2192 
TCGA-B4-5838 TCGA-BP-4174 TCGA-BP-4177 TCGA-BP-4803 TCGA-BP-4969 TCGA-BP-4994 
         166         1879         1670          204         1794         1308 
TCGA-BP-5185 TCGA-CJ-4871 TCGA-CJ-4875 TCGA-CJ-4897 TCGA-CW-5585 TCGA-CW-5588 
        1132         2423         2353         1808         2609         2017 
TCGA-CZ-4866 TCGA-CZ-5456 TCGA-CZ-5460 
        1868         1712         1430 

$`15Q GAIN WILD-TYPE`
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 
        1120         1436           16          735         1493         1491 
TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3326 
        1130         1508         1478         1106         1186         1137 
TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3347 TCGA-A3-3349 
        1485          665         1043          945         1610         1385 
TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 
         910         2688         1307         2504         1559          319 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 
         873         2270         2274         1621         1070          630 
TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-A8CQ TCGA-AK-3425 
         567          574          861         1993            3         3343 
TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 
        2566         2223         2017         1853         2087         2044 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 
        1745         1423         1471         1280         1217         1779 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
        1481         1397          874         1143         1168          951 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4699 TCGA-B0-4706 
         853          369         1238           43          110           26 
TCGA-B0-4710 TCGA-B0-4718 TCGA-B0-4813 TCGA-B0-4819 TCGA-B0-5097 TCGA-B0-5108 
          96          616           18          183          665          911 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 
        1092          359          797          657          535           59 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 
         493          554          652         1132          449         2408 
TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 
        3431         1487         3076         1420         1727         1835 
TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 
        2583         2741         1732         1605         1203         3668 
TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
        2414         3117         1459         2931         2722         1865 
TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 
        2963          992         1092           51          374          648 
TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR 
         952          358          315          417          656          507 
TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
         291          175            7           38           16          141 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
          11            7          511          826          838          762 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 
         750          523          777          788          700          636 
TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
         722           36          822           26          737          522 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
         505          194          434           15         1046          435 
TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J 
         830          519           53          256          150           66 
TCGA-B8-A7U6 TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
         110         3377         2881         2746         3074         2839 
TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4173 TCGA-BP-4176 
        3037           13         2718          701         1893         1955 
TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 
        2964         1625          845         1888         1133          645 
TCGA-BP-4335 TCGA-BP-4338 TCGA-BP-4344 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 
         461         2859         1666         1367          372          970 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4765 
         374         2208         2372         2361          182         2184 
TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 
        1462          400         1876         1885         1843          411 
TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4795 
        1731         2080          354         1854         1489          620 
TCGA-BP-4797 TCGA-BP-4801 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 
        1107         1124         1459          211         2660         2172 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 
        1935         1785         1834         1862         1871          205 
TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4975 
        1746          433         1487         1502         1384         1433 
TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4987 
        1632          454         1014         1413          785         1124 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 
         118         1413          501          177         1371          932 
TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 
        1266          563         1177         1126          840         1140 
TCGA-BP-5008 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5177 
        1071          193         2412         2257          932          293 
TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 
        2263         1495         1165         1291         1133          693 
TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 
         406          822         1011          967          714          408 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 
         749         1018          603         1355         1063          951 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4639 TCGA-CJ-4640 
          29         1820         1416         1924         2308         1998 
TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4872 
        1628         1793          646         2554         1498         1435 
TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 
        2259         2283         1955         2186         2014         1883 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 
        1759         2125         1952         1946         2085         1521 
TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4899 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 
         750          841         1528         1450         1520         1560 
TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4916 
        1792         1496         1499         1531         1657         1373 
TCGA-CJ-5671 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
        1943         2430         2575          552         1883         1889 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CW-5581 
        2231         2038         1855         1906         2548         2799 
TCGA-CW-5583 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6088 TCGA-CW-6090 
        2489         2226         2378         2271         3222         2552 
TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4858 TCGA-CZ-4859 
        3146          774         1404           18         1943         1787 
TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 
        1843         1928         2830         1929         1789           25 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5461 TCGA-CZ-5463 TCGA-CZ-5464 
        1683         1732         1683          330          662         1740 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 
        1446          685           59          946          386         2439 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
        2067         1997          373          435          693         1905 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 
        1329         1398         1470          370          355         1130 
TCGA-DV-5574 TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
         723         1729          551          119          206          127 
TCGA-GK-A6C7 
          61 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
               166                  3 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              2609               3668 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              1670               1238 
[1] "166.0 - 2609.0 (1670.0)" "3.0 - 3668.0 (1238.0)"  
[1] "hr=" "1.7"
D27V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  15Q GAIN MUTATED        10        4         7        5
  15Q GAIN WILD-TYPE     234       52       119       74
D27V3, multiclass
           clus
vv          15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  STAGE I                 10                234
  STAGE II                 4                 52
  STAGE III                7                119
  STAGE IV                 5                 74
[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"
                    vv
clus                  T1  T2  T3  T4
  15Q GAIN MUTATED    10   4  11   1
  15Q GAIN WILD-TYPE 240  63 166  10
D27V4, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  T1               10                240
  T2                4                 63
  T3               11                166
  T4                1                 10
[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"
D27V5, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    10   2
  15Q GAIN WILD-TYPE 220  16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     10    2
  15Q GAIN WILD-TYPE  220   16
   clus
vv  15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  0               10                220
  1                2                 16
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  15Q GAIN MUTATED    21   5   0
  15Q GAIN WILD-TYPE 396  73   9
D27V6, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  M0               21                396
  M1                5                 73
  MX                0                  9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V7, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     8  18
  15Q GAIN WILD-TYPE 170 309
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      8   18
  15Q GAIN WILD-TYPE  170  309
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE                8                170
  MALE                 18                309
[1] 2 2
[1] FALSE
D27V8, continuous
D27V9, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  15Q GAIN MUTATED       0                         1    25
  15Q GAIN WILD-TYPE     8                        32   432
D27V10, multiclass
                           clus
vv                          15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  ASIAN                                    0                  8
  BLACK OR AFRICAN AMERICAN                1                 32
  WHITE                                   25                432
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V11, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     1  16
  15Q GAIN WILD-TYPE  23 314
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      1   16
  15Q GAIN WILD-TYPE   23  314
                        clus
vv                       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 23
  NOT HISPANIC OR LATINO               16                314
[1] 2 2
[1] FALSE

Clustering(28) Variable = 16P GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                  0   1
  16P GAIN MUTATED    73   6
  16P GAIN WILD-TYPE 265  20
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                79                285 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 6                 20 
$`16P GAIN MUTATED`
TCGA-A3-3313 TCGA-A3-3319 TCGA-A3-3325 TCGA-A3-3358 TCGA-A3-3372 TCGA-A3-3382 
         735         1130          751         1307          735          574 
TCGA-A3-3387 TCGA-AK-3433 TCGA-AK-3440 TCGA-AK-3453 TCGA-B0-4699 TCGA-B0-5113 
         617         2192         1745         1397          110          359 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 TCGA-B2-4098 
        1132          449         1487         1727         1835           51 
TCGA-B2-5639 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5838 TCGA-B8-4620 
         417            7           38           16          166          777 
TCGA-B8-4621 TCGA-B8-A54I TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4166 TCGA-BP-4167 
         788          150         3074         2839           13         2718 
TCGA-BP-4174 TCGA-BP-4338 TCGA-BP-4351 TCGA-BP-4756 TCGA-BP-4768 TCGA-BP-4781 
        1879         2859          970          374          400         2080 
TCGA-BP-4782 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4967 TCGA-BP-4969 
         354          204         1459         2172          205         1794 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4977 TCGA-BP-4989 TCGA-BP-4994 TCGA-BP-4995 
        1487         1502          454          118         1308         1371 
TCGA-BP-5175 TCGA-BP-5198 TCGA-BP-5200 TCGA-CJ-4636 TCGA-CJ-4871 TCGA-CJ-4873 
         932          603         1063         1924         2423         2259 
TCGA-CJ-4875 TCGA-CJ-4885 TCGA-CJ-4889 TCGA-CJ-4897 TCGA-CJ-4901 TCGA-CJ-4903 
        2353         2125         1946         1808         1450         1560 
TCGA-CJ-4907 TCGA-CJ-5671 TCGA-CJ-5676 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CW-5581 
        1499         1943         2575         1883         1889         2799 
TCGA-CW-5588 TCGA-CW-5591 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4866 TCGA-CZ-5456 
        2017         2271         1943         1787         1868         1712 
TCGA-CZ-5457 TCGA-CZ-5460 TCGA-CZ-5469 TCGA-CZ-5984 TCGA-DV-5568 TCGA-DV-5573 
        1683         1430          946         2067          370         1130 
TCGA-EU-5905 
         119 

$`16P GAIN WILD-TYPE`
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3320 
        1120         1436           16         1493         1491         1508 
TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 
        1478         1106         1186         1137         1485          665 
TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 
        1043          945         1610         1385          910         2688 
TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 
        2504         1559          319          873         2270         2274 
TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3383 
        1621         1314         1070          630          567          861 
TCGA-A3-3385 TCGA-A3-A8CQ TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
        1993            3         3343         2566         2223         2017 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3443 TCGA-AK-3444 
         480         1853         2087         2044         1423         1471 
TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3456 
        1280         1217         1779         1481          874         1143 
TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 
        1168          951          853          369         1238           43 
TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4718 TCGA-B0-4813 TCGA-B0-4819 TCGA-B0-5097 
          26           96          616           18          183          665 
TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 
         911         1092          797          657          535           59 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5693 
         493          554          652         2408         3431         3076 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
        1420         2583         2741         1732         1605         1203 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
        3668         2414         3117         1459         2931         2722 
TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4099 TCGA-B2-4101 
        1865         2963          992         1092          374          648 
TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 
         952          358          315          656          507          291 
TCGA-B4-5378 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 
         175          141           11            7          511          826 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4622 TCGA-B8-5158 
         838          762          750          523          700          636 
TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
         722           36          822           26          737          522 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
         505          194          434           15         1046          435 
TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54J TCGA-B8-A7U6 
         830          519           53          256           66          110 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4165 TCGA-BP-4169 TCGA-BP-4173 
        3377         2881         2746         3037          701         1893 
TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 
        1955         1670         2964         1625          845         1888 
TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4344 TCGA-BP-4347 TCGA-BP-4349 
        1133          645          461         1666         1367          372 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4765 TCGA-BP-4766 
        2208         2372         2361          182         2184         1462 
TCGA-BP-4769 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4784 
        1876         1885         1843          411         1731         1854 
TCGA-BP-4789 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4801 TCGA-BP-4807 TCGA-BP-4959 
        1489          620         1107         1124          211         2660 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4968 
        1935         1785         1834         1862         1871         1746 
TCGA-BP-4970 TCGA-BP-4973 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4982 TCGA-BP-4983 
         433         1384         1433         1632         1014         1413 
TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4998 
         785         1124         1413          501          177          932 
TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 
        1266          563         1177         1126          840         1140 
TCGA-BP-5008 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5177 TCGA-BP-5180 
        1071          193         2412         2257          293         2263 
TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
        1495         1165         1291         1133         1132          693 
TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 
         406          822         1011          967          714          408 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5199 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 
         749         1018         1355          951           29         1820 
TCGA-CJ-4635 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 
        1416         2308         1998         1628         1793          646 
TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4872 TCGA-CJ-4874 TCGA-CJ-4876 TCGA-CJ-4878 
        2554         1498         1435         2283         1955         2186 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4886 TCGA-CJ-4890 TCGA-CJ-4892 
        2014         1883         1759         1952         2085         1521 
TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4899 TCGA-CJ-4902 TCGA-CJ-4904 TCGA-CJ-4905 
         750          841         1528         1520         1792         1496 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-5675 TCGA-CJ-5681 TCGA-CJ-5684 
        1531         1657         1373         2430          552         2231 
TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CW-5583 TCGA-CW-5585 
        2038         1855         1906         2548         2489         2609 
TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CZ-4853 
        2226         2378         3222         2552         3146          774 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-5451 
        1404           18         1843         1928         2830         1929 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5461 TCGA-CZ-5463 
        1789           25         1732         1683          330          662 
TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5470 TCGA-CZ-5982 
        1740         1446          685           59          386         2439 
TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 
        1997          373          435          693         1905         1329 
TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-EU-5904 
        1398         1470          355          723         1729          551 
TCGA-EU-5906 TCGA-EU-5907 TCGA-GK-A6C7 
         206          127           61 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 7                  3 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              3074               3668 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              1430               1217 
[1] "7.0 - 3074.0 (1430.0)" "3.0 - 3668.0 (1217.0)"
[1] "hr=" "1.1"
D28V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  16P GAIN MUTATED        45        8        33       18
  16P GAIN WILD-TYPE     199       48        93       61
D28V3, multiclass
           clus
vv          16P GAIN MUTATED 16P GAIN WILD-TYPE
  STAGE I                 45                199
  STAGE II                 8                 48
  STAGE III               33                 93
  STAGE IV                18                 61
[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"
                    vv
clus                  T1  T2  T3  T4
  16P GAIN MUTATED    45  10  46   3
  16P GAIN WILD-TYPE 205  57 131   8
D28V4, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  T1               45                205
  T2               10                 57
  T3               46                131
  T4                3                  8
[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"
D28V5, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    50   1
  16P GAIN WILD-TYPE 180  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     50    1
  16P GAIN WILD-TYPE  180   17
   clus
vv  16P GAIN MUTATED 16P GAIN WILD-TYPE
  0               50                180
  1                1                 17
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  16P GAIN MUTATED    85  18   1
  16P GAIN WILD-TYPE 332  60   8
D28V6, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  M0               85                332
  M1               18                 60
  MX                1                  8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V7, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    35  69
  16P GAIN WILD-TYPE 143 258
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     35   69
  16P GAIN WILD-TYPE  143  258
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE               35                143
  MALE                 69                258
[1] 2 2
[1] FALSE
D28V8, continuous
D28V9, continuous
[1] "Remove cluster labels:" "16P GAIN MUTATED"      
clus
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 1                  7 
        TCGA-A3-A8CQ         TCGA-B2-A4SR         TCGA-B8-5158 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-B8-5164         TCGA-B8-A54F         TCGA-B8-A54G 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-G6-A5PC 
"16P GAIN WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16P GAIN MUTATED       1                         4    99
  16P GAIN WILD-TYPE     7                        29   358
D28V10, multiclass
                           clus
vv                          16P GAIN MUTATED 16P GAIN WILD-TYPE
  ASIAN                                    1                  7
  BLACK OR AFRICAN AMERICAN                4                 29
  WHITE                                   99                358
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V11, binary
                    cls
clus                   0   1
  16P GAIN MUTATED     4  63
  16P GAIN WILD-TYPE  20 267
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      4   63
  16P GAIN WILD-TYPE   20  267
                        clus
vv                       16P GAIN MUTATED 16P GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                 20
  NOT HISPANIC OR LATINO               63                267
[1] 2 2
[1] FALSE

Clustering(29) Variable = 16Q GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                  0   1
  16Q GAIN MUTATED    68   5
  16Q GAIN WILD-TYPE 270  21
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                73                291 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 5                 21 
$`16Q GAIN MUTATED`
TCGA-A3-3313 TCGA-A3-3325 TCGA-A3-3358 TCGA-A3-3382 TCGA-A3-3387 TCGA-AK-3433 
         735          751         1307          574          617         2192 
TCGA-AK-3440 TCGA-AK-3453 TCGA-B0-4699 TCGA-B0-5113 TCGA-B0-5400 TCGA-B0-5692 
        1745         1397          110          359         1132         1487 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B2-4098 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5838 
        1727         1835           51            7           38          166 
TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-A54I TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4166 
         777          788          150         3074         2839           13 
TCGA-BP-4167 TCGA-BP-4174 TCGA-BP-4338 TCGA-BP-4351 TCGA-BP-4756 TCGA-BP-4768 
        2718         1879         2859          970          374          400 
TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4967 
        2080          354          204         1459         2172          205 
TCGA-BP-4969 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4977 TCGA-BP-4989 TCGA-BP-4994 
        1794         1487         1502          454          118         1308 
TCGA-BP-5175 TCGA-BP-5198 TCGA-BP-5200 TCGA-CJ-4636 TCGA-CJ-4871 TCGA-CJ-4873 
         932          603         1063         1924         2423         2259 
TCGA-CJ-4875 TCGA-CJ-4885 TCGA-CJ-4889 TCGA-CJ-4897 TCGA-CJ-4901 TCGA-CJ-4903 
        2353         2125         1946         1808         1450         1560 
TCGA-CJ-4907 TCGA-CJ-5671 TCGA-CJ-5676 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CW-5581 
        1499         1943         2575         1883         1889         2799 
TCGA-CW-5588 TCGA-CW-5591 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4866 TCGA-CZ-5456 
        2017         2271         1943         1787         1868         1712 
TCGA-CZ-5457 TCGA-CZ-5460 TCGA-CZ-5469 TCGA-CZ-5984 TCGA-DV-5568 TCGA-DV-5573 
        1683         1430          946         2067          370         1130 
TCGA-EU-5905 
         119 

$`16Q GAIN WILD-TYPE`
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 
        1120         1436           16         1493         1491         1130 
TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3326 TCGA-A3-3331 
        1508         1478         1106         1186         1137         1485 
TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 
         665         1043          945         1610         1385          910 
TCGA-A3-3357 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 
        2688         2504         1559          319          873         2270 
TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 
        2274          735         1621         1314         1070          630 
TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-A8CQ TCGA-AK-3425 TCGA-AK-3427 
         567          861         1993            3         3343         2566 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 
        2223         2017          480         1853         2087         2044 
TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 
        1423         1471         1280         1217         1779         1481 
TCGA-AK-3454 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 
         874         1143         1168          951          853          369 
TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4718 TCGA-B0-4813 
        1238           43           26           96          616           18 
TCGA-B0-4819 TCGA-B0-5097 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5115 TCGA-B0-5116 
         183          665          911         1092          797          657 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5402 
         535           59          493          554          652          449 
TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5699 
        2408         3431         3076         1420         2583         2741 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 
        1732         1605         1203         3668         2414         3117 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 
        1459         2931         2722         1865         2963          992 
TCGA-B2-3924 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 
        1092          374          648          952          358          315 
TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5835 
         417          656          507          291          175           16 
TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
         141           11            7          511          826          838 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 
         762          750          523          700          636          722 
TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
          36          822           26          737          522          505 
TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D 
         194          434           15         1046          435          830 
TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4158 
         519           53          256           66          110         3377 
TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4165 TCGA-BP-4169 TCGA-BP-4173 TCGA-BP-4176 
        2881         2746         3037          701         1893         1955 
TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 
        1670         2964         1625          845         1888         1133 
TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4344 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4758 
         645          461         1666         1367          372         2208 
TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 
        2372         2361          182         2184         1462         1876 
TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4784 TCGA-BP-4789 
        1885         1843          411         1731         1854         1489 
TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4801 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4961 
         620         1107         1124          211         2660         1935 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4968 TCGA-BP-4970 
        1785         1834         1862         1871         1746          433 
TCGA-BP-4973 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4986 
        1384         1433         1632         1014         1413          785 
TCGA-BP-4987 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 
        1124         1413          501          177         1371          932 
TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 
        1266          563         1177         1126          840         1140 
TCGA-BP-5008 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5177 TCGA-BP-5180 
        1071          193         2412         2257          293         2263 
TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
        1495         1165         1291         1133         1132          693 
TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 
         406          822         1011          967          714          408 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5199 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 
         749         1018         1355          951           29         1820 
TCGA-CJ-4635 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 
        1416         2308         1998         1628         1793          646 
TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4872 TCGA-CJ-4874 TCGA-CJ-4876 TCGA-CJ-4878 
        2554         1498         1435         2283         1955         2186 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4886 TCGA-CJ-4890 TCGA-CJ-4892 
        2014         1883         1759         1952         2085         1521 
TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4899 TCGA-CJ-4902 TCGA-CJ-4904 TCGA-CJ-4905 
         750          841         1528         1520         1792         1496 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-5675 TCGA-CJ-5681 TCGA-CJ-5684 
        1531         1657         1373         2430          552         2231 
TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CW-5583 TCGA-CW-5585 
        2038         1855         1906         2548         2489         2609 
TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CZ-4853 
        2226         2378         3222         2552         3146          774 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-5451 
        1404           18         1843         1928         2830         1929 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5461 TCGA-CZ-5463 
        1789           25         1732         1683          330          662 
TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5470 TCGA-CZ-5982 
        1740         1446          685           59          386         2439 
TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 
        1997          373          435          693         1905         1329 
TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-EU-5904 
        1398         1470          355          723         1729          551 
TCGA-EU-5906 TCGA-EU-5907 TCGA-GK-A6C7 
         206          127           61 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 7                  3 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              3074               3668 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              1487               1186 
[1] "7.0 - 3074.0 (1487.0)" "3.0 - 3668.0 (1186.0)"
[1] "hr=" "1.1"
D29V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  16Q GAIN MUTATED        42        8        32       14
  16Q GAIN WILD-TYPE     202       48        94       65
D29V3, multiclass
           clus
vv          16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  STAGE I                 42                202
  STAGE II                 8                 48
  STAGE III               32                 94
  STAGE IV                14                 65
[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"
                    vv
clus                  T1  T2  T3  T4
  16Q GAIN MUTATED    42   8  44   2
  16Q GAIN WILD-TYPE 208  59 133   9
D29V4, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  T1               42                208
  T2                8                 59
  T3               44                133
  T4                2                  9
[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"
D29V5, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    47   1
  16Q GAIN WILD-TYPE 183  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     47    1
  16Q GAIN WILD-TYPE  183   17
   clus
vv  16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  0               47                183
  1                1                 17
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  16Q GAIN MUTATED    80  15   1
  16Q GAIN WILD-TYPE 337  63   8
D29V6, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  M0               80                337
  M1               15                 63
  MX                1                  8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V7, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    34  62
  16Q GAIN WILD-TYPE 144 265
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     34   62
  16Q GAIN WILD-TYPE  144  265
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE               34                144
  MALE                 62                265
[1] 2 2
[1] FALSE
D29V8, continuous
D29V9, continuous
[1] "Remove cluster labels:" "16Q GAIN MUTATED"      
clus
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 1                  7 
        TCGA-A3-A8CQ         TCGA-B2-A4SR         TCGA-B8-5158 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B8-5164         TCGA-B8-A54F         TCGA-B8-A54G 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-G6-A5PC 
"16Q GAIN WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16Q GAIN MUTATED       1                         4    91
  16Q GAIN WILD-TYPE     7                        29   366
D29V10, multiclass
                           clus
vv                          16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  ASIAN                                    1                  7
  BLACK OR AFRICAN AMERICAN                4                 29
  WHITE                                   91                366
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V11, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     4  57
  16Q GAIN WILD-TYPE  20 273
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      4   57
  16Q GAIN WILD-TYPE   20  273
                        clus
vv                       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                 20
  NOT HISPANIC OR LATINO               57                273
[1] 2 2
[1] FALSE

Clustering(30) Variable = 17P GAIN MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                  0   1
  17P GAIN MUTATED    18   2
  17P GAIN WILD-TYPE 320  24
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                20                344 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 2                 24 
$`17P GAIN MUTATED`
TCGA-A3-3313 TCGA-A3-3325 TCGA-A3-3363 TCGA-AK-3453 TCGA-B4-5838 TCGA-B8-4621 
         735          751          319         1397          166          788 
TCGA-B8-5551 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4756 TCGA-BP-4768 TCGA-BP-4781 
          15         1955         1670          374          400         2080 
TCGA-BP-5185 TCGA-BP-5200 TCGA-CJ-4873 TCGA-CJ-4901 TCGA-CJ-4907 TCGA-CZ-4866 
        1132         1063         2259         1450         1499         1868 
TCGA-CZ-5469 TCGA-EU-5905 
         946          119 

$`17P GAIN WILD-TYPE`
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 
        1120         1436           16         1493         1491         1130 
TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3326 TCGA-A3-3331 
        1508         1478         1106         1186         1137         1485 
TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 
         665         1043          945         1610         1385          910 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3365 TCGA-A3-3367 
        2688         1307         2504         1559          873         2270 
TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 
        2274          735         1621         1314         1070          630 
TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A8CQ 
         567          574          861         1993          617            3 
TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 
        3343         2566         2223         2017          480         1853 
TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 
        2192         2087         2044         1745         1423         1471 
TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3456 
        1280         1217         1779         1481          874         1143 
TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 
        1168          951          853          369         1238           43 
TCGA-B0-4699 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4718 TCGA-B0-4813 TCGA-B0-4819 
         110           26           96          616           18          183 
TCGA-B0-5097 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 
         665          911         1092          359          797          657 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
         535           59          493          554          652         1132 
TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 
         449         2408         3431         1487         3076         1420 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
        1727         1835         2583         2741         1732         1605 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
        1203         3668         2414         3117         1459         2931 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
        2722         1865         2963          992         1092           51 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 
         374          648          952          358          315          417 
TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 
         656          507          291          175            7           38 
TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 
          16          141           11            7          511          826 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 
         838          762          750          523          777          700 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
         636          722           36          822           26          737 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5552 TCGA-B8-5553 
         522          505          194          434         1046          435 
TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J 
         830          519           53          256          150           66 
TCGA-B8-A7U6 TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
         110         3377         2881         2746         3074         2839 
TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4173 TCGA-BP-4174 
        3037           13         2718          701         1893         1879 
TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 
        2964         1625          845         1888         1133          645 
TCGA-BP-4335 TCGA-BP-4338 TCGA-BP-4344 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 
         461         2859         1666         1367          372          970 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4765 TCGA-BP-4766 
        2208         2372         2361          182         2184         1462 
TCGA-BP-4769 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4782 
        1876         1885         1843          411         1731          354 
TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4801 TCGA-BP-4803 
        1854         1489          620         1107         1124          204 
TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
        1459          211         2660         2172         1935         1785 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 
        1834         1862         1871          205         1746         1794 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4975 TCGA-BP-4976 
         433         1487         1502         1384         1433         1632 
TCGA-BP-4977 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4989 
         454         1014         1413          785         1124          118 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 
        1413          501          177         1308         1371          932 
TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 
        1266          563         1177         1126          840         1140 
TCGA-BP-5008 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5177 
        1071          193         2412         2257          932          293 
TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 
        2263         1495         1165         1291         1133          693 
TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 
         406          822         1011          967          714          408 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5201 TCGA-BP-5202 
         749         1018          603         1355          951           29 
TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4642 
        1820         1416         1924         2308         1998         1628 
TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 
        1793          646         2554         1498         2423         1435 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 
        2283         2353         1955         2186         2014         1883 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 
        1759         2125         1952         1946         2085         1521 
TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4902 TCGA-CJ-4903 
         750          841         1808         1528         1520         1560 
TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-5671 
        1792         1496         1531         1657         1373         1943 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
        2430         2575          552         1883         1889         2231 
TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CW-5581 TCGA-CW-5583 
        2038         1855         1906         2548         2799         2489 
TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6088 
        2609         2226         2017         2378         2271         3222 
TCGA-CW-6090 TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4858 
        2552         3146          774         1404           18         1943 
TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-5451 TCGA-CZ-5452 
        1787         1843         1928         2830         1929         1789 
TCGA-CZ-5453 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
          25         1712         1683         1732         1683         1430 
TCGA-CZ-5461 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5468 
         330          662         1740         1446          685           59 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 
         386         2439         2067         1997          373          435 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 
         693         1905         1329         1398         1470          370 
TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5906 
         355         1130          723         1729          551          206 
TCGA-EU-5907 TCGA-GK-A6C7 
         127           61 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                15                  3 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              2259               3668 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
            1004.5             1311.0 
[1] "15.0 - 2259.0 (1004.5)" "3.0 - 3668.0 (1311.0)" 
[1] "hr=" "1.7"
D30V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  17P GAIN MUTATED        14        4         7        0
  17P GAIN WILD-TYPE     230       52       119       79
D30V3, multiclass
           clus
vv          17P GAIN MUTATED 17P GAIN WILD-TYPE
  STAGE I                 14                230
  STAGE II                 4                 52
  STAGE III                7                119
  STAGE IV                 0                 79
[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"
                    vv
clus                  T1  T2  T3  T4
  17P GAIN MUTATED    14   4   7   0
  17P GAIN WILD-TYPE 236  63 170  11
D30V4, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  T1               14                236
  T2                4                 63
  T3                7                170
  T4                0                 11
[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"
D30V5, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    10   2
  17P GAIN WILD-TYPE 220  16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     10    2
  17P GAIN WILD-TYPE  220   16
   clus
vv  17P GAIN MUTATED 17P GAIN WILD-TYPE
  0               10                220
  1                2                 16
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  17P GAIN MUTATED    25   0   0
  17P GAIN WILD-TYPE 392  78   9
D30V6, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  M0               25                392
  M1                0                 78
  MX                0                  9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V7, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     8  17
  17P GAIN WILD-TYPE 170 310
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      8   17
  17P GAIN WILD-TYPE  170  310
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE                8                170
  MALE                 17                310
[1] 2 2
[1] FALSE
D30V8, continuous
D30V9, continuous
[1] "Remove cluster labels:" "17P GAIN MUTATED"      
clus
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 1                  7 
        TCGA-A3-A8CQ         TCGA-B2-A4SR         TCGA-B8-5158 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-B8-5164         TCGA-B8-A54F         TCGA-B8-A54G 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G6-A5PC 
"17P GAIN WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17P GAIN MUTATED       2                         3    20
  17P GAIN WILD-TYPE     6                        30   437
D30V10, multiclass
                           clus
vv                          17P GAIN MUTATED 17P GAIN WILD-TYPE
  ASIAN                                    2                  6
  BLACK OR AFRICAN AMERICAN                3                 30
  WHITE                                   20                437
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V11, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     0  14
  17P GAIN WILD-TYPE  24 316
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      0   14
  17P GAIN WILD-TYPE   24  316
                        clus
vv                       17P GAIN MUTATED 17P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 24
  NOT HISPANIC OR LATINO               14                316
[1] 2 2
[1] FALSE

Clustering(31) Variable = 17Q GAIN MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                  0   1
  17Q GAIN MUTATED    21   2
  17Q GAIN WILD-TYPE 317  24
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                23                341 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 2                 24 
$`17Q GAIN MUTATED`
TCGA-A3-3313 TCGA-A3-3325 TCGA-A3-3363 TCGA-AK-3453 TCGA-B4-5835 TCGA-B4-5838 
         735          751          319         1397           16          166 
TCGA-B8-4621 TCGA-B8-5551 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4756 TCGA-BP-4758 
         788           15         1955         1670          374         2208 
TCGA-BP-4768 TCGA-BP-4781 TCGA-BP-5182 TCGA-BP-5185 TCGA-BP-5200 TCGA-CJ-4873 
         400         2080         1165         1132         1063         2259 
TCGA-CJ-4901 TCGA-CJ-4907 TCGA-CZ-4866 TCGA-CZ-5469 TCGA-EU-5905 
        1450         1499         1868          946          119 

$`17Q GAIN WILD-TYPE`
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 
        1120         1436           16         1493         1491         1130 
TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3326 TCGA-A3-3331 
        1508         1478         1106         1186         1137         1485 
TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 
         665         1043          945         1610         1385          910 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3365 TCGA-A3-3367 
        2688         1307         2504         1559          873         2270 
TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 
        2274          735         1621         1314         1070          630 
TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A8CQ 
         567          574          861         1993          617            3 
TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 
        3343         2566         2223         2017          480         1853 
TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 
        2192         2087         2044         1745         1423         1471 
TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3456 
        1280         1217         1779         1481          874         1143 
TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 
        1168          951          853          369         1238           43 
TCGA-B0-4699 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4718 TCGA-B0-4813 TCGA-B0-4819 
         110           26           96          616           18          183 
TCGA-B0-5097 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 
         665          911         1092          359          797          657 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
         535           59          493          554          652         1132 
TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 
         449         2408         3431         1487         3076         1420 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
        1727         1835         2583         2741         1732         1605 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
        1203         3668         2414         3117         1459         2931 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
        2722         1865         2963          992         1092           51 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 
         374          648          952          358          315          417 
TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 
         656          507          291          175            7           38 
TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
         141           11            7          511          826          838 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 
         762          750          523          777          700          636 
TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
         722           36          822           26          737          522 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D 
         505          194          434         1046          435          830 
TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 
         519           53          256          150           66          110 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 
        3377         2881         2746         3074         2839         3037 
TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4325 
          13         2718          701         1893         1879         2964 
TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 
        1625          845         1888         1133          645          461 
TCGA-BP-4338 TCGA-BP-4344 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4759 
        2859         1666         1367          372          970         2372 
TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4774 
        2361          182         2184         1462         1876         1885 
TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4789 
        1843          411         1731          354         1854         1489 
TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 
         620         1107         1124          204         1459          211 
TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 
        2660         2172         1935         1785         1834         1862 
TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 
        1871          205         1746         1794          433         1487 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4982 
        1502         1384         1433         1632          454         1014 
TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
        1413          785         1124          118         1413          501 
TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 
         177         1308         1371          932         1266          563 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5169 
        1177         1126          840         1140         1071          193 
TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5181 
        2412         2257          932          293         2263         1495 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 
        1291         1133          693          406          822         1011 
TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 
         967          714          408          749         1018          603 
TCGA-BP-5199 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 
        1355          951           29         1820         1416         1924 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 
        2308         1998         1628         1793          646         2554 
TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 
        1498         2423         1435         2283         2353         1955 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 
        2186         2014         1883         1759         2125         1952 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4897 
        1946         2085         1521          750          841         1808 
TCGA-CJ-4899 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4908 
        1528         1520         1560         1792         1496         1531 
TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-5671 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5681 
        1657         1373         1943         2430         2575          552 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6031 
        1883         1889         2231         2038         1855         1906 
TCGA-CJ-6032 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 
        2548         2799         2489         2609         2226         2017 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CZ-4853 
        2378         2271         3222         2552         3146          774 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-4863 
        1404           18         1943         1787         1843         1928 
TCGA-CZ-4864 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5456 TCGA-CZ-5457 
        2830         1929         1789           25         1712         1683 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5463 TCGA-CZ-5464 
        1732         1683         1430          330          662         1740 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 
        1446          685           59          386         2439         2067 
TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 
        1997          373          435          693         1905         1329 
TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 
        1398         1470          370          355         1130          723 
TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5906 TCGA-EU-5907 TCGA-GK-A6C7 
        1729          551          206          127           61 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                15                  3 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              2259               3668 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              1063               1314 
[1] "15.0 - 2259.0 (1063.0)" "3.0 - 3668.0 (1314.0)" 
[1] "hr=" "1.5"
D31V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  17Q GAIN MUTATED        17        4         8        2
  17Q GAIN WILD-TYPE     227       52       118       77
D31V3, multiclass
           clus
vv          17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  STAGE I                 17                227
  STAGE II                 4                 52
  STAGE III                8                118
  STAGE IV                 2                 77
[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"
                    vv
clus                  T1  T2  T3  T4
  17Q GAIN MUTATED    17   4   9   1
  17Q GAIN WILD-TYPE 233  63 168  10
D31V4, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  T1               17                233
  T2                4                 63
  T3                9                168
  T4                1                 10
[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"
D31V5, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    13   2
  17Q GAIN WILD-TYPE 217  16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     13    2
  17Q GAIN WILD-TYPE  217   16
   clus
vv  17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  0               13                217
  1                2                 16
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  17Q GAIN MUTATED    29   2   0
  17Q GAIN WILD-TYPE 388  76   9
D31V6, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  M0               29                388
  M1                2                 76
  MX                0                  9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V7, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    11  20
  17Q GAIN WILD-TYPE 167 307
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     11   20
  17Q GAIN WILD-TYPE  167  307
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE               11                167
  MALE                 20                307
[1] 2 2
[1] FALSE
D31V8, continuous
D31V9, continuous
[1] "Remove cluster labels:" "17Q GAIN MUTATED"      
clus
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 1                  7 
        TCGA-A3-A8CQ         TCGA-B2-A4SR         TCGA-B8-5158 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-B8-5164         TCGA-B8-A54F         TCGA-B8-A54G 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-G6-A5PC 
"17Q GAIN WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17Q GAIN MUTATED       2                         3    26
  17Q GAIN WILD-TYPE     6                        30   431
D31V10, multiclass
                           clus
vv                          17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  ASIAN                                    2                  6
  BLACK OR AFRICAN AMERICAN                3                 30
  WHITE                                   26                431
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V11, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED     0  17
  17Q GAIN WILD-TYPE  24 313
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      0   17
  17Q GAIN WILD-TYPE   24  313
                        clus
vv                       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 24
  NOT HISPANIC OR LATINO               17                313
[1] 2 2
[1] FALSE

Clustering(32) Variable = 18P GAIN MUTATION ANALYSIS
D32V1, survival
                    sevent
clus2                  0   1
  18P GAIN MUTATED    22   0
  18P GAIN WILD-TYPE 316  26
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                22                342 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 0                 26 
$`18P GAIN MUTATED`
TCGA-A3-3308 TCGA-A3-3325 TCGA-A3-3374 TCGA-A3-3382 TCGA-AK-3433 TCGA-B0-4710 
          16          751         1314          574         2192           96 
TCGA-B0-5113 TCGA-B0-5693 TCGA-B2-5633 TCGA-B4-5838 TCGA-BP-4177 TCGA-BP-4351 
         359         3076          358          166         1670          970 
TCGA-BP-4768 TCGA-BP-4789 TCGA-BP-4992 TCGA-CJ-4635 TCGA-CJ-4872 TCGA-CJ-4897 
         400         1489          501         1416         1435         1808 
TCGA-CJ-4905 TCGA-CW-5583 TCGA-CW-5585 TCGA-CZ-5457 
        1496         2489         2609         1683 

$`18P GAIN WILD-TYPE`
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 
        1120         1436          735         1493         1491         1130 
TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3326 TCGA-A3-3331 
        1508         1478         1106         1186         1137         1485 
TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 
         665         1043          945         1610         1385          910 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
        2688         1307         2504         1559          319          873 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 
        2270         2274          735         1621         1070          630 
TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A8CQ TCGA-AK-3425 
         567          861         1993          617            3         3343 
TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 
        2566         2223         2017          480         1853         2087 
TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 
        2044         1745         1423         1471         1280         1217 
TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3456 TCGA-AK-3458 
        1779         1481         1397          874         1143         1168 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4699 
         951          853          369         1238           43          110 
TCGA-B0-4706 TCGA-B0-4718 TCGA-B0-4813 TCGA-B0-4819 TCGA-B0-5097 TCGA-B0-5108 
          26          616           18          183          665          911 
TCGA-B0-5110 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 
        1092          797          657          535           59          493 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 
         554          652         1132          449         2408         3431 
TCGA-B0-5692 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 
        1487         1420         1727         1835         2583         2741 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 
        1732         1605         1203         3668         2414         3117 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 
        1459         2931         2722         1865         2963          992 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5635 
        1092           51          374          648          952          315 
TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 
         417          656          507          291          175            7 
TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 
          38           16          141           11            7          511 
TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 
         826          838          762          750          523          777 
TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 
         788          700          636          722           36          822 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 
          26          737          522          505          194          434 
TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G 
          15         1046          435          830          519           53 
TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4158 TCGA-BP-4160 
         256          150           66          110         3377         2881 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 
        2746         3074         2839         3037           13         2718 
TCGA-BP-4169 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4325 TCGA-BP-4326 
         701         1893         1879         1955         2964         1625 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4338 
         845         1888         1133          645          461         2859 
TCGA-BP-4344 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 
        1666         1367          372          374         2208         2372 
TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4774 
        2361          182         2184         1462         1876         1885 
TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 
        1843          411         1731         2080          354         1854 
TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 
         620         1107         1124          204         1459          211 
TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 
        2660         2172         1935         1785         1834         1862 
TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 
        1871          205         1746         1794          433         1487 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4982 
        1502         1384         1433         1632          454         1014 
TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4993 
        1413          785         1124          118         1413          177 
TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 
        1308         1371          932         1266          563         1177 
TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5169 TCGA-BP-5170 
        1126          840         1140         1071          193         2412 
TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 
        2257          932          293         2263         1495         1165 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 
        1291         1133         1132          693          406          822 
TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
        1011          967          714          408          749         1018 
TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 
         603         1355         1063          951           29         1820 
TCGA-CJ-4636 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 
        1924         2308         1998         1628         1793          646 
TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 
        2554         1498         2423         2259         2283         2353 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
        1955         2186         2014         1883         1759         2125 
TCGA-CJ-4886 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 
        1952         1946         2085         1521          750          841 
TCGA-CJ-4899 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4907 
        1528         1450         1520         1560         1792         1499 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-5671 TCGA-CJ-5675 TCGA-CJ-5676 
        1531         1657         1373         1943         2430         2575 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 
         552         1883         1889         2231         2038         1855 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CW-5581 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 
        1906         2548         2799         2226         2017         2378 
TCGA-CW-5591 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4854 
        2271         3222         2552         3146          774         1404 
TCGA-CZ-4856 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 
          18         1943         1787         1843         1928         2830 
TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5456 TCGA-CZ-5458 
        1868         1929         1789           25         1712         1732 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 
        1683         1430          330          662         1740         1446 
TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 
         685           59          946          386         2439         2067 
TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 
        1997          373          435          693         1905         1329 
TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 
        1398         1470          370          355         1130          723 
TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-GK-A6C7 
        1729          551          119          206          127           61 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                16                  3 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              3076               3668 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
            1365.0             1285.5 
[1] "16.0 - 3076.0 (1365.0)" "3.0 - 3668.0 (1285.5)" 
[1] "hr="     "2.6e+07"
D32V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  18P GAIN MUTATED        13        2         8        2
  18P GAIN WILD-TYPE     231       54       118       77
D32V3, multiclass
           clus
vv          18P GAIN MUTATED 18P GAIN WILD-TYPE
  STAGE I                 13                231
  STAGE II                 2                 54
  STAGE III                8                118
  STAGE IV                 2                 77
[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"
                    vv
clus                  T1  T2  T3  T4
  18P GAIN MUTATED    13   2  10   0
  18P GAIN WILD-TYPE 237  65 167  11
D32V4, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  T1               13                237
  T2                2                 65
  T3               10                167
  T4                0                 11
[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"
D32V5, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    12   1
  18P GAIN WILD-TYPE 218  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     12    1
  18P GAIN WILD-TYPE  218   17
   clus
vv  18P GAIN MUTATED 18P GAIN WILD-TYPE
  0               12                218
  1                1                 17
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  18P GAIN MUTATED    23   2   0
  18P GAIN WILD-TYPE 394  76   9
D32V6, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  M0               23                394
  M1                2                 76
  MX                0                  9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V7, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    13  12
  18P GAIN WILD-TYPE 165 315
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     13   12
  18P GAIN WILD-TYPE  165  315
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE               13                165
  MALE                 12                315
[1] 2 2
[1] FALSE
D32V8, continuous
[1] "Remove cluster labels:" "18P GAIN MUTATED"      
clus
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 2                 35 
        TCGA-A3-A8CQ         TCGA-AK-3426         TCGA-AK-3430 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-B0-4838         TCGA-B2-5639         TCGA-B4-5377 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-B4-5378         TCGA-B4-5832         TCGA-B4-5834 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-B4-5835         TCGA-B4-5836         TCGA-B4-5843 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-B4-5844         TCGA-CZ-4854         TCGA-CZ-4856 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CZ-4858         TCGA-CZ-4860         TCGA-CZ-4861 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CZ-4862         TCGA-CZ-5456         TCGA-CZ-5465 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CZ-5469         TCGA-CZ-5982         TCGA-DV-5565 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DV-5566         TCGA-DV-5567         TCGA-DV-5568 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DV-5569         TCGA-DV-5573         TCGA-DV-5574 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DV-5575         TCGA-DV-5576         TCGA-EU-5904 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EU-5905         TCGA-EU-5907 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
D32V9, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18P GAIN MUTATED       0                         1    24
  18P GAIN WILD-TYPE     8                        32   433
D32V10, multiclass
                           clus
vv                          18P GAIN MUTATED 18P GAIN WILD-TYPE
  ASIAN                                    0                  8
  BLACK OR AFRICAN AMERICAN                1                 32
  WHITE                                   24                433
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V11, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     2  15
  18P GAIN WILD-TYPE  22 315
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      2   15
  18P GAIN WILD-TYPE   22  315
                        clus
vv                       18P GAIN MUTATED 18P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                 22
  NOT HISPANIC OR LATINO               15                315
[1] 2 2
[1] FALSE

Clustering(33) Variable = 18Q GAIN MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                  0   1
  18Q GAIN MUTATED    21   0
  18Q GAIN WILD-TYPE 317  26
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                21                343 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 0                 26 
$`18Q GAIN MUTATED`
TCGA-A3-3308 TCGA-A3-3325 TCGA-A3-3374 TCGA-A3-3382 TCGA-AK-3433 TCGA-B0-4710 
          16          751         1314          574         2192           96 
TCGA-B0-5113 TCGA-B0-5693 TCGA-B2-5633 TCGA-B4-5838 TCGA-BP-4177 TCGA-BP-4351 
         359         3076          358          166         1670          970 
TCGA-BP-4768 TCGA-BP-4789 TCGA-BP-4992 TCGA-CJ-4635 TCGA-CJ-4897 TCGA-CJ-4905 
         400         1489          501         1416         1808         1496 
TCGA-CW-5583 TCGA-CW-5585 TCGA-CZ-5457 
        2489         2609         1683 

$`18Q GAIN WILD-TYPE`
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 
        1120         1436          735         1493         1491         1130 
TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3326 TCGA-A3-3331 
        1508         1478         1106         1186         1137         1485 
TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 
         665         1043          945         1610         1385          910 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
        2688         1307         2504         1559          319          873 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 
        2270         2274          735         1621         1070          630 
TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A8CQ TCGA-AK-3425 
         567          861         1993          617            3         3343 
TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 
        2566         2223         2017          480         1853         2087 
TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 
        2044         1745         1423         1471         1280         1217 
TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3456 TCGA-AK-3458 
        1779         1481         1397          874         1143         1168 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4699 
         951          853          369         1238           43          110 
TCGA-B0-4706 TCGA-B0-4718 TCGA-B0-4813 TCGA-B0-4819 TCGA-B0-5097 TCGA-B0-5108 
          26          616           18          183          665          911 
TCGA-B0-5110 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 
        1092          797          657          535           59          493 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 
         554          652         1132          449         2408         3431 
TCGA-B0-5692 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 
        1487         1420         1727         1835         2583         2741 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 
        1732         1605         1203         3668         2414         3117 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 
        1459         2931         2722         1865         2963          992 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5635 
        1092           51          374          648          952          315 
TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 
         417          656          507          291          175            7 
TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 
          38           16          141           11            7          511 
TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 
         826          838          762          750          523          777 
TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 
         788          700          636          722           36          822 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 
          26          737          522          505          194          434 
TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G 
          15         1046          435          830          519           53 
TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4158 TCGA-BP-4160 
         256          150           66          110         3377         2881 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 
        2746         3074         2839         3037           13         2718 
TCGA-BP-4169 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4325 TCGA-BP-4326 
         701         1893         1879         1955         2964         1625 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4338 
         845         1888         1133          645          461         2859 
TCGA-BP-4344 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 
        1666         1367          372          374         2208         2372 
TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4774 
        2361          182         2184         1462         1876         1885 
TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 
        1843          411         1731         2080          354         1854 
TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 
         620         1107         1124          204         1459          211 
TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 
        2660         2172         1935         1785         1834         1862 
TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 
        1871          205         1746         1794          433         1487 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4982 
        1502         1384         1433         1632          454         1014 
TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4993 
        1413          785         1124          118         1413          177 
TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 
        1308         1371          932         1266          563         1177 
TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5169 TCGA-BP-5170 
        1126          840         1140         1071          193         2412 
TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 
        2257          932          293         2263         1495         1165 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 
        1291         1133         1132          693          406          822 
TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
        1011          967          714          408          749         1018 
TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 
         603         1355         1063          951           29         1820 
TCGA-CJ-4636 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 
        1924         2308         1998         1628         1793          646 
TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 
        2554         1498         2423         1435         2259         2283 
TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 
        2353         1955         2186         2014         1883         1759 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 
        2125         1952         1946         2085         1521          750 
TCGA-CJ-4894 TCGA-CJ-4899 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 
         841         1528         1450         1520         1560         1792 
TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-5671 TCGA-CJ-5675 
        1499         1531         1657         1373         1943         2430 
TCGA-CJ-5676 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 
        2575          552         1883         1889         2231         2038 
TCGA-CJ-6027 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CW-5581 TCGA-CW-5587 TCGA-CW-5588 
        1855         1906         2548         2799         2226         2017 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CZ-4853 
        2378         2271         3222         2552         3146          774 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-4863 
        1404           18         1943         1787         1843         1928 
TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5456 
        2830         1868         1929         1789           25         1712 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5463 TCGA-CZ-5464 
        1732         1683         1430          330          662         1740 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 
        1446          685           59          946          386         2439 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
        2067         1997          373          435          693         1905 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 
        1329         1398         1470          370          355         1130 
TCGA-DV-5574 TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
         723         1729          551          119          206          127 
TCGA-GK-A6C7 
          61 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                16                  3 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              3076               3668 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              1314               1291 
[1] "16.0 - 3076.0 (1314.0)" "3.0 - 3668.0 (1291.0)" 
[1] "hr="     "2.6e+07"
D33V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  18Q GAIN MUTATED        12        2         9        2
  18Q GAIN WILD-TYPE     232       54       117       77
D33V3, multiclass
           clus
vv          18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  STAGE I                 12                232
  STAGE II                 2                 54
  STAGE III                9                117
  STAGE IV                 2                 77
[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"
                    vv
clus                  T1  T2  T3  T4
  18Q GAIN MUTATED    12   2  11   0
  18Q GAIN WILD-TYPE 238  65 166  11
D33V4, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  T1               12                238
  T2                2                 65
  T3               11                166
  T4                0                 11
[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"
D33V5, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    11   1
  18Q GAIN WILD-TYPE 219  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     11    1
  18Q GAIN WILD-TYPE  219   17
   clus
vv  18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  0               11                219
  1                1                 17
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  18Q GAIN MUTATED    23   2   0
  18Q GAIN WILD-TYPE 394  76   9
D33V6, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  M0               23                394
  M1                2                 76
  MX                0                  9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V7, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    13  12
  18Q GAIN WILD-TYPE 165 315
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     13   12
  18Q GAIN WILD-TYPE  165  315
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE               13                165
  MALE                 12                315
[1] 2 2
[1] FALSE
D33V8, continuous
[1] "Remove cluster labels:" "18Q GAIN MUTATED"      
clus
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 2                 35 
        TCGA-A3-A8CQ         TCGA-AK-3426         TCGA-AK-3430 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B0-4838         TCGA-B2-5639         TCGA-B4-5377 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B4-5378         TCGA-B4-5832         TCGA-B4-5834 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B4-5835         TCGA-B4-5836         TCGA-B4-5843 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B4-5844         TCGA-CZ-4854         TCGA-CZ-4856 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CZ-4858         TCGA-CZ-4860         TCGA-CZ-4861 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CZ-4862         TCGA-CZ-5456         TCGA-CZ-5465 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CZ-5469         TCGA-CZ-5982         TCGA-DV-5565 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DV-5566         TCGA-DV-5567         TCGA-DV-5568 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DV-5569         TCGA-DV-5573         TCGA-DV-5574 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DV-5575         TCGA-DV-5576         TCGA-EU-5904 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EU-5905         TCGA-EU-5907 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
D33V9, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18Q GAIN MUTATED       0                         1    24
  18Q GAIN WILD-TYPE     8                        32   433
D33V10, multiclass
                           clus
vv                          18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  ASIAN                                    0                  8
  BLACK OR AFRICAN AMERICAN                1                 32
  WHITE                                   24                433
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V11, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     2  15
  18Q GAIN WILD-TYPE  22 315
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      2   15
  18Q GAIN WILD-TYPE   22  315
                        clus
vv                       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                 22
  NOT HISPANIC OR LATINO               15                315
[1] 2 2
[1] FALSE

Clustering(34) Variable = 19P GAIN MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                  0   1
  19P GAIN MUTATED    34   4
  19P GAIN WILD-TYPE 304  22
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                38                326 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 4                 22 
$`19P GAIN MUTATED`
TCGA-A3-3325 TCGA-A3-3374 TCGA-A3-3382 TCGA-AK-3433 TCGA-AK-3440 TCGA-AK-3453 
         751         1314          574         2192         1745         1397 
TCGA-B0-4699 TCGA-B0-4710 TCGA-B4-5832 TCGA-B4-5838 TCGA-BP-4166 TCGA-BP-4351 
         110           96            7          166           13          970 
TCGA-BP-4768 TCGA-BP-4967 TCGA-BP-4969 TCGA-BP-4994 TCGA-BP-5185 TCGA-BP-5198 
         400          205         1794         1308         1132          603 
TCGA-BP-5200 TCGA-CJ-4635 TCGA-CJ-4871 TCGA-CJ-4873 TCGA-CJ-4897 TCGA-CJ-4907 
        1063         1416         2423         2259         1808         1499 
TCGA-CJ-5671 TCGA-CJ-5676 TCGA-CJ-5682 TCGA-CW-5591 TCGA-CZ-4854 TCGA-CZ-4866 
        1943         2575         1883         2271         1404         1868 
TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5464 TCGA-CZ-5469 
        1712         1683         1430          330         1740          946 
TCGA-CZ-5984 TCGA-EU-5905 
        2067          119 

$`19P GAIN WILD-TYPE`
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 
        1120         1436           16          735         1493         1491 
TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3326 
        1130         1508         1478         1106         1186         1137 
TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3347 TCGA-A3-3349 
        1485          665         1043          945         1610         1385 
TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 
         910         2688         1307         2504         1559          319 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 
         873         2270         2274          735         1621         1070 
TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A8CQ 
         630          567          861         1993          617            3 
TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 
        3343         2566         2223         2017          480         1853 
TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 
        2087         2044         1423         1471         1280         1217 
TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
        1779         1481          874         1143         1168          951 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4706 TCGA-B0-4718 
         853          369         1238           43           26          616 
TCGA-B0-4813 TCGA-B0-4819 TCGA-B0-5097 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 
          18          183          665          911         1092          359 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
         797          657          535           59          493          554 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 
         652         1132          449         2408         3431         1487 
TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 
        3076         1420         1727         1835         2583         2741 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 
        1732         1605         1203         3668         2414         3117 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 
        1459         2931         2722         1865         2963          992 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 
        1092           51          374          648          952          358 
TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 
         315          417          656          507          291          175 
TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 
          38           16          141           11            7          511 
TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 
         826          838          762          750          523          777 
TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 
         788          700          636          722           36          822 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 
          26          737          522          505          194          434 
TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G 
          15         1046          435          830          519           53 
TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4158 TCGA-BP-4160 
         256          150           66          110         3377         2881 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4167 TCGA-BP-4169 
        2746         3074         2839         3037         2718          701 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 
        1893         1879         1955         1670         2964         1625 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4338 
         845         1888         1133          645          461         2859 
TCGA-BP-4344 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 
        1666         1367          372          374         2208         2372 
TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4774 
        2361          182         2184         1462         1876         1885 
TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 
        1843          411         1731         2080          354         1854 
TCGA-BP-4789 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 
        1489          620         1107         1124          204         1459 
TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
         211         2660         2172         1935         1785         1834 
TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
        1862         1871         1746          433         1487         1502 
TCGA-BP-4973 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4982 TCGA-BP-4983 
        1384         1433         1632          454         1014         1413 
TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 
         785         1124          118         1413          501          177 
TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
        1371          932         1266          563         1177         1126 
TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 
         840         1140         1071          193         2412         2257 
TCGA-BP-5175 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 
         932          293         2263         1495         1165         1291 
TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 
        1133          693          406          822         1011          967 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5199 TCGA-BP-5201 
         714          408          749         1018         1355          951 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4636 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4642 
          29         1820         1924         2308         1998         1628 
TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4872 TCGA-CJ-4874 
        1793          646         2554         1498         1435         2283 
TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 
        2353         1955         2186         2014         1883         1759 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 
        2125         1952         1946         2085         1521          750 
TCGA-CJ-4894 TCGA-CJ-4899 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 
         841         1528         1450         1520         1560         1792 
TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-5675 TCGA-CJ-5681 
        1496         1531         1657         1373         2430          552 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6031 TCGA-CJ-6032 
        1889         2231         2038         1855         1906         2548 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 
        2799         2489         2609         2226         2017         2378 
TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4858 
        3222         2552         3146          774           18         1943 
TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-5451 TCGA-CZ-5452 
        1787         1843         1928         2830         1929         1789 
TCGA-CZ-5453 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 
          25         1732         1683          662         1446          685 
TCGA-CZ-5468 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 
          59          386         2439         1997          373          435 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 
         693         1905         1329         1398         1470          370 
TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5906 
         355         1130          723         1729          551          206 
TCGA-EU-5907 TCGA-GK-A6C7 
         127           61 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 7                  3 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              2575               3668 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            1400.5             1252.0 
[1] "7.0 - 2575.0 (1400.5)" "3.0 - 3668.0 (1252.0)"
[1] "hr=" "1.6"
D34V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  19P GAIN MUTATED        15        7        14       15
  19P GAIN WILD-TYPE     229       49       112       64
D34V3, multiclass
           clus
vv          19P GAIN MUTATED 19P GAIN WILD-TYPE
  STAGE I                 15                229
  STAGE II                 7                 49
  STAGE III               14                112
  STAGE IV                15                 64
[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"
                    vv
clus                  T1  T2  T3  T4
  19P GAIN MUTATED    16   7  26   2
  19P GAIN WILD-TYPE 234  60 151   9
D34V4, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  T1               16                234
  T2                7                 60
  T3               26                151
  T4                2                  9
[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"
D34V5, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    22   3
  19P GAIN WILD-TYPE 208  15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     22    3
  19P GAIN WILD-TYPE  208   15
   clus
vv  19P GAIN MUTATED 19P GAIN WILD-TYPE
  0               22                208
  1                3                 15
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  19P GAIN MUTATED    36  15   0
  19P GAIN WILD-TYPE 381  63   9
D34V6, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  M0               36                381
  M1               15                 63
  MX                0                  9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V7, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    14  37
  19P GAIN WILD-TYPE 164 290
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     14   37
  19P GAIN WILD-TYPE  164  290
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE               14                164
  MALE                 37                290
[1] 2 2
[1] FALSE
D34V8, continuous
D34V9, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19P GAIN MUTATED       0                         1    50
  19P GAIN WILD-TYPE     8                        32   407
D34V10, multiclass
                           clus
vv                          19P GAIN MUTATED 19P GAIN WILD-TYPE
  ASIAN                                    0                  8
  BLACK OR AFRICAN AMERICAN                1                 32
  WHITE                                   50                407
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V11, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     3  33
  19P GAIN WILD-TYPE  21 297
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      3   33
  19P GAIN WILD-TYPE   21  297
                        clus
vv                       19P GAIN MUTATED 19P GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                 21
  NOT HISPANIC OR LATINO               33                297
[1] 2 2
[1] FALSE

Clustering(35) Variable = 19Q GAIN MUTATION ANALYSIS
D35V1, survival
                    sevent
clus2                  0   1
  19Q GAIN MUTATED    36   4
  19Q GAIN WILD-TYPE 302  22
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                40                324 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 4                 22 
$`19Q GAIN MUTATED`
TCGA-A3-3325 TCGA-A3-3336 TCGA-A3-3374 TCGA-A3-3382 TCGA-AK-3433 TCGA-AK-3436 
         751         1043         1314          574         2192         2044 
TCGA-AK-3440 TCGA-AK-3453 TCGA-B0-4699 TCGA-B0-4710 TCGA-B4-5832 TCGA-B4-5838 
        1745         1397          110           96            7          166 
TCGA-BP-4166 TCGA-BP-4351 TCGA-BP-4768 TCGA-BP-4967 TCGA-BP-4969 TCGA-BP-4994 
          13          970          400          205         1794         1308 
TCGA-BP-5185 TCGA-BP-5198 TCGA-BP-5200 TCGA-CJ-4635 TCGA-CJ-4871 TCGA-CJ-4873 
        1132          603         1063         1416         2423         2259 
TCGA-CJ-4897 TCGA-CJ-4907 TCGA-CJ-5671 TCGA-CJ-5676 TCGA-CJ-5682 TCGA-CW-5591 
        1808         1499         1943         2575         1883         2271 
TCGA-CZ-4854 TCGA-CZ-4866 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5460 TCGA-CZ-5461 
        1404         1868         1712         1683         1430          330 
TCGA-CZ-5464 TCGA-CZ-5469 TCGA-CZ-5984 TCGA-EU-5905 
        1740          946         2067          119 

$`19Q GAIN WILD-TYPE`
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 
        1120         1436           16          735         1493         1491 
TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3326 
        1130         1508         1478         1106         1186         1137 
TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3343 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 
        1485          665          945         1610         1385          910 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
        2688         1307         2504         1559          319          873 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 
        2270         2274          735         1621         1070          630 
TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A8CQ TCGA-AK-3425 
         567          861         1993          617            3         3343 
TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 
        2566         2223         2017          480         1853         2087 
TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 
        1423         1471         1280         1217         1779         1481 
TCGA-AK-3454 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 
         874         1143         1168          951          853          369 
TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4706 TCGA-B0-4718 TCGA-B0-4813 TCGA-B0-4819 
        1238           43           26          616           18          183 
TCGA-B0-5097 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 
         665          911         1092          359          797          657 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
         535           59          493          554          652         1132 
TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 
         449         2408         3431         1487         3076         1420 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
        1727         1835         2583         2741         1732         1605 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
        1203         3668         2414         3117         1459         2931 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
        2722         1865         2963          992         1092           51 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 
         374          648          952          358          315          417 
TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5835 
         656          507          291          175           38           16 
TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
         141           11            7          511          826          838 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 
         762          750          523          777          788          700 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
         636          722           36          822           26          737 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
         522          505          194          434           15         1046 
TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I 
         435          830          519           53          256          150 
TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 
          66          110         3377         2881         2746         3074 
TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4173 TCGA-BP-4174 
        2839         3037         2718          701         1893         1879 
TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 
        1955         1670         2964         1625          845         1888 
TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4338 TCGA-BP-4344 TCGA-BP-4347 
        1133          645          461         2859         1666         1367 
TCGA-BP-4349 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 
         372          374         2208         2372         2361          182 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 
        2184         1462         1876         1885         1843          411 
TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4795 
        1731         2080          354         1854         1489          620 
TCGA-BP-4797 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 
        1107         1124          204         1459          211         2660 
TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 
        2172         1935         1785         1834         1862         1871 
TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4975 
        1746          433         1487         1502         1384         1433 
TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4987 
        1632          454         1014         1413          785         1124 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 
         118         1413          501          177         1371          932 
TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 
        1266          563         1177         1126          840         1140 
TCGA-BP-5008 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5177 
        1071          193         2412         2257          932          293 
TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 
        2263         1495         1165         1291         1133          693 
TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 
         406          822         1011          967          714          408 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5199 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 
         749         1018         1355          951           29         1820 
TCGA-CJ-4636 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 
        1924         2308         1998         1628         1793          646 
TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4872 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 
        2554         1498         1435         2283         2353         1955 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 
        2186         2014         1883         1759         2125         1952 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4899 
        1946         2085         1521          750          841         1528 
TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4908 
        1450         1520         1560         1792         1496         1531 
TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-5675 TCGA-CJ-5681 TCGA-CJ-5683 TCGA-CJ-5684 
        1657         1373         2430          552         1889         2231 
TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CW-5581 TCGA-CW-5583 
        2038         1855         1906         2548         2799         2489 
TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-6088 TCGA-CW-6090 
        2609         2226         2017         2378         3222         2552 
TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4862 
        3146          774           18         1943         1787         1843 
TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5458 
        1928         2830         1929         1789           25         1732 
TCGA-CZ-5459 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5470 
        1683          662         1446          685           59          386 
TCGA-CZ-5982 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
        2439         1997          373          435          693         1905 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 
        1329         1398         1470          370          355         1130 
TCGA-DV-5574 TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5906 TCGA-EU-5907 TCGA-GK-A6C7 
         723         1729          551          206          127           61 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 7                  3 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              2575               3668 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            1400.5             1252.0 
[1] "7.0 - 2575.0 (1400.5)" "3.0 - 3668.0 (1252.0)"
[1] "hr=" "1.5"
D35V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  19Q GAIN MUTATED        16        7        17       17
  19Q GAIN WILD-TYPE     228       49       109       62
D35V3, multiclass
           clus
vv          19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  STAGE I                 16                228
  STAGE II                 7                 49
  STAGE III               17                109
  STAGE IV                17                 62
[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"
                    vv
clus                  T1  T2  T3  T4
  19Q GAIN MUTATED    17   9  29   2
  19Q GAIN WILD-TYPE 233  58 148   9
D35V4, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  T1               17                233
  T2                9                 58
  T3               29                148
  T4                2                  9
[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"
D35V5, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    25   3
  19Q GAIN WILD-TYPE 205  15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     25    3
  19Q GAIN WILD-TYPE  205   15
   clus
vv  19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  0               25                205
  1                3                 15
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  19Q GAIN MUTATED    40  17   0
  19Q GAIN WILD-TYPE 377  61   9
D35V6, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  M0               40                377
  M1               17                 61
  MX                0                  9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V7, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    16  41
  19Q GAIN WILD-TYPE 162 286
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     16   41
  19Q GAIN WILD-TYPE  162  286
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE               16                162
  MALE                 41                286
[1] 2 2
[1] FALSE
D35V8, continuous
D35V9, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19Q GAIN MUTATED       1                         1    55
  19Q GAIN WILD-TYPE     7                        32   402
D35V10, multiclass
                           clus
vv                          19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  ASIAN                                    1                  7
  BLACK OR AFRICAN AMERICAN                1                 32
  WHITE                                   55                402
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V11, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     3  38
  19Q GAIN WILD-TYPE  21 292
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      3   38
  19Q GAIN WILD-TYPE   21  292
                        clus
vv                       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                 21
  NOT HISPANIC OR LATINO               38                292
[1] 2 2
[1] FALSE

Clustering(36) Variable = 20P GAIN MUTATION ANALYSIS
D36V1, survival
                    sevent
clus2                  0   1
  20P GAIN MUTATED    69   8
  20P GAIN WILD-TYPE 269  18
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                77                287 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 8                 18 
$`20P GAIN MUTATED`
TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3325 TCGA-A3-3358 TCGA-A3-3372 
          16          735         1493          751         1307          735 
TCGA-A3-3374 TCGA-A3-3382 TCGA-A3-3385 TCGA-AK-3427 TCGA-AK-3429 TCGA-AK-3433 
        1314          574         1993         2566         2017         2192 
TCGA-AK-3440 TCGA-AK-3445 TCGA-AK-3453 TCGA-B0-4699 TCGA-B0-4819 TCGA-B0-5113 
        1745         1280         1397          110          183          359 
TCGA-B0-5116 TCGA-B4-5832 TCGA-B4-5838 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 
         657            7          166          777          788          700 
TCGA-B8-5158 TCGA-B8-5163 TCGA-B8-5551 TCGA-B8-A54I TCGA-BP-4166 TCGA-BP-4167 
         636          822           15          150           13         2718 
TCGA-BP-4176 TCGA-BP-4338 TCGA-BP-4351 TCGA-BP-4761 TCGA-BP-4768 TCGA-BP-4781 
        1955         2859          970          182          400         2080 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4967 TCGA-BP-4969 TCGA-BP-4983 
         204         1459         2172          205         1794         1413 
TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-5175 TCGA-BP-5185 TCGA-BP-5191 TCGA-BP-5198 
         501         1308          932         1132          967          603 
TCGA-BP-5200 TCGA-CJ-4635 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4875 
        1063         1416         2423         1435         2259         2353 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4897 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 
        2014         1883         1808         1450         1520         1560 
TCGA-CJ-4907 TCGA-CJ-5671 TCGA-CJ-5676 TCGA-CJ-5682 TCGA-CW-5588 TCGA-CW-5591 
        1499         1943         2575         1883         2017         2271 
TCGA-CZ-4854 TCGA-CZ-4858 TCGA-CZ-4866 TCGA-CZ-5456 TCGA-CZ-5460 TCGA-CZ-5461 
        1404         1943         1868         1712         1430          330 
TCGA-CZ-5464 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5984 TCGA-EU-5905 
        1740           59          946         2067          119 

$`20P GAIN WILD-TYPE`
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 
        1120         1436         1491         1130         1508         1478 
TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 
        1106         1186         1137         1485          665         1043 
TCGA-A3-3343 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3359 
         945         1610         1385          910         2688         2504 
TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 
        1559          319          873         2270         2274         1621 
TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3387 TCGA-A3-A8CQ 
        1070          630          567          861          617            3 
TCGA-AK-3425 TCGA-AK-3428 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 
        3343         2223          480         1853         2087         2044 
TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 
        1423         1471         1217         1779         1481          874 
TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 
        1143         1168          951          853          369         1238 
TCGA-AS-3778 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4718 TCGA-B0-4813 TCGA-B0-5097 
          43           26           96          616           18          665 
TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5115 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 
         911         1092          797          535           59          493 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 
         554          652         1132          449         2408         3431 
TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 
        1487         3076         1420         1727         1835         2583 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
        2741         1732         1605         1203         3668         2414 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 
        3117         1459         2931         2722         1865         2963 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 
         992         1092           51          374          648          952 
TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 
         358          315          417          656          507          291 
TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 
         175           38           16          141           11            7 
TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 
         511          826          838          762          750          523 
TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
         722           36           26          737          522          505 
TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54F 
         194          434         1046          435          830          519 
TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4158 TCGA-BP-4160 
          53          256           66          110         3377         2881 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4169 TCGA-BP-4173 
        2746         3074         2839         3037          701         1893 
TCGA-BP-4174 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 
        1879         1670         2964         1625          845         1888 
TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4344 TCGA-BP-4347 TCGA-BP-4349 
        1133          645          461         1666         1367          372 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4765 TCGA-BP-4766 
         374         2208         2372         2361         2184         1462 
TCGA-BP-4769 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4782 
        1876         1885         1843          411         1731          354 
TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4801 TCGA-BP-4807 
        1854         1489          620         1107         1124          211 
TCGA-BP-4959 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 
        2660         1935         1785         1834         1862         1871 
TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4975 
        1746          433         1487         1502         1384         1433 
TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4982 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4989 
        1632          454         1014          785         1124          118 
TCGA-BP-4991 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 
        1413          177         1371          932         1266          563 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5169 
        1177         1126          840         1140         1071          193 
TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 
        2412         2257          293         2263         1495         1165 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 
        1291         1133          693          406          822         1011 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5199 TCGA-BP-5201 
         714          408          749         1018         1355          951 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4636 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4642 
          29         1820         1924         2308         1998         1628 
TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4874 TCGA-CJ-4876 
        1793          646         2554         1498         2283         1955 
TCGA-CJ-4878 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4889 TCGA-CJ-4890 
        2186         1759         2125         1952         1946         2085 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4899 TCGA-CJ-4904 TCGA-CJ-4905 
        1521          750          841         1528         1792         1496 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-5675 TCGA-CJ-5681 TCGA-CJ-5683 
        1531         1657         1373         2430          552         1889 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CW-5581 
        2231         2038         1855         1906         2548         2799 
TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-6088 TCGA-CW-6090 
        2489         2609         2226         2378         3222         2552 
TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-4863 
        3146          774           18         1787         1843         1928 
TCGA-CZ-4864 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5457 TCGA-CZ-5458 
        2830         1929         1789           25         1683         1732 
TCGA-CZ-5459 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5470 TCGA-CZ-5982 
        1683          662         1446          685          386         2439 
TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 
        1997          373          435          693         1905         1329 
TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 
        1398         1470          370          355         1130          723 
TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5906 TCGA-EU-5907 TCGA-GK-A6C7 
        1729          551          206          127           61 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 7                  3 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              2859               3668 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              1397               1217 
[1] "7.0 - 2859.0 (1397.0)" "3.0 - 3668.0 (1217.0)"
[1] "hr=" "1.7"
D36V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  20P GAIN MUTATED        33       12        39       26
  20P GAIN WILD-TYPE     211       44        87       53
D36V3, multiclass
           clus
vv          20P GAIN MUTATED 20P GAIN WILD-TYPE
  STAGE I                 33                211
  STAGE II                12                 44
  STAGE III               39                 87
  STAGE IV                26                 53
[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"
                    vv
clus                  T1  T2  T3  T4
  20P GAIN MUTATED    34  13  57   6
  20P GAIN WILD-TYPE 216  54 120   5
D36V4, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  T1               34                216
  T2               13                 54
  T3               57                120
  T4                6                  5
[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"
D36V5, binary
                    cls
clus                   0   1
  20P GAIN MUTATED    47   5
  20P GAIN WILD-TYPE 183  13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     47    5
  20P GAIN WILD-TYPE  183   13
   clus
vv  20P GAIN MUTATED 20P GAIN WILD-TYPE
  0               47                183
  1                5                 13
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  20P GAIN MUTATED    83  26   1
  20P GAIN WILD-TYPE 334  52   8
D36V6, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  M0               83                334
  M1               26                 52
  MX                1                  8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V7, binary
                    cls
clus                   0   1
  20P GAIN MUTATED    24  86
  20P GAIN WILD-TYPE 154 241
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     24   86
  20P GAIN WILD-TYPE  154  241
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE               24                154
  MALE                 86                241
[1] 2 2
[1] FALSE
D36V8, continuous
D36V9, continuous
[1] "Remove cluster labels:" "20P GAIN MUTATED"      
clus
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 2                  6 
        TCGA-A3-A8CQ         TCGA-B2-A4SR         TCGA-B8-5164 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-B8-A54F         TCGA-B8-A54G         TCGA-G6-A5PC 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20P GAIN MUTATED       1                         6   103
  20P GAIN WILD-TYPE     7                        27   354
D36V10, multiclass
                           clus
vv                          20P GAIN MUTATED 20P GAIN WILD-TYPE
  ASIAN                                    1                  7
  BLACK OR AFRICAN AMERICAN                6                 27
  WHITE                                  103                354
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V11, binary
                    cls
clus                   0   1
  20P GAIN MUTATED     3  69
  20P GAIN WILD-TYPE  21 261
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      3   69
  20P GAIN WILD-TYPE   21  261
                        clus
vv                       20P GAIN MUTATED 20P GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                 21
  NOT HISPANIC OR LATINO               69                261
[1] 2 2
[1] FALSE

Clustering(37) Variable = 20Q GAIN MUTATION ANALYSIS
D37V1, survival
                    sevent
clus2                  0   1
  20Q GAIN MUTATED    70   9
  20Q GAIN WILD-TYPE 268  17
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                79                285 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 9                 17 
$`20Q GAIN MUTATED`
TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3319 TCGA-A3-3325 TCGA-A3-3347 
          16          735         1493         1130          751         1610 
TCGA-A3-3358 TCGA-A3-3372 TCGA-A3-3374 TCGA-A3-3382 TCGA-A3-3385 TCGA-AK-3427 
        1307          735         1314          574         1993         2566 
TCGA-AK-3429 TCGA-AK-3433 TCGA-AK-3440 TCGA-AK-3445 TCGA-AK-3453 TCGA-B0-4699 
        2017         2192         1745         1280         1397          110 
TCGA-B0-4819 TCGA-B0-5113 TCGA-B0-5116 TCGA-B4-5832 TCGA-B4-5838 TCGA-B8-4620 
         183          359          657            7          166          777 
TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5163 TCGA-B8-5551 TCGA-B8-A54I 
         788          700          636          822           15          150 
TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4176 TCGA-BP-4338 TCGA-BP-4351 TCGA-BP-4761 
          13         2718         1955         2859          970          182 
TCGA-BP-4768 TCGA-BP-4781 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4967 
         400         2080          204         1459         2172          205 
TCGA-BP-4969 TCGA-BP-4983 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-5175 TCGA-BP-5185 
        1794         1413          501         1308          932         1132 
TCGA-BP-5191 TCGA-BP-5198 TCGA-BP-5200 TCGA-CJ-4635 TCGA-CJ-4871 TCGA-CJ-4872 
         967          603         1063         1416         2423         1435 
TCGA-CJ-4873 TCGA-CJ-4875 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4897 TCGA-CJ-4901 
        2259         2353         2014         1883         1808         1450 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4907 TCGA-CJ-5671 TCGA-CJ-5676 TCGA-CJ-5682 
        1520         1560         1499         1943         2575         1883 
TCGA-CW-5588 TCGA-CW-5591 TCGA-CZ-4854 TCGA-CZ-4858 TCGA-CZ-4866 TCGA-CZ-5456 
        2017         2271         1404         1943         1868         1712 
TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5464 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5984 
        1430          330         1740           59          946         2067 
TCGA-EU-5905 
         119 

$`20Q GAIN WILD-TYPE`
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3317 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 
        1120         1436         1491         1508         1478         1106 
TCGA-A3-3324 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 
        1186         1137         1485          665         1043          945 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 
        1385          910         2688         2504         1559          319 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 
         873         2270         2274         1621         1070          630 
TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3387 TCGA-A3-A8CQ TCGA-AK-3425 TCGA-AK-3428 
         567          861          617            3         3343         2223 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3443 TCGA-AK-3444 
         480         1853         2087         2044         1423         1471 
TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3456 TCGA-AK-3458 
        1217         1779         1481          874         1143         1168 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4706 
         951          853          369         1238           43           26 
TCGA-B0-4710 TCGA-B0-4718 TCGA-B0-4813 TCGA-B0-5097 TCGA-B0-5108 TCGA-B0-5110 
          96          616           18          665          911         1092 
TCGA-B0-5115 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
         797          535           59          493          554          652 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 
        1132          449         2408         3431         1487         3076 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 
        1420         1727         1835         2583         2741         1732 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 
        1605         1203         3668         2414         3117         1459 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 
        2931         2722         1865         2963          992         1092 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 
          51          374          648          952          358          315 
TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 
         417          656          507          291          175           38 
TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 
          16          141           11            7          511          826 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-5159 TCGA-B8-5162 
         838          762          750          523          722           36 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 
          26          737          522          505          194          434 
TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H 
        1046          435          830          519           53          256 
TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 
          66          110         3377         2881         2746         3074 
TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4169 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4177 
        2839         3037          701         1893         1879         1670 
TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 
        2964         1625          845         1888         1133          645 
TCGA-BP-4335 TCGA-BP-4344 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4756 TCGA-BP-4758 
         461         1666         1367          372          374         2208 
TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4774 
        2372         2361         2184         1462         1876         1885 
TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4789 
        1843          411         1731          354         1854         1489 
TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4801 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4961 
         620         1107         1124          211         2660         1935 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4968 TCGA-BP-4970 
        1785         1834         1862         1871         1746          433 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 
        1487         1502         1384         1433         1632          454 
TCGA-BP-4982 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4993 
        1014          785         1124          118         1413          177 
TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
        1371          932         1266          563         1177         1126 
TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 
         840         1140         1071          193         2412         2257 
TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
         293         2263         1495         1165         1291         1133 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 
         693          406          822         1011          714          408 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5199 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 
         749         1018         1355          951           29         1820 
TCGA-CJ-4636 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 
        1924         2308         1998         1628         1793          646 
TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4874 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4884 
        2554         1498         2283         1955         2186         1759 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 
        2125         1952         1946         2085         1521          750 
TCGA-CJ-4894 TCGA-CJ-4899 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 
         841         1528         1792         1496         1531         1657 
TCGA-CJ-4916 TCGA-CJ-5675 TCGA-CJ-5681 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 
        1373         2430          552         1889         2231         2038 
TCGA-CJ-6027 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 
        1855         1906         2548         2799         2489         2609 
TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CZ-4853 
        2226         2378         3222         2552         3146          774 
TCGA-CZ-4856 TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-5451 
          18         1787         1843         1928         2830         1929 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5463 
        1789           25         1683         1732         1683          662 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5985 TCGA-CZ-5986 
        1446          685          386         2439         1997          373 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 
         435          693         1905         1329         1398         1470 
TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-EU-5904 
         370          355         1130          723         1729          551 
TCGA-EU-5906 TCGA-EU-5907 TCGA-GK-A6C7 
         206          127           61 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 7                  3 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              2859               3668 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              1397               1217 
[1] "7.0 - 2859.0 (1397.0)" "3.0 - 3668.0 (1217.0)"
[1] "hr=" "2"  
D37V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  20Q GAIN MUTATED        34       12        41       26
  20Q GAIN WILD-TYPE     210       44        85       53
D37V3, multiclass
           clus
vv          20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  STAGE I                 34                210
  STAGE II                12                 44
  STAGE III               41                 85
  STAGE IV                26                 53
[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"
                    vv
clus                  T1  T2  T3  T4
  20Q GAIN MUTATED    36  13  59   5
  20Q GAIN WILD-TYPE 214  54 118   6
D37V4, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  T1               36                214
  T2               13                 54
  T3               59                118
  T4                5                  6
[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"
D37V5, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED    48   6
  20Q GAIN WILD-TYPE 182  12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     48    6
  20Q GAIN WILD-TYPE  182   12
   clus
vv  20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  0               48                182
  1                6                 12
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  20Q GAIN MUTATED    86  26   1
  20Q GAIN WILD-TYPE 331  52   8
D37V6, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  M0               86                331
  M1               26                 52
  MX                1                  8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V7, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED    27  86
  20Q GAIN WILD-TYPE 151 241
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     27   86
  20Q GAIN WILD-TYPE  151  241
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE               27                151
  MALE                 86                241
[1] 2 2
[1] FALSE
D37V8, continuous
D37V9, continuous
[1] "Remove cluster labels:" "20Q GAIN MUTATED"      
clus
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 2                  6 
        TCGA-A3-A8CQ         TCGA-B2-A4SR         TCGA-B8-5164 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-B8-A54F         TCGA-B8-A54G         TCGA-G6-A5PC 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20Q GAIN MUTATED       2                         6   105
  20Q GAIN WILD-TYPE     6                        27   352
D37V10, multiclass
                           clus
vv                          20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  ASIAN                                    2                  6
  BLACK OR AFRICAN AMERICAN                6                 27
  WHITE                                  105                352
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V11, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED     3  71
  20Q GAIN WILD-TYPE  21 259
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      3   71
  20Q GAIN WILD-TYPE   21  259
                        clus
vv                       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                 21
  NOT HISPANIC OR LATINO               71                259
[1] 2 2
[1] FALSE

Clustering(38) Variable = 21Q GAIN MUTATION ANALYSIS
D38V1, survival
                    sevent
clus2                  0   1
  21Q GAIN MUTATED    31   4
  21Q GAIN WILD-TYPE 307  22
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                35                329 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 4                 22 
$`21Q GAIN MUTATED`
TCGA-A3-3316 TCGA-A3-3322 TCGA-A3-3372 TCGA-A3-3382 TCGA-AK-3429 TCGA-AK-3445 
        1493         1478          735          574         2017         1280 
TCGA-B0-5113 TCGA-B0-5116 TCGA-B0-5696 TCGA-B4-5832 TCGA-B8-5163 TCGA-B8-A54F 
         359          657         1727            7          822          519 
TCGA-BP-4167 TCGA-BP-4176 TCGA-BP-4338 TCGA-BP-4351 TCGA-BP-4781 TCGA-BP-4969 
        2718         1955         2859          970         2080         1794 
TCGA-BP-4995 TCGA-BP-5185 TCGA-BP-5191 TCGA-CJ-4635 TCGA-CJ-4873 TCGA-CJ-5676 
        1371         1132          967         1416         2259         2575 
TCGA-CJ-6027 TCGA-CW-5591 TCGA-CZ-4854 TCGA-CZ-4866 TCGA-CZ-5460 TCGA-CZ-5461 
        1855         2271         1404         1868         1430          330 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-DV-5568 TCGA-DV-5573 TCGA-EU-5905 
          59          946          370         1130          119 

$`21Q GAIN WILD-TYPE`
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3319 
        1120         1436           16          735         1491         1130 
TCGA-A3-3320 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 
        1508         1106         1186          751         1137         1485 
TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 
         665         1043          945         1610         1385          910 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
        2688         1307         2504         1559          319          873 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 
        2270         2274         1621         1314         1070          630 
TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A8CQ TCGA-AK-3425 
         567          861         1993          617            3         3343 
TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 
        2566         2223          480         1853         2192         2087 
TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3447 TCGA-AK-3450 
        2044         1745         1423         1471         1217         1779 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
        1481         1397          874         1143         1168          951 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4699 TCGA-B0-4706 
         853          369         1238           43          110           26 
TCGA-B0-4710 TCGA-B0-4718 TCGA-B0-4813 TCGA-B0-4819 TCGA-B0-5097 TCGA-B0-5108 
          96          616           18          183          665          911 
TCGA-B0-5110 TCGA-B0-5115 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
        1092          797          535           59          493          554 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 
         652         1132          449         2408         3431         1487 
TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 
        3076         1420         1835         2583         2741         1732 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 
        1605         1203         3668         2414         3117         1459 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 
        2931         2722         1865         2963          992         1092 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 
          51          374          648          952          358          315 
TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 
         417          656          507          291          175           38 
TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 
          16          141          166           11            7          511 
TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 
         826          838          762          750          523          777 
TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5164 
         788          700          636          722           36           26 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 
         737          522          505          194          434           15 
TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I 
        1046          435          830           53          256          150 
TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 
          66          110         3377         2881         2746         3074 
TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4169 TCGA-BP-4173 TCGA-BP-4174 
        2839         3037           13          701         1893         1879 
TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 
        1670         2964         1625          845         1888         1133 
TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4344 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4756 
         645          461         1666         1367          372          374 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4765 TCGA-BP-4766 
        2208         2372         2361          182         2184         1462 
TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 
         400         1876         1885         1843          411         1731 
TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4801 
         354         1854         1489          620         1107         1124 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 
         204         1459          211         2660         2172         1935 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 
        1785         1834         1862         1871          205         1746 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4975 TCGA-BP-4976 
         433         1487         1502         1384         1433         1632 
TCGA-BP-4977 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4989 
         454         1014         1413          785         1124          118 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-4999 
        1413          501          177         1308          932         1266 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 
         563         1177         1126          840         1140         1071 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5177 TCGA-BP-5180 
         193         2412         2257          932          293         2263 
TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5187 
        1495         1165         1291         1133          693          406 
TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
         822         1011          714          408          749         1018 
TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 
         603         1355         1063          951           29         1820 
TCGA-CJ-4636 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 
        1924         2308         1998         1628         1793          646 
TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4874 TCGA-CJ-4875 
        2554         1498         2423         1435         2283         2353 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
        1955         2186         2014         1883         1759         2125 
TCGA-CJ-4886 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 
        1952         1946         2085         1521          750          841 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 
        1808         1528         1450         1520         1560         1792 
TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-5671 
        1496         1499         1531         1657         1373         1943 
TCGA-CJ-5675 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 
        2430          552         1883         1889         2231         2038 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5587 
        1906         2548         2799         2489         2609         2226 
TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CZ-4853 
        2017         2378         3222         2552         3146          774 
TCGA-CZ-4856 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 
          18         1943         1787         1843         1928         2830 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 
        1929         1789           25         1712         1683         1732 
TCGA-CZ-5459 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5470 
        1683          662         1740         1446          685          386 
TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 
        2439         2067         1997          373          435          693 
TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5569 TCGA-DV-5574 
        1905         1329         1398         1470          355          723 
TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5906 TCGA-EU-5907 TCGA-GK-A6C7 
        1729          551          206          127           61 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 7                  3 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              2859               3668 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              1371               1291 
[1] "7.0 - 2859.0 (1371.0)" "3.0 - 3668.0 (1291.0)"
[1] "hr=" "1.7"
D38V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  21Q GAIN MUTATED        20        3        17        9
  21Q GAIN WILD-TYPE     224       53       109       70
D38V3, multiclass
           clus
vv          21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  STAGE I                 20                224
  STAGE II                 3                 53
  STAGE III               17                109
  STAGE IV                 9                 70
[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"
                    vv
clus                  T1  T2  T3  T4
  21Q GAIN MUTATED    21   3  24   1
  21Q GAIN WILD-TYPE 229  64 153  10
D38V4, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  T1               21                229
  T2                3                 64
  T3               24                153
  T4                1                 10
[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"
D38V5, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    20   1
  21Q GAIN WILD-TYPE 210  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     20    1
  21Q GAIN WILD-TYPE  210   17
   clus
vv  21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  0               20                210
  1                1                 17
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  21Q GAIN MUTATED    39   9   1
  21Q GAIN WILD-TYPE 378  69   8
D38V6, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  M0               39                378
  M1                9                 69
  MX                1                  8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V7, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    15  34
  21Q GAIN WILD-TYPE 163 293
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     15   34
  21Q GAIN WILD-TYPE  163  293
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE               15                163
  MALE                 34                293
[1] 2 2
[1] FALSE
D38V8, continuous
D38V9, continuous
[1] "Remove cluster labels:" "21Q GAIN MUTATED"      
clus
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 1                  7 
        TCGA-A3-A8CQ         TCGA-B2-A4SR         TCGA-B8-4621 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-B8-5158         TCGA-B8-5164         TCGA-B8-A54G 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G6-A5PC 
"21Q GAIN WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  21Q GAIN MUTATED       0                         1    48
  21Q GAIN WILD-TYPE     8                        32   409
D38V10, multiclass
                           clus
vv                          21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  ASIAN                                    0                  8
  BLACK OR AFRICAN AMERICAN                1                 32
  WHITE                                   48                409
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V11, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     3  30
  21Q GAIN WILD-TYPE  21 300
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      3   30
  21Q GAIN WILD-TYPE   21  300
                        clus
vv                       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                 21
  NOT HISPANIC OR LATINO               30                300
[1] 2 2
[1] FALSE

Clustering(39) Variable = 22Q GAIN MUTATION ANALYSIS
D39V1, survival
                    sevent
clus2                  0   1
  22Q GAIN MUTATED    29   1
  22Q GAIN WILD-TYPE 309  25
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                30                334 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 1                 25 
$`22Q GAIN MUTATED`
TCGA-A3-3306 TCGA-A3-3319 TCGA-A3-3374 TCGA-A3-3382 TCGA-AK-3433 TCGA-AK-3440 
        1120         1130         1314          574         2192         1745 
TCGA-B0-4699 TCGA-B0-5113 TCGA-B0-5400 TCGA-B4-5832 TCGA-B4-5838 TCGA-BP-4166 
         110          359         1132            7          166           13 
TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4351 TCGA-BP-4765 TCGA-BP-4781 TCGA-BP-4975 
        1879         1955          970         2184         2080         1433 
TCGA-BP-4994 TCGA-BP-5185 TCGA-BP-5198 TCGA-BP-5200 TCGA-CJ-4903 TCGA-CJ-4907 
        1308         1132          603         1063         1560         1499 
TCGA-CJ-5671 TCGA-CJ-5676 TCGA-CJ-5682 TCGA-CW-5588 TCGA-CW-5591 TCGA-CZ-5984 
        1943         2575         1883         2017         2271         2067 

$`22Q GAIN WILD-TYPE`
TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3320 
        1436           16          735         1493         1491         1508 
TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 
        1478         1106         1186          751         1137         1485 
TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 
         665         1043          945         1610         1385          910 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
        2688         1307         2504         1559          319          873 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 
        2270         2274          735         1621         1070          630 
TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A8CQ TCGA-AK-3425 
         567          861         1993          617            3         3343 
TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 
        2566         2223         2017          480         1853         2087 
TCGA-AK-3436 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 
        2044         1423         1471         1280         1217         1779 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
        1481         1397          874         1143         1168          951 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4706 TCGA-B0-4710 
         853          369         1238           43           26           96 
TCGA-B0-4718 TCGA-B0-4813 TCGA-B0-4819 TCGA-B0-5097 TCGA-B0-5108 TCGA-B0-5110 
         616           18          183          665          911         1092 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
         797          657          535           59          493          554 
TCGA-B0-5399 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 
         652          449         2408         3431         1487         3076 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 
        1420         1727         1835         2583         2741         1732 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 
        1605         1203         3668         2414         3117         1459 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 
        2931         2722         1865         2963          992         1092 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 
          51          374          648          952          358          315 
TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 
         417          656          507          291          175           38 
TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 
          16          141           11            7          511          826 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 
         838          762          750          523          777          788 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 
         700          636          722           36          822           26 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 
         737          522          505          194          434           15 
TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H 
        1046          435          830          519           53          256 
TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4161 
         150           66          110         3377         2881         2746 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4173 
        3074         2839         3037         2718          701         1893 
TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 
        1670         2964         1625          845         1888         1133 
TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4338 TCGA-BP-4344 TCGA-BP-4347 TCGA-BP-4349 
         645          461         2859         1666         1367          372 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4766 
         374         2208         2372         2361          182         1462 
TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 
         400         1876         1885         1843          411         1731 
TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4801 
         354         1854         1489          620         1107         1124 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 
         204         1459          211         2660         2172         1935 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 
        1785         1834         1862         1871          205         1746 
TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4976 
        1794          433         1487         1502         1384         1632 
TCGA-BP-4977 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4989 
         454         1014         1413          785         1124          118 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 
        1413          501          177         1371          932         1266 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 
         563         1177         1126          840         1140         1071 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5177 TCGA-BP-5180 
         193         2412         2257          932          293         2263 
TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5187 
        1495         1165         1291         1133          693          406 
TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
         822         1011          967          714          408          749 
TCGA-BP-5196 TCGA-BP-5199 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 
        1018         1355          951           29         1820         1416 
TCGA-CJ-4636 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 
        1924         2308         1998         1628         1793          646 
TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 
        2554         1498         2423         1435         2259         2283 
TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 
        2353         1955         2186         2014         1883         1759 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 
        2125         1952         1946         2085         1521          750 
TCGA-CJ-4894 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4904 
         841         1808         1528         1450         1520         1792 
TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-5675 TCGA-CJ-5681 
        1496         1531         1657         1373         2430          552 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6031 TCGA-CJ-6032 
        1889         2231         2038         1855         1906         2548 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-6088 
        2799         2489         2609         2226         2378         3222 
TCGA-CW-6090 TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4858 
        2552         3146          774         1404           18         1943 
TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 
        1787         1843         1928         2830         1868         1929 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 
        1789           25         1712         1683         1732         1683 
TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 
        1430          330          662         1740         1446          685 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5985 TCGA-CZ-5986 
          59          946          386         2439         1997          373 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 
         435          693         1905         1329         1398         1470 
TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-EU-5904 
         370          355         1130          723         1729          551 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-GK-A6C7 
         119          206          127           61 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 7                  3 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              2575               3668 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
            1373.5             1273.0 
[1] "7.0 - 2575.0 (1373.5)" "3.0 - 3668.0 (1273.0)"
[1] "hr=" "2.3"
D39V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  22Q GAIN MUTATED        17        4        12        7
  22Q GAIN WILD-TYPE     227       52       114       72
D39V3, multiclass
           clus
vv          22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  STAGE I                 17                227
  STAGE II                 4                 52
  STAGE III               12                114
  STAGE IV                 7                 72
[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"
                    vv
clus                  T1  T2  T3  T4
  22Q GAIN MUTATED    17   4  16   3
  22Q GAIN WILD-TYPE 233  63 161   8
D39V4, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  T1               17                233
  T2                4                 63
  T3               16                161
  T4                3                  8
[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"
D39V5, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    18   1
  22Q GAIN WILD-TYPE 212  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     18    1
  22Q GAIN WILD-TYPE  212   17
   clus
vv  22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  0               18                212
  1                1                 17
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  22Q GAIN MUTATED    33   7   0
  22Q GAIN WILD-TYPE 384  71   9
D39V6, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  M0               33                384
  M1                7                 71
  MX                0                  9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V7, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    11  29
  22Q GAIN WILD-TYPE 167 298
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     11   29
  22Q GAIN WILD-TYPE  167  298
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE               11                167
  MALE                 29                298
[1] 2 2
[1] FALSE
D39V8, continuous
D39V9, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  22Q GAIN MUTATED       0                         1    39
  22Q GAIN WILD-TYPE     8                        32   418
D39V10, multiclass
                           clus
vv                          22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  ASIAN                                    0                  8
  BLACK OR AFRICAN AMERICAN                1                 32
  WHITE                                   39                418
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V11, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED     1  21
  22Q GAIN WILD-TYPE  23 309
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      1   21
  22Q GAIN WILD-TYPE   23  309
                        clus
vv                       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 23
  NOT HISPANIC OR LATINO               21                309
[1] 2 2
[1] FALSE

Clustering(40) Variable = XQ GAIN MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                 0   1
  XQ GAIN MUTATED    18   3
  XQ GAIN WILD-TYPE 320  23
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               21               343 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                3                23 
$`XQ GAIN MUTATED`
TCGA-A3-3383 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3436 TCGA-AK-3453 TCGA-B8-A54I 
         861         2223         2017         2044         1397          150 
TCGA-BP-4162 TCGA-BP-4174 TCGA-BP-4338 TCGA-BP-4969 TCGA-BP-4989 TCGA-CJ-4885 
        3074         1879         2859         1794          118         2125 
TCGA-CJ-4899 TCGA-CJ-5681 TCGA-CW-5591 TCGA-CZ-4854 TCGA-CZ-5456 TCGA-CZ-5458 
        1528          552         2271         1404         1712         1732 
TCGA-CZ-5464 TCGA-CZ-5468 TCGA-EU-5905 
        1740           59          119 

$`XQ GAIN WILD-TYPE`
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 
        1120         1436           16          735         1493         1491 
TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 
        1130         1508         1478         1106         1186          751 
TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3347 
        1137         1485          665         1043          945         1610 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 
        1385          910         2688         1307         2504         1559 
TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 
         319          873         2270         2274          735         1621 
TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3385 
        1314         1070          630          567          574         1993 
TCGA-A3-3387 TCGA-A3-A8CQ TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3430 TCGA-AK-3431 
         617            3         3343         2566          480         1853 
TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 
        2192         2087         1745         1423         1471         1280 
TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3456 TCGA-AK-3458 
        1217         1779         1481          874         1143         1168 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4699 
         951          853          369         1238           43          110 
TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4718 TCGA-B0-4813 TCGA-B0-4819 TCGA-B0-5097 
          26           96          616           18          183          665 
TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 
         911         1092          359          797          657          535 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
          59          493          554          652         1132          449 
TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5696 
        2408         3431         1487         3076         1420         1727 
TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
        1835         2583         2741         1732         1605         1203 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
        3668         2414         3117         1459         2931         2722 
TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
        1865         2963          992         1092           51          374 
TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 
         648          952          358          315          417          656 
TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 
         507          291          175            7           38           16 
TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 
         141          166           11            7          511          826 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 
         838          762          750          523          777          788 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 
         700          636          722           36          822           26 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 
         737          522          505          194          434           15 
TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H 
        1046          435          830          519           53          256 
TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4163 
          66          110         3377         2881         2746         2839 
TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4173 TCGA-BP-4176 
        3037           13         2718          701         1893         1955 
TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 
        1670         2964         1625          845         1888         1133 
TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4344 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 
         645          461         1666         1367          372          970 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4765 
         374         2208         2372         2361          182         2184 
TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 
        1462          400         1876         1885         1843          411 
TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4795 
        1731         2080          354         1854         1489          620 
TCGA-BP-4797 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 
        1107         1124          204         1459          211         2660 
TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 
        2172         1935         1785         1834         1862         1871 
TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 
         205         1746          433         1487         1502         1384 
TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4986 
        1433         1632          454         1014         1413          785 
TCGA-BP-4987 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 
        1124         1413          501          177         1308         1371 
TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 
         932         1266          563         1177         1126          840 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5175 
        1140         1071          193         2412         2257          932 
TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
         293         2263         1495         1165         1291         1133 
TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 
        1132          693          406          822         1011          967 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 
         714          408          749         1018          603         1355 
TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 
        1063          951           29         1820         1416         1924 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 
        2308         1998         1628         1793          646         2554 
TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 
        1498         2423         1435         2259         2283         2353 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4886 
        1955         2186         2014         1883         1759         1952 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4897 
        1946         2085         1521          750          841         1808 
TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 
        1450         1520         1560         1792         1496         1499 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-5671 TCGA-CJ-5675 TCGA-CJ-5676 
        1531         1657         1373         1943         2430         2575 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6031 
        1883         1889         2231         2038         1855         1906 
TCGA-CJ-6032 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 
        2548         2799         2489         2609         2226         2017 
TCGA-CW-5589 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4856 
        2378         3222         2552         3146          774           18 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 
        1943         1787         1843         1928         2830         1868 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5457 TCGA-CZ-5459 TCGA-CZ-5460 
        1929         1789           25         1683         1683         1430 
TCGA-CZ-5461 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5469 TCGA-CZ-5470 
         330          662         1446          685          946          386 
TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 
        2439         2067         1997          373          435          693 
TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 
        1905         1329         1398         1470          370          355 
TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5906 TCGA-EU-5907 
        1130          723         1729          551          206          127 
TCGA-GK-A6C7 
          61 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               59                 3 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             3074              3668 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             1732              1217 
[1] "59.0 - 3074.0 (1732.0)" "3.0 - 3668.0 (1217.0)" 
[1] "hr=" "1.8"
D40V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  XQ GAIN MUTATED         9        4         7        9
  XQ GAIN WILD-TYPE     235       52       119       70
D40V3, multiclass
           clus
vv          XQ GAIN MUTATED XQ GAIN WILD-TYPE
  STAGE I                 9               235
  STAGE II                4                52
  STAGE III               7               119
  STAGE IV                9                70
[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"
                   vv
clus                 T1  T2  T3  T4
  XQ GAIN MUTATED     9   5  15   0
  XQ GAIN WILD-TYPE 241  62 162  11
D40V4, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  T1               9               241
  T2               5                62
  T3              15               162
  T4               0                11
[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"
D40V5, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    16   1
  XQ GAIN WILD-TYPE 214  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     16    1
  XQ GAIN WILD-TYPE  214   17
   clus
vv  XQ GAIN MUTATED XQ GAIN WILD-TYPE
  0              16               214
  1               1                17
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  XQ GAIN MUTATED    19   9   1
  XQ GAIN WILD-TYPE 398  69   8
D40V6, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  M0              19               398
  M1               9                69
  MX               1                 8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V7, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    11  18
  XQ GAIN WILD-TYPE 167 309
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     11   18
  XQ GAIN WILD-TYPE  167  309
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE              11               167
  MALE                18               309
[1] 2 2
[1] FALSE
D40V8, continuous
D40V9, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XQ GAIN MUTATED       1                         1    27
  XQ GAIN WILD-TYPE     7                        32   430
D40V10, multiclass
                           clus
vv                          XQ GAIN MUTATED XQ GAIN WILD-TYPE
  ASIAN                                   1                 7
  BLACK OR AFRICAN AMERICAN               1                32
  WHITE                                  27               430
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V11, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     0  17
  XQ GAIN WILD-TYPE  24 313
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      0   17
  XQ GAIN WILD-TYPE   24  313
                        clus
vv                       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                24
  NOT HISPANIC OR LATINO              17               313
[1] 2 2
[1] FALSE

Clustering(41) Variable = 1P LOSS MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                 0   1
  1P LOSS MUTATED    35   6
  1P LOSS WILD-TYPE 303  20
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               41               323 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                6                20 
$`1P LOSS MUTATED`
TCGA-A3-3313 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3380 TCGA-AK-3427 TCGA-AK-3433 
         735         1621         1314          567         2566         2192 
TCGA-AK-3440 TCGA-AK-3447 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4699 TCGA-B0-5117 
        1745         1217          369         1238          110          535 
TCGA-B0-5402 TCGA-B0-5703 TCGA-B2-3923 TCGA-B2-4098 TCGA-B4-5835 TCGA-B4-5838 
         449         1203          992           51           16          166 
TCGA-B8-4619 TCGA-B8-5549 TCGA-BP-4176 TCGA-BP-4334 TCGA-BP-4768 TCGA-BP-4775 
         523          194         1955          645          400         1843 
TCGA-BP-4781 TCGA-BP-4968 TCGA-BP-4986 TCGA-BP-4994 TCGA-BP-5004 TCGA-BP-5201 
        2080         1746          785         1308         1126          951 
TCGA-CJ-4640 TCGA-CJ-4876 TCGA-CJ-4894 TCGA-CJ-4897 TCGA-CJ-4901 TCGA-CJ-4907 
        1998         1955          841         1808         1450         1499 
TCGA-CW-5588 TCGA-CZ-4866 TCGA-CZ-5457 TCGA-CZ-5469 TCGA-EU-5907 
        2017         1868         1683          946          127 

$`1P LOSS WILD-TYPE`
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 
        1120         1436           16         1493         1491         1130 
TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 
        1508         1478         1106         1186          751         1137 
TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3347 TCGA-A3-3349 
        1485          665         1043          945         1610         1385 
TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 
         910         2688         1307         2504         1559          319 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3376 TCGA-A3-3378 
         873         2270         2274          735         1070          630 
TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A8CQ TCGA-AK-3425 
         574          861         1993          617            3         3343 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 
        2223         2017          480         1853         2087         2044 
TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 
        1423         1471         1280         1779         1481         1397 
TCGA-AK-3454 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3778 
         874         1143         1168          951          853           43 
TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4718 TCGA-B0-4813 TCGA-B0-4819 TCGA-B0-5097 
          26           96          616           18          183          665 
TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 
         911         1092          359          797          657           59 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5690 TCGA-B0-5691 
         493          554          652         1132         2408         3431 
TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 
        1487         3076         1420         1727         1835         2583 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 
        2741         1732         1605         3668         2414         3117 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3924 
        1459         2931         2722         1865         2963         1092 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 
         374          648          952          358          315          417 
TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 
         656          507          291          175            7           38 
TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
         141           11            7          511          826          838 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 
         762          750          777          788          700          636 
TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
         722           36          822           26          737          522 
TCGA-B8-5546 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D 
         505          434           15         1046          435          830 
TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 
         519           53          256          150           66          110 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 
        3377         2881         2746         3074         2839         3037 
TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4177 
          13         2718          701         1893         1879         1670 
TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4335 
        2964         1625          845         1888         1133          461 
TCGA-BP-4338 TCGA-BP-4344 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4756 
        2859         1666         1367          372          970          374 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4765 TCGA-BP-4766 
        2208         2372         2361          182         2184         1462 
TCGA-BP-4769 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4782 TCGA-BP-4784 
        1876         1885          411         1731          354         1854 
TCGA-BP-4789 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 
        1489          620         1107         1124          204         1459 
TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
         211         2660         2172         1935         1785         1834 
TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 
        1862         1871          205         1794          433         1487 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4982 
        1502         1384         1433         1632          454         1014 
TCGA-BP-4983 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 
        1413         1124          118         1413          501          177 
TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5006 
        1371          932         1266          563         1177          840 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5175 
        1140         1071          193         2412         2257          932 
TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
         293         2263         1495         1165         1291         1133 
TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 
        1132          693          406          822         1011          967 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 
         714          408          749         1018          603         1355 
TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4639 
        1063           29         1820         1416         1924         2308 
TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
        1628         1793          646         2554         1498         2423 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4878 TCGA-CJ-4881 
        1435         2259         2283         2353         2186         2014 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4889 TCGA-CJ-4890 
        1883         1759         2125         1952         1946         2085 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4899 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 
        1521          750         1528         1520         1560         1792 
TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-5671 TCGA-CJ-5675 
        1496         1531         1657         1373         1943         2430 
TCGA-CJ-5676 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 
        2575          552         1883         1889         2231         2038 
TCGA-CJ-6027 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 
        1855         1906         2548         2799         2489         2609 
TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 
        2226         2378         2271         3222         2552         3146 
TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4862 
         774         1404           18         1943         1787         1843 
TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5456 
        1928         2830         1929         1789           25         1712 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5463 TCGA-CZ-5464 
        1732         1683         1430          330          662         1740 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 
        1446          685           59          386         2439         2067 
TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 
        1997          373          435          693         1905         1329 
TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 
        1398         1470          370          355         1130          723 
TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-GK-A6C7 
        1729          551          119          206           61 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               16                 3 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             2566              3668 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             1203              1355 
[1] "16.0 - 2566.0 (1203.0)" "3.0 - 3668.0 (1355.0)" 
[1] "hr=" "2.6"
D41V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  1P LOSS MUTATED        29        8        10        8
  1P LOSS WILD-TYPE     215       48       116       71
D41V3, multiclass
           clus
vv          1P LOSS MUTATED 1P LOSS WILD-TYPE
  STAGE I                29               215
  STAGE II                8                48
  STAGE III              10               116
  STAGE IV                8                71
[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"
                   vv
clus                 T1  T2  T3  T4
  1P LOSS MUTATED    30   9  12   4
  1P LOSS WILD-TYPE 220  58 165   7
D41V4, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  T1              30               220
  T2               9                58
  T3              12               165
  T4               4                 7
[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"
D41V5, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    26   1
  1P LOSS WILD-TYPE 204  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     26    1
  1P LOSS WILD-TYPE  204   17
   clus
vv  1P LOSS MUTATED 1P LOSS WILD-TYPE
  0              26               204
  1               1                17
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  1P LOSS MUTATED    49   6   0
  1P LOSS WILD-TYPE 368  72   9
D41V6, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  M0              49               368
  M1               6                72
  MX               0                 9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V7, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    15  40
  1P LOSS WILD-TYPE 163 287
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     15   40
  1P LOSS WILD-TYPE  163  287
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE              15               163
  MALE                40               287
[1] 2 2
[1] FALSE
D41V8, continuous
D41V9, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1P LOSS MUTATED       1                         6    47
  1P LOSS WILD-TYPE     7                        27   410
D41V10, multiclass
                           clus
vv                          1P LOSS MUTATED 1P LOSS WILD-TYPE
  ASIAN                                   1                 7
  BLACK OR AFRICAN AMERICAN               6                27
  WHITE                                  47               410
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V11, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     5  37
  1P LOSS WILD-TYPE  19 293
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      5   37
  1P LOSS WILD-TYPE   19  293
                        clus
vv                       1P LOSS MUTATED 1P LOSS WILD-TYPE
  HISPANIC OR LATINO                   5                19
  NOT HISPANIC OR LATINO              37               293
[1] 2 2
[1] FALSE

Clustering(42) Variable = 1Q LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                 0   1
  1Q LOSS MUTATED    23   3
  1Q LOSS WILD-TYPE 315  23
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               26               338 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                3                23 
$`1Q LOSS MUTATED`
TCGA-A3-3374 TCGA-A3-3380 TCGA-AK-3427 TCGA-AK-3433 TCGA-AK-3440 TCGA-AK-3465 
        1314          567         2566         2192         1745          369 
TCGA-AS-3777 TCGA-B0-4699 TCGA-B0-5117 TCGA-B2-3923 TCGA-B4-5838 TCGA-B8-4619 
        1238          110          535          992          166          523 
TCGA-B8-5549 TCGA-BP-4334 TCGA-BP-4768 TCGA-BP-4775 TCGA-BP-4968 TCGA-BP-4986 
         194          645          400         1843         1746          785 
TCGA-BP-4994 TCGA-CJ-4897 TCGA-CJ-4901 TCGA-CJ-4907 TCGA-CW-5588 TCGA-CZ-4866 
        1308         1808         1450         1499         2017         1868 
TCGA-CZ-5457 TCGA-CZ-5469 
        1683          946 

$`1Q LOSS WILD-TYPE`
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 
        1120         1436           16          735         1493         1491 
TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 
        1130         1508         1478         1106         1186          751 
TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3347 
        1137         1485          665         1043          945         1610 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 
        1385          910         2688         1307         2504         1559 
TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 
         319          873         2270         2274          735         1621 
TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 
        1070          630          574          861         1993          617 
TCGA-A3-A8CQ TCGA-AK-3425 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 
           3         3343         2223         2017          480         1853 
TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 
        2087         2044         1423         1471         1280         1217 
TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3456 TCGA-AK-3458 
        1779         1481         1397          874         1143         1168 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4718 
         951          853           43           26           96          616 
TCGA-B0-4813 TCGA-B0-4819 TCGA-B0-5097 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 
          18          183          665          911         1092          359 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
         797          657           59          493          554          652 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 
        1132          449         2408         3431         1487         3076 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 
        1420         1727         1835         2583         2741         1732 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 
        1605         1203         3668         2414         3117         1459 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3924 TCGA-B2-4098 
        2931         2722         1865         2963         1092           51 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 
         374          648          952          358          315          417 
TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 
         656          507          291          175            7           38 
TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 
          16          141           11            7          511          826 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 
         838          762          750          777          788          700 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
         636          722           36          822           26          737 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
         522          505          434           15         1046          435 
TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J 
         830          519           53          256          150           66 
TCGA-B8-A7U6 TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
         110         3377         2881         2746         3074         2839 
TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4173 TCGA-BP-4174 
        3037           13         2718          701         1893         1879 
TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 
        1955         1670         2964         1625          845         1888 
TCGA-BP-4332 TCGA-BP-4335 TCGA-BP-4338 TCGA-BP-4344 TCGA-BP-4347 TCGA-BP-4349 
        1133          461         2859         1666         1367          372 
TCGA-BP-4351 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 
         970          374         2208         2372         2361          182 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 
        2184         1462         1876         1885          411         1731 
TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4795 TCGA-BP-4797 
        2080          354         1854         1489          620         1107 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 
        1124          204         1459          211         2660         2172 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 
        1935         1785         1834         1862         1871          205 
TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4975 
        1794          433         1487         1502         1384         1433 
TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4987 TCGA-BP-4989 
        1632          454         1014         1413         1124          118 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 
        1413          501          177         1371          932         1266 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 
         563         1177         1126          840         1140         1071 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5177 TCGA-BP-5180 
         193         2412         2257          932          293         2263 
TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
        1495         1165         1291         1133         1132          693 
TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 
         406          822         1011          967          714          408 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 
         749         1018          603         1355         1063          951 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4639 TCGA-CJ-4640 
          29         1820         1416         1924         2308         1998 
TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
        1628         1793          646         2554         1498         2423 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
        1435         2259         2283         2353         1955         2186 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4889 
        2014         1883         1759         2125         1952         1946 
TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4899 TCGA-CJ-4902 
        2085         1521          750          841         1528         1520 
TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4916 
        1560         1792         1496         1531         1657         1373 
TCGA-CJ-5671 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
        1943         2430         2575          552         1883         1889 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CW-5581 
        2231         2038         1855         1906         2548         2799 
TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6088 
        2489         2609         2226         2378         2271         3222 
TCGA-CW-6090 TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4858 
        2552         3146          774         1404           18         1943 
TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-5451 TCGA-CZ-5452 
        1787         1843         1928         2830         1929         1789 
TCGA-CZ-5453 TCGA-CZ-5456 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 
          25         1712         1732         1683         1430          330 
TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5470 
         662         1740         1446          685           59          386 
TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 
        2439         2067         1997          373          435          693 
TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 
        1905         1329         1398         1470          370          355 
TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 
        1130          723         1729          551          119          206 
TCGA-EU-5907 TCGA-GK-A6C7 
         127           61 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
              110                 3 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
             2566              3668 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
             1273              1299 
[1] "110.0 - 2566.0 (1273.0)" "3.0 - 3668.0 (1299.0)"  
[1] "hr=" "1.9"
D42V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  1Q LOSS MUTATED        19        5         8        4
  1Q LOSS WILD-TYPE     225       51       118       75
D42V3, multiclass
           clus
vv          1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  STAGE I                19               225
  STAGE II                5                51
  STAGE III               8               118
  STAGE IV                4                75
[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"
                   vv
clus                 T1  T2  T3  T4
  1Q LOSS MUTATED    19   5   9   3
  1Q LOSS WILD-TYPE 231  62 168   8
D42V4, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  T1              19               231
  T2               5                62
  T3               9               168
  T4               3                 8
[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"
D42V5, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED    17   1
  1Q LOSS WILD-TYPE 213  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     17    1
  1Q LOSS WILD-TYPE  213   17
   clus
vv  1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  0              17               213
  1               1                17
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  1Q LOSS MUTATED    33   3   0
  1Q LOSS WILD-TYPE 384  75   9
D42V6, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  M0              33               384
  M1               3                75
  MX               0                 9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V7, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED    11  25
  1Q LOSS WILD-TYPE 167 302
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     11   25
  1Q LOSS WILD-TYPE  167  302
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE              11               167
  MALE                25               302
[1] 2 2
[1] FALSE
D42V8, continuous
D42V9, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1Q LOSS MUTATED       1                         2    32
  1Q LOSS WILD-TYPE     7                        31   425
D42V10, multiclass
                           clus
vv                          1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  ASIAN                                   1                 7
  BLACK OR AFRICAN AMERICAN               2                31
  WHITE                                  32               425
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V11, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     3  27
  1Q LOSS WILD-TYPE  21 303
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      3   27
  1Q LOSS WILD-TYPE   21  303
                        clus
vv                       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                21
  NOT HISPANIC OR LATINO              27               303
[1] 2 2
[1] FALSE

Clustering(43) Variable = 2P LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                 0   1
  2P LOSS MUTATED    10   3
  2P LOSS WILD-TYPE 328  23
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               13               351 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                3                23 
$`2P LOSS MUTATED`
TCGA-A3-3313 TCGA-A3-3374 TCGA-AK-3433 TCGA-AK-3440 TCGA-AK-3447 TCGA-AK-3465 
         735         1314         2192         1745         1217          369 
TCGA-AS-3777 TCGA-B0-4699 TCGA-B0-5117 TCGA-B2-3923 TCGA-BP-4334 TCGA-BP-4994 
        1238          110          535          992          645         1308 
TCGA-BP-5175 
         932 

$`2P LOSS WILD-TYPE`
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 
        1120         1436           16         1493         1491         1130 
TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 
        1508         1478         1106         1186          751         1137 
TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3347 TCGA-A3-3349 
        1485          665         1043          945         1610         1385 
TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 
         910         2688         1307         2504         1559          319 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 
         873         2270         2274          735         1621         1070 
TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 
         630          567          574          861         1993          617 
TCGA-A3-A8CQ TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 
           3         3343         2566         2223         2017          480 
TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 
        1853         2087         2044         1423         1471         1280 
TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3456 TCGA-AK-3458 
        1779         1481         1397          874         1143         1168 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4718 
         951          853           43           26           96          616 
TCGA-B0-4813 TCGA-B0-4819 TCGA-B0-5097 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 
          18          183          665          911         1092          359 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
         797          657           59          493          554          652 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 
        1132          449         2408         3431         1487         3076 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 
        1420         1727         1835         2583         2741         1732 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 
        1605         1203         3668         2414         3117         1459 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3924 TCGA-B2-4098 
        2931         2722         1865         2963         1092           51 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 
         374          648          952          358          315          417 
TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 
         656          507          291          175            7           38 
TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 
          16          141          166           11            7          511 
TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 
         826          838          762          750          523          777 
TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 
         788          700          636          722           36          822 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 
          26          737          522          505          194          434 
TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G 
          15         1046          435          830          519           53 
TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4158 TCGA-BP-4160 
         256          150           66          110         3377         2881 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 
        2746         3074         2839         3037           13         2718 
TCGA-BP-4169 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 
         701         1893         1879         1955         1670         2964 
TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4335 TCGA-BP-4338 
        1625          845         1888         1133          461         2859 
TCGA-BP-4344 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4756 TCGA-BP-4758 
        1666         1367          372          970          374         2208 
TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 
        2372         2361          182         2184         1462          400 
TCGA-BP-4769 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 
        1876         1885         1843          411         1731         2080 
TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4801 
         354         1854         1489          620         1107         1124 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 
         204         1459          211         2660         2172         1935 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 
        1785         1834         1862         1871          205         1746 
TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4975 
        1794          433         1487         1502         1384         1433 
TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4987 
        1632          454         1014         1413          785         1124 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 
         118         1413          501          177         1371          932 
TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 
        1266          563         1177         1126          840         1140 
TCGA-BP-5008 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5177 TCGA-BP-5180 
        1071          193         2412         2257          293         2263 
TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
        1495         1165         1291         1133         1132          693 
TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 
         406          822         1011          967          714          408 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 
         749         1018          603         1355         1063          951 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4639 TCGA-CJ-4640 
          29         1820         1416         1924         2308         1998 
TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
        1628         1793          646         2554         1498         2423 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
        1435         2259         2283         2353         1955         2186 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4889 
        2014         1883         1759         2125         1952         1946 
TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4897 TCGA-CJ-4899 
        2085         1521          750          841         1808         1528 
TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 
        1450         1520         1560         1792         1496         1499 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-5671 TCGA-CJ-5675 TCGA-CJ-5676 
        1531         1657         1373         1943         2430         2575 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 
         552         1883         1889         2231         2038         1855 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5587 
        1906         2548         2799         2489         2609         2226 
TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 
        2017         2378         2271         3222         2552         3146 
TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4862 
         774         1404           18         1943         1787         1843 
TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 
        1928         2830         1868         1929         1789           25 
TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 
        1712         1683         1732         1683         1430          330 
TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5469 
         662         1740         1446          685           59          946 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 
         386         2439         2067         1997          373          435 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 
         693         1905         1329         1398         1470          370 
TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5905 
         355         1130          723         1729          551          119 
TCGA-EU-5906 TCGA-EU-5907 TCGA-GK-A6C7 
         206          127           61 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
              110                 3 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             2192              3668 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
              992              1355 
[1] "110.0 - 2192.0 (992.0)" "3.0 - 3668.0 (1355.0)" 
[1] "hr=" "4.1"
D43V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  2P LOSS MUTATED         8        3         2        1
  2P LOSS WILD-TYPE     236       53       124       78
D43V3, multiclass
           clus
vv          2P LOSS MUTATED 2P LOSS WILD-TYPE
  STAGE I                 8               236
  STAGE II                3                53
  STAGE III               2               124
  STAGE IV                1                78
[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"
                   vv
clus                 T1  T2  T3  T4
  2P LOSS MUTATED     8   3   2   1
  2P LOSS WILD-TYPE 242  64 175  10
D43V4, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  T1               8               242
  T2               3                64
  T3               2               175
  T4               1                10
[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"
D43V5, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     6   0
  2P LOSS WILD-TYPE 224  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      6    0
  2P LOSS WILD-TYPE  224   18
   clus
vv  2P LOSS MUTATED 2P LOSS WILD-TYPE
  0               6               224
  1               0                18
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  2P LOSS MUTATED    13   1   0
  2P LOSS WILD-TYPE 404  77   9
D43V6, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  M0              13               404
  M1               1                77
  MX               0                 9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V7, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     4  10
  2P LOSS WILD-TYPE 174 317
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      4   10
  2P LOSS WILD-TYPE  174  317
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE               4               174
  MALE                10               317
[1] 2 2
[1] FALSE
D43V8, continuous
D43V9, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2P LOSS MUTATED       1                         3    10
  2P LOSS WILD-TYPE     7                        30   447
D43V10, multiclass
                           clus
vv                          2P LOSS MUTATED 2P LOSS WILD-TYPE
  ASIAN                                   1                 7
  BLACK OR AFRICAN AMERICAN               3                30
  WHITE                                  10               447
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V11, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     0  10
  2P LOSS WILD-TYPE  24 320
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      0   10
  2P LOSS WILD-TYPE   24  320
                        clus
vv                       2P LOSS MUTATED 2P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                24
  NOT HISPANIC OR LATINO              10               320
[1] 2 2
[1] FALSE

Clustering(44) Variable = 2Q LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                 0   1
  2Q LOSS MUTATED    10   2
  2Q LOSS WILD-TYPE 328  24
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               12               352 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                2                24 
$`2Q LOSS MUTATED`
TCGA-A3-3374 TCGA-AK-3433 TCGA-AK-3440 TCGA-AK-3447 TCGA-AK-3465 TCGA-AS-3777 
        1314         2192         1745         1217          369         1238 
TCGA-B0-4699 TCGA-B0-5117 TCGA-B2-3923 TCGA-BP-4334 TCGA-BP-4994 TCGA-BP-5175 
         110          535          992          645         1308          932 

$`2Q LOSS WILD-TYPE`
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 
        1120         1436           16          735         1493         1491 
TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 
        1130         1508         1478         1106         1186          751 
TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3347 
        1137         1485          665         1043          945         1610 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 
        1385          910         2688         1307         2504         1559 
TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 
         319          873         2270         2274          735         1621 
TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 
        1070          630          567          574          861         1993 
TCGA-A3-3387 TCGA-A3-A8CQ TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
         617            3         3343         2566         2223         2017 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3443 TCGA-AK-3444 
         480         1853         2087         2044         1423         1471 
TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3456 
        1280         1779         1481         1397          874         1143 
TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4706 TCGA-B0-4710 
        1168          951          853           43           26           96 
TCGA-B0-4718 TCGA-B0-4813 TCGA-B0-4819 TCGA-B0-5097 TCGA-B0-5108 TCGA-B0-5110 
         616           18          183          665          911         1092 
TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
         359          797          657           59          493          554 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 
         652         1132          449         2408         3431         1487 
TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 
        3076         1420         1727         1835         2583         2741 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 
        1732         1605         1203         3668         2414         3117 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3924 
        1459         2931         2722         1865         2963         1092 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 
          51          374          648          952          358          315 
TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 
         417          656          507          291          175            7 
TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 
          38           16          141          166           11            7 
TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 
         511          826          838          762          750          523 
TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 
         777          788          700          636          722           36 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 
         822           26          737          522          505          194 
TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54F 
         434           15         1046          435          830          519 
TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4158 
          53          256          150           66          110         3377 
TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 
        2881         2746         3074         2839         3037           13 
TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 
        2718          701         1893         1879         1955         1670 
TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4335 
        2964         1625          845         1888         1133          461 
TCGA-BP-4338 TCGA-BP-4344 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4756 
        2859         1666         1367          372          970          374 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4765 TCGA-BP-4766 
        2208         2372         2361          182         2184         1462 
TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 
         400         1876         1885         1843          411         1731 
TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4795 TCGA-BP-4797 
        2080          354         1854         1489          620         1107 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 
        1124          204         1459          211         2660         2172 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 
        1935         1785         1834         1862         1871          205 
TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 
        1746         1794          433         1487         1502         1384 
TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4986 
        1433         1632          454         1014         1413          785 
TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 
        1124          118         1413          501          177         1371 
TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 
         932         1266          563         1177         1126          840 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5177 
        1140         1071          193         2412         2257          293 
TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 
        2263         1495         1165         1291         1133         1132 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 
         693          406          822         1011          967          714 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 
         408          749         1018          603         1355         1063 
TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4639 
         951           29         1820         1416         1924         2308 
TCGA-CJ-4640 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
        1998         1628         1793          646         2554         1498 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 
        2423         1435         2259         2283         2353         1955 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 
        2186         2014         1883         1759         2125         1952 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4897 
        1946         2085         1521          750          841         1808 
TCGA-CJ-4899 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 
        1528         1450         1520         1560         1792         1496 
TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-5671 TCGA-CJ-5675 
        1499         1531         1657         1373         1943         2430 
TCGA-CJ-5676 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 
        2575          552         1883         1889         2231         2038 
TCGA-CJ-6027 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 
        1855         1906         2548         2799         2489         2609 
TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6088 TCGA-CW-6090 
        2226         2017         2378         2271         3222         2552 
TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4858 TCGA-CZ-4859 
        3146          774         1404           18         1943         1787 
TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 
        1843         1928         2830         1868         1929         1789 
TCGA-CZ-5453 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
          25         1712         1683         1732         1683         1430 
TCGA-CZ-5461 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5468 
         330          662         1740         1446          685           59 
TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
         946          386         2439         2067         1997          373 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 
         435          693         1905         1329         1398         1470 
TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-EU-5904 
         370          355         1130          723         1729          551 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-GK-A6C7 
         119          206          127           61 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
              110                 3 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             2192              3668 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
           1104.5            1342.0 
[1] "110.0 - 2192.0 (1104.5)" "3.0 - 3668.0 (1342.0)"  
[1] "hr=" "2.8"
D44V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  2Q LOSS MUTATED         7        3         3        1
  2Q LOSS WILD-TYPE     237       53       123       78
D44V3, multiclass
           clus
vv          2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  STAGE I                 7               237
  STAGE II                3                53
  STAGE III               3               123
  STAGE IV                1                78
[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"
                   vv
clus                 T1  T2  T3  T4
  2Q LOSS MUTATED     7   3   3   1
  2Q LOSS WILD-TYPE 243  64 174  10
D44V4, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  T1               7               243
  T2               3                64
  T3               3               174
  T4               1                10
[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"
D44V5, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     6   0
  2Q LOSS WILD-TYPE 224  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      6    0
  2Q LOSS WILD-TYPE  224   18
   clus
vv  2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  0               6               224
  1               0                18
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  2Q LOSS MUTATED    13   1   0
  2Q LOSS WILD-TYPE 404  77   9
D44V6, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  M0              13               404
  M1               1                77
  MX               0                 9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V7, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     4  10
  2Q LOSS WILD-TYPE 174 317
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      4   10
  2Q LOSS WILD-TYPE  174  317
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE               4               174
  MALE                10               317
[1] 2 2
[1] FALSE
D44V8, continuous
D44V9, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2Q LOSS MUTATED       1                         2    11
  2Q LOSS WILD-TYPE     7                        31   446
D44V10, multiclass
                           clus
vv                          2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  ASIAN                                   1                 7
  BLACK OR AFRICAN AMERICAN               2                31
  WHITE                                  11               446
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V11, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     0  11
  2Q LOSS WILD-TYPE  24 319
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      0   11
  2Q LOSS WILD-TYPE   24  319
                        clus
vv                       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                24
  NOT HISPANIC OR LATINO              11               319
[1] 2 2
[1] FALSE

Clustering(45) Variable = 3P LOSS MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                 0   1
  3P LOSS MUTATED   246  18
  3P LOSS WILD-TYPE  92   8
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
              264               100 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               18                 8 
$`3P LOSS MUTATED`
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 
        1120         1436          735         1493         1491         1130 
TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3331 
        1508         1478         1106         1186          751         1485 
TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3347 TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 
         665         1043         1610          910         2688         1307 
TCGA-A3-3359 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 
        2504          873         2270         2274          735         1621 
TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3387 
        1070          630          567          574          861          617 
TCGA-A3-A8CQ TCGA-AK-3425 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 
           3         3343         2017          480         1853         2192 
TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 
        2087         2044         1280         1779         1481          874 
TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4706 TCGA-B0-4710 
        1168          951          853           43           26           96 
TCGA-B0-4813 TCGA-B0-4819 TCGA-B0-5097 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 
          18          183          665          911         1092          359 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5399 TCGA-B0-5402 
         797          657           59          493          652          449 
TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 
        2408         1487         3076         1420         1727         1835 
TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5706 
        2583         2741         1732         1605         1203         2414 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3924 
        3117         1459         2931         2722         1865         1092 
TCGA-B2-4099 TCGA-B2-5633 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 
         374          358          417          656          507          291 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 
           7           38          141          166           11            7 
TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 
         511          826          777          700          636          722 
TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5549 TCGA-B8-5551 TCGA-B8-5552 
          36          822           26          194           15         1046 
TCGA-B8-5553 TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J 
         435          519           53          256          150           66 
TCGA-B8-A7U6 TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4163 TCGA-BP-4166 TCGA-BP-4167 
         110         3377         2881         2839           13         2718 
TCGA-BP-4169 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4325 TCGA-BP-4329 TCGA-BP-4330 
         701         1879         1955         2964          845         1888 
TCGA-BP-4332 TCGA-BP-4338 TCGA-BP-4344 TCGA-BP-4347 TCGA-BP-4351 TCGA-BP-4758 
        1133         2859         1666         1367          970         2208 
TCGA-BP-4761 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4774 TCGA-BP-4776 
         182         2184         1462          400         1885          411 
TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4789 TCGA-BP-4797 TCGA-BP-4801 
        1731         2080          354         1489         1107         1124 
TCGA-BP-4803 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
         204          211         2660         2172         1935         1785 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 
        1834         1862         1871         1487         1502         1384 
TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4987 
        1433          454         1014         1413          785         1124 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 
         118         1413          501          177         1371          932 
TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5008 TCGA-BP-5169 
        1266          563         1126          840         1071          193 
TCGA-BP-5174 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
        2257         2263         1495         1165         1291         1133 
TCGA-BP-5185 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5194 TCGA-BP-5195 
        1132          406          822         1011          408          749 
TCGA-BP-5196 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 
        1018         1355         1063          951           29         1820 
TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4640 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 
        1416         1924         1998         1628         1793          646 
TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4876 
        2554         1498         2423         2259         2283         1955 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4886 TCGA-CJ-4892 TCGA-CJ-4893 
        2186         2014         1883         1952         1521          750 
TCGA-CJ-4894 TCGA-CJ-4899 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 
         841         1528         1450         1520         1560         1792 
TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4916 TCGA-CJ-5671 TCGA-CJ-5675 
        1496         1499         1531         1373         1943         2430 
TCGA-CJ-5676 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-6027 TCGA-CJ-6032 
        2575         1883         1889         2231         1855         2548 
TCGA-CW-5583 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6088 
        2489         2226         2017         2378         2271         3222 
TCGA-CW-6090 TCGA-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4863 
        2552          774           18         1943         1787         1928 
TCGA-CZ-4864 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5457 TCGA-CZ-5458 
        2830         1929         1789           25         1683         1732 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 
        1683         1430          330          662         1740         1446 
TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
         685           59         2439         2067         1997          373 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 
         435          693         1905         1329         1398          370 
TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-EU-5906 TCGA-EU-5907 TCGA-GK-A6C7 
        1130          723         1729          206          127           61 

$`3P LOSS WILD-TYPE`
TCGA-A3-3308 TCGA-A3-3326 TCGA-A3-3343 TCGA-A3-3349 TCGA-A3-3362 TCGA-A3-3363 
          16         1137          945         1385         1559          319 
TCGA-A3-3374 TCGA-A3-3385 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3440 TCGA-AK-3443 
        1314         1993         2566         2223         1745         1423 
TCGA-AK-3444 TCGA-AK-3447 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3465 TCGA-AS-3777 
        1471         1217         1397         1143          369         1238 
TCGA-B0-4699 TCGA-B0-4718 TCGA-B0-5117 TCGA-B0-5121 TCGA-B0-5400 TCGA-B0-5691 
         110          616          535          554         1132         3431 
TCGA-B0-5705 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-4098 TCGA-B2-4101 TCGA-B2-4102 
        3668         2963          992           51          648          952 
TCGA-B2-5635 TCGA-B4-5378 TCGA-B4-5835 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
         315          175           16          838          762          750 
TCGA-B8-4619 TCGA-B8-4621 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5550 
         523          788          737          522          505          434 
TCGA-B8-A54D TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4165 TCGA-BP-4173 TCGA-BP-4177 
         830         2746         3074         3037         1893         1670 
TCGA-BP-4326 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4349 TCGA-BP-4756 TCGA-BP-4759 
        1625          645          461          372          374         2372 
TCGA-BP-4760 TCGA-BP-4769 TCGA-BP-4775 TCGA-BP-4784 TCGA-BP-4795 TCGA-BP-4804 
        2361         1876         1843         1854          620         1459 
TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4976 TCGA-BP-4994 
         205         1746         1794          433         1632         1308 
TCGA-BP-5001 TCGA-BP-5007 TCGA-BP-5170 TCGA-BP-5175 TCGA-BP-5177 TCGA-BP-5186 
        1177         1140         2412          932          293          693 
TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5198 TCGA-CJ-4639 TCGA-CJ-4872 TCGA-CJ-4875 
         967          714          603         2308         1435         2353 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4897 TCGA-CJ-4912 
        1759         2125         1946         2085         1808         1657 
TCGA-CJ-5681 TCGA-CJ-5686 TCGA-CJ-6031 TCGA-CW-5581 TCGA-CW-5585 TCGA-CW-6093 
         552         2038         1906         2799         2609         3146 
TCGA-CZ-4854 TCGA-CZ-4862 TCGA-CZ-4866 TCGA-CZ-5456 TCGA-CZ-5469 TCGA-CZ-5470 
        1404         1843         1868         1712          946          386 
TCGA-DV-5567 TCGA-DV-5569 TCGA-EU-5904 TCGA-EU-5905 
        1470          355          551          119 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                3                16 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             3377              3668 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           1318.0            1227.5 
[1] "3.0 - 3377.0 (1318.0)"  "16.0 - 3668.0 (1227.5)"
[1] "hr=" "1.2"
D45V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  3P LOSS MUTATED       172       41       102       49
  3P LOSS WILD-TYPE      72       15        24       30
D45V3, multiclass
           clus
vv          3P LOSS MUTATED 3P LOSS WILD-TYPE
  STAGE I               172                72
  STAGE II               41                15
  STAGE III             102                24
  STAGE IV               49                30
[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"
                   vv
clus                 T1  T2  T3  T4
  3P LOSS MUTATED   176  49 135   4
  3P LOSS WILD-TYPE  74  18  42   7
D45V4, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  T1             176                74
  T2              49                18
  T3             135                42
  T4               4                 7
[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"
D45V5, binary
                   cls
clus                  0   1
  3P LOSS MUTATED   162  12
  3P LOSS WILD-TYPE  68   6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED    162   12
  3P LOSS WILD-TYPE   68    6
   clus
vv  3P LOSS MUTATED 3P LOSS WILD-TYPE
  0             162                68
  1              12                 6
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  3P LOSS MUTATED   306  50   7
  3P LOSS WILD-TYPE 111  28   2
D45V6, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  M0             306               111
  M1              50                28
  MX               7                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V7, binary
                   cls
clus                  0   1
  3P LOSS MUTATED   117 247
  3P LOSS WILD-TYPE  61  80
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED    117  247
  3P LOSS WILD-TYPE   61   80
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE             117                61
  MALE               247                80
[1] 2 2
[1] FALSE
D45V8, continuous
D45V9, continuous
[1] "Remove cluster labels:" "3P LOSS WILD-TYPE"     
clus
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                6                 2 
     TCGA-A3-A8CQ      TCGA-B2-A4SR      TCGA-B8-5158      TCGA-B8-5164 
"3P LOSS MUTATED" "3P LOSS MUTATED" "3P LOSS MUTATED" "3P LOSS MUTATED" 
     TCGA-B8-A54F      TCGA-B8-A54G 
"3P LOSS MUTATED" "3P LOSS MUTATED" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3P LOSS MUTATED       5                        19   334
  3P LOSS WILD-TYPE     3                        14   123
D45V10, multiclass
                           clus
vv                          3P LOSS MUTATED 3P LOSS WILD-TYPE
  ASIAN                                   5                 3
  BLACK OR AFRICAN AMERICAN              19                14
  WHITE                                 334               123
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V11, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    19 233
  3P LOSS WILD-TYPE   5  97
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     19  233
  3P LOSS WILD-TYPE    5   97
                        clus
vv                       3P LOSS MUTATED 3P LOSS WILD-TYPE
  HISPANIC OR LATINO                  19                 5
  NOT HISPANIC OR LATINO             233                97
[1] 2 2
[1] FALSE

Clustering(46) Variable = 3Q LOSS MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                 0   1
  3Q LOSS MUTATED    65   9
  3Q LOSS WILD-TYPE 273  17
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               74               290 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                9                17 
$`3Q LOSS MUTATED`
TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3324 TCGA-A3-3347 TCGA-A3-3357 
         735         1491         1478         1186         1610         2688 
TCGA-A3-3365 TCGA-A3-3372 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3387 TCGA-AK-3425 
         873          735          567          574          617         3343 
TCGA-AK-3433 TCGA-AK-3460 TCGA-B0-5115 TCGA-B0-5120 TCGA-B0-5712 TCGA-B2-3924 
        2192          951          797          493         2722         1092 
TCGA-B2-5639 TCGA-B8-4148 TCGA-B8-5163 TCGA-B8-A54I TCGA-BP-4158 TCGA-BP-4166 
         417          826          822          150         3377           13 
TCGA-BP-4169 TCGA-BP-4344 TCGA-BP-4347 TCGA-BP-4351 TCGA-BP-4768 TCGA-BP-4777 
         701         1666         1367          970          400         1731 
TCGA-BP-4781 TCGA-BP-4797 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4963 TCGA-BP-4977 
        2080         1107         1124          204         1834          454 
TCGA-BP-4986 TCGA-BP-4992 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5008 TCGA-BP-5180 
         785          501          932         1266         1071         2263 
TCGA-BP-5185 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5195 TCGA-BP-5199 TCGA-BP-5200 
        1132          406          822          749         1355         1063 
TCGA-CJ-4635 TCGA-CJ-4642 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4882 TCGA-CJ-4904 
        1416         1628         2259         2283         1883         1792 
TCGA-CJ-4907 TCGA-CJ-5682 TCGA-CJ-6027 TCGA-CW-6090 TCGA-CZ-4863 TCGA-CZ-4864 
        1499         1883         1855         2552         1928         2830 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5457 TCGA-CZ-5459 TCGA-CZ-5461 TCGA-CZ-5463 
        1929         1789         1683         1683          330          662 
TCGA-CZ-5468 TCGA-CZ-5984 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-DV-5573 TCGA-DV-5574 
          59         2067          373          435         1130          723 
TCGA-EU-5907 TCGA-GK-A6C7 
         127           61 

$`3Q LOSS WILD-TYPE`
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3316 TCGA-A3-3319 TCGA-A3-3320 
        1120         1436           16         1493         1130         1508 
TCGA-A3-3323 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 
        1106          751         1137         1485          665         1043 
TCGA-A3-3343 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 
         945         1385          910         1307         2504         1559 
TCGA-A3-3363 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 
         319         2270         2274         1621         1314         1070 
TCGA-A3-3378 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-A8CQ TCGA-AK-3427 TCGA-AK-3428 
         630          861         1993            3         2566         2223 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
        2017          480         1853         2087         2044         1745 
TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 
        1423         1471         1280         1217         1779         1481 
TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3461 TCGA-AK-3465 
        1397          874         1143         1168          853          369 
TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4699 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4718 
        1238           43          110           26           96          616 
TCGA-B0-4813 TCGA-B0-4819 TCGA-B0-5097 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 
          18          183          665          911         1092          359 
TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
         657          535           59          554          652         1132 
TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 
         449         2408         3431         1487         3076         1420 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
        1727         1835         2583         2741         1732         1605 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
        1203         3668         2414         3117         1459         2931 
TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 
        1865         2963          992           51          374          648 
TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 
         952          358          315          656          507          291 
TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
         175            7           38           16          141          166 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
          11            7          511          838          762          750 
TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 
         523          777          788          700          636          722 
TCGA-B8-5162 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 
          36           26          737          522          505          194 
TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54F 
         434           15         1046          435          830          519 
TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4160 TCGA-BP-4161 
          53          256           66          110         2881         2746 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4167 TCGA-BP-4173 TCGA-BP-4174 
        3074         2839         3037         2718         1893         1879 
TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 
        1955         1670         2964         1625          845         1888 
TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4338 TCGA-BP-4349 TCGA-BP-4756 
        1133          645          461         2859          372          374 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4765 TCGA-BP-4766 
        2208         2372         2361          182         2184         1462 
TCGA-BP-4769 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4782 TCGA-BP-4784 
        1876         1885         1843          411          354         1854 
TCGA-BP-4789 TCGA-BP-4795 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 
        1489          620         1459          211         2660         2172 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 
        1935         1785         1862         1871          205         1746 
TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4975 
        1794          433         1487         1502         1384         1433 
TCGA-BP-4976 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 
        1632         1014         1413         1124          118         1413 
TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
         177         1308         1371          563         1177         1126 
TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5175 
         840         1140          193         2412         2257          932 
TCGA-BP-5177 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 
         293         1495         1165         1291         1133          693 
TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5196 TCGA-BP-5198 
        1011          967          714          408         1018          603 
TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4636 TCGA-CJ-4639 TCGA-CJ-4640 
         951           29         1820         1924         2308         1998 
TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 
        1793          646         2554         1498         2423         1435 
TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4884 TCGA-CJ-4885 
        2353         1955         2186         2014         1759         2125 
TCGA-CJ-4886 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 
        1952         1946         2085         1521          750          841 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 
        1808         1528         1450         1520         1560         1496 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-5671 TCGA-CJ-5675 TCGA-CJ-5676 
        1531         1657         1373         1943         2430         2575 
TCGA-CJ-5681 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6031 TCGA-CJ-6032 
         552         1889         2231         2038         1906         2548 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 
        2799         2489         2609         2226         2017         2378 
TCGA-CW-5591 TCGA-CW-6088 TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 
        2271         3222         3146          774         1404           18 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-4866 TCGA-CZ-5453 TCGA-CZ-5456 
        1943         1787         1843         1868           25         1712 
TCGA-CZ-5458 TCGA-CZ-5460 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5469 
        1732         1430         1740         1446          685          946 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5985 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 
         386         2439         1997          693         1905         1329 
TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5575 TCGA-EU-5904 
        1398         1470          370          355         1729          551 
TCGA-EU-5905 TCGA-EU-5906 
         119          206 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               13                 3 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             3377              3668 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
           1115.5            1372.0 
[1] "13.0 - 3377.0 (1115.5)" "3.0 - 3668.0 (1372.0)" 
[1] "hr=" "2.1"
D46V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  3Q LOSS MUTATED        46       14        23       13
  3Q LOSS WILD-TYPE     198       42       103       66
D46V3, multiclass
           clus
vv          3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  STAGE I                46               198
  STAGE II               14                42
  STAGE III              23               103
  STAGE IV               13                66
[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"
                   vv
clus                 T1  T2  T3  T4
  3Q LOSS MUTATED    49  16  31   0
  3Q LOSS WILD-TYPE 201  51 146  11
D46V4, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  T1              49               201
  T2              16                51
  T3              31               146
  T4               0                11
[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"
D46V5, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    37   2
  3Q LOSS WILD-TYPE 193  16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     37    2
  3Q LOSS WILD-TYPE  193   16
   clus
vv  3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  0              37               193
  1               2                16
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  3Q LOSS MUTATED    80  14   2
  3Q LOSS WILD-TYPE 337  64   7
D46V6, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  M0              80               337
  M1              14                64
  MX               2                 7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V7, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    19  77
  3Q LOSS WILD-TYPE 159 250
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     19   77
  3Q LOSS WILD-TYPE  159  250
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE              19               159
  MALE                77               250
[1] 2 2
[1] FALSE
D46V8, continuous
D46V9, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3Q LOSS MUTATED       1                         5    88
  3Q LOSS WILD-TYPE     7                        28   369
D46V10, multiclass
                           clus
vv                          3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  ASIAN                                   1                 7
  BLACK OR AFRICAN AMERICAN               5                28
  WHITE                                  88               369
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V11, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     5  54
  3Q LOSS WILD-TYPE  19 276
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      5   54
  3Q LOSS WILD-TYPE   19  276
                        clus
vv                       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   5                19
  NOT HISPANIC OR LATINO              54               276
[1] 2 2
[1] FALSE

Clustering(47) Variable = 4P LOSS MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                 0   1
  4P LOSS MUTATED    33   4
  4P LOSS WILD-TYPE 305  22
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               37               327 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                4                22 
$`4P LOSS MUTATED`
TCGA-A3-3316 TCGA-A3-3373 TCGA-A3-3380 TCGA-A3-3385 TCGA-AK-3436 TCGA-AK-3458 
        1493         1621          567         1993         2044         1168 
TCGA-B0-4710 TCGA-B0-5113 TCGA-B0-5116 TCGA-B0-5399 TCGA-B4-5835 TCGA-B4-5838 
          96          359          657          652           16          166 
TCGA-B8-4154 TCGA-B8-5158 TCGA-B8-5162 TCGA-B8-5549 TCGA-BP-4161 TCGA-BP-4351 
         750          636           36          194         2746          970 
TCGA-BP-4768 TCGA-BP-5183 TCGA-BP-5196 TCGA-BP-5198 TCGA-CJ-4878 TCGA-CJ-4894 
         400         1291         1018          603         2186          841 
TCGA-CJ-4897 TCGA-CJ-4903 TCGA-CJ-4907 TCGA-CJ-5676 TCGA-CW-5588 TCGA-CW-6090 
        1808         1560         1499         2575         2017         2552 
TCGA-CZ-4858 TCGA-CZ-4866 TCGA-CZ-5457 TCGA-CZ-5461 TCGA-CZ-5465 TCGA-CZ-5469 
        1943         1868         1683          330         1446          946 
TCGA-EU-5907 
         127 

$`4P LOSS WILD-TYPE`
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3319 
        1120         1436           16          735         1491         1130 
TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 
        1508         1478         1106         1186          751         1137 
TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3347 TCGA-A3-3349 
        1485          665         1043          945         1610         1385 
TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 
         910         2688         1307         2504         1559          319 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3374 TCGA-A3-3376 
         873         2270         2274          735         1314         1070 
TCGA-A3-3378 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3387 TCGA-A3-A8CQ TCGA-AK-3425 
         630          574          861          617            3         3343 
TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 
        2566         2223         2017          480         1853         2192 
TCGA-AK-3434 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 
        2087         1745         1423         1471         1280         1217 
TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3456 TCGA-AK-3460 
        1779         1481         1397          874         1143          951 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4699 TCGA-B0-4706 
         853          369         1238           43          110           26 
TCGA-B0-4718 TCGA-B0-4813 TCGA-B0-4819 TCGA-B0-5097 TCGA-B0-5108 TCGA-B0-5110 
         616           18          183          665          911         1092 
TCGA-B0-5115 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5400 
         797          535           59          493          554         1132 
TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 
         449         2408         3431         1487         3076         1420 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
        1727         1835         2583         2741         1732         1605 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
        1203         3668         2414         3117         1459         2931 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
        2722         1865         2963          992         1092           51 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 
         374          648          952          358          315          417 
TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 
         656          507          291          175            7           38 
TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
         141           11            7          511          826          838 
TCGA-B8-4153 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5159 
         762          523          777          788          700          722 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5550 
         822           26          737          522          505          434 
TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G 
          15         1046          435          830          519           53 
TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4158 TCGA-BP-4160 
         256          150           66          110         3377         2881 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 
        3074         2839         3037           13         2718          701 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 
        1893         1879         1955         1670         2964         1625 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4338 
         845         1888         1133          645          461         2859 
TCGA-BP-4344 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 
        1666         1367          372          374         2208         2372 
TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4774 
        2361          182         2184         1462         1876         1885 
TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 
        1843          411         1731         2080          354         1854 
TCGA-BP-4789 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 
        1489          620         1107         1124          204         1459 
TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
         211         2660         2172         1935         1785         1834 
TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 
        1862         1871          205         1746         1794          433 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 
        1487         1502         1384         1433         1632          454 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 
        1014         1413          785         1124          118         1413 
TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 
         501          177         1308         1371          932         1266 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 
         563         1177         1126          840         1140         1071 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5177 TCGA-BP-5180 
         193         2412         2257          932          293         2263 
TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 
        1495         1165         1133         1132          693          406 
TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
         822         1011          967          714          408          749 
TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 
        1355         1063          951           29         1820         1416 
TCGA-CJ-4636 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 
        1924         2308         1998         1628         1793          646 
TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 
        2554         1498         2423         1435         2259         2283 
TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
        2353         1955         2014         1883         1759         2125 
TCGA-CJ-4886 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4899 
        1952         1946         2085         1521          750         1528 
TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 
        1450         1520         1792         1496         1531         1657 
TCGA-CJ-4916 TCGA-CJ-5671 TCGA-CJ-5675 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
        1373         1943         2430          552         1883         1889 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CW-5581 
        2231         2038         1855         1906         2548         2799 
TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6088 
        2489         2609         2226         2378         2271         3222 
TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4859 TCGA-CZ-4862 
        3146          774         1404           18         1787         1843 
TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5456 
        1928         2830         1929         1789           25         1712 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5466 
        1732         1683         1430          662         1740          685 
TCGA-CZ-5468 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
          59          386         2439         2067         1997          373 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 
         435          693         1905         1329         1398         1470 
TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-EU-5904 
         370          355         1130          723         1729          551 
TCGA-EU-5905 TCGA-EU-5906 TCGA-GK-A6C7 
         119          206           61 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               16                 3 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             2746              3668 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             1018              1314 
[1] "16.0 - 2746.0 (1018.0)" "3.0 - 3668.0 (1314.0)" 
[1] "hr=" "1.8"
D47V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  4P LOSS MUTATED        20        6        26       19
  4P LOSS WILD-TYPE     224       50       100       60
D47V3, multiclass
           clus
vv          4P LOSS MUTATED 4P LOSS WILD-TYPE
  STAGE I                20               224
  STAGE II                6                50
  STAGE III              26               100
  STAGE IV               19                60
[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"
                   vv
clus                 T1  T2  T3  T4
  4P LOSS MUTATED    21   8  38   4
  4P LOSS WILD-TYPE 229  59 139   7
D47V4, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  T1              21               229
  T2               8                59
  T3              38               139
  T4               4                 7
[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"
D47V5, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    32   3
  4P LOSS WILD-TYPE 198  15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     32    3
  4P LOSS WILD-TYPE  198   15
   clus
vv  4P LOSS MUTATED 4P LOSS WILD-TYPE
  0              32               198
  1               3                15
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  4P LOSS MUTATED    53  18   0
  4P LOSS WILD-TYPE 364  60   9
D47V6, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  M0              53               364
  M1              18                60
  MX               0                 9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V7, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    24  47
  4P LOSS WILD-TYPE 154 280
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     24   47
  4P LOSS WILD-TYPE  154  280
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE              24               154
  MALE                47               280
[1] 2 2
[1] FALSE
D47V8, continuous
D47V9, continuous
[1] "Remove cluster labels:" "4P LOSS MUTATED"       
clus
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                1                 7 
       TCGA-A3-A8CQ        TCGA-B2-A4SR        TCGA-B8-4621        TCGA-B8-5164 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-B8-A54F        TCGA-B8-A54G        TCGA-G6-A5PC 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4P LOSS MUTATED       1                         1    67
  4P LOSS WILD-TYPE     7                        32   390
D47V10, multiclass
                           clus
vv                          4P LOSS MUTATED 4P LOSS WILD-TYPE
  ASIAN                                   1                 7
  BLACK OR AFRICAN AMERICAN               1                32
  WHITE                                  67               390
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V11, binary
                   cls
clus                  0   1
  4P LOSS MUTATED     5  48
  4P LOSS WILD-TYPE  19 282
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      5   48
  4P LOSS WILD-TYPE   19  282
                        clus
vv                       4P LOSS MUTATED 4P LOSS WILD-TYPE
  HISPANIC OR LATINO                   5                19
  NOT HISPANIC OR LATINO              48               282
[1] 2 2
[1] FALSE

Clustering(48) Variable = 4Q LOSS MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                 0   1
  4Q LOSS MUTATED    29   3
  4Q LOSS WILD-TYPE 309  23
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               32               332 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                3                23 
$`4Q LOSS MUTATED`
TCGA-A3-3316 TCGA-A3-3373 TCGA-A3-3380 TCGA-AK-3436 TCGA-AK-3458 TCGA-B0-4710 
        1493         1621          567         2044         1168           96 
TCGA-B0-5113 TCGA-B0-5116 TCGA-B4-5838 TCGA-B8-5158 TCGA-B8-5162 TCGA-B8-5549 
         359          657          166          636           36          194 
TCGA-BP-4161 TCGA-BP-4351 TCGA-BP-4768 TCGA-BP-5183 TCGA-BP-5196 TCGA-BP-5198 
        2746          970          400         1291         1018          603 
TCGA-CJ-4881 TCGA-CJ-4897 TCGA-CJ-4903 TCGA-CJ-4907 TCGA-CJ-5676 TCGA-CW-5588 
        2014         1808         1560         1499         2575         2017 
TCGA-CW-6090 TCGA-CZ-4858 TCGA-CZ-4866 TCGA-CZ-5457 TCGA-CZ-5461 TCGA-CZ-5465 
        2552         1943         1868         1683          330         1446 
TCGA-CZ-5469 TCGA-EU-5907 
         946          127 

$`4Q LOSS WILD-TYPE`
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3319 
        1120         1436           16          735         1491         1130 
TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 
        1508         1478         1106         1186          751         1137 
TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3347 TCGA-A3-3349 
        1485          665         1043          945         1610         1385 
TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 
         910         2688         1307         2504         1559          319 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3374 TCGA-A3-3376 
         873         2270         2274          735         1314         1070 
TCGA-A3-3378 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A8CQ 
         630          574          861         1993          617            3 
TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 
        3343         2566         2223         2017          480         1853 
TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 
        2192         2087         1745         1423         1471         1280 
TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3456 
        1217         1779         1481         1397          874         1143 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4699 
         951          853          369         1238           43          110 
TCGA-B0-4706 TCGA-B0-4718 TCGA-B0-4813 TCGA-B0-4819 TCGA-B0-5097 TCGA-B0-5108 
          26          616           18          183          665          911 
TCGA-B0-5110 TCGA-B0-5115 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
        1092          797          535           59          493          554 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 
         652         1132          449         2408         3431         1487 
TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 
        3076         1420         1727         1835         2583         2741 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 
        1732         1605         1203         3668         2414         3117 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 
        1459         2931         2722         1865         2963          992 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 
        1092           51          374          648          952          358 
TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 
         315          417          656          507          291          175 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 
           7           38           16          141           11            7 
TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 
         511          826          838          762          750          523 
TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 
         777          788          700          722          822           26 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
         737          522          505          434           15         1046 
TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I 
         435          830          519           53          256          150 
TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4162 TCGA-BP-4163 
          66          110         3377         2881         3074         2839 
TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4173 TCGA-BP-4174 
        3037           13         2718          701         1893         1879 
TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 
        1955         1670         2964         1625          845         1888 
TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4338 TCGA-BP-4344 TCGA-BP-4347 
        1133          645          461         2859         1666         1367 
TCGA-BP-4349 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 
         372          374         2208         2372         2361          182 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 
        2184         1462         1876         1885         1843          411 
TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4795 
        1731         2080          354         1854         1489          620 
TCGA-BP-4797 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 
        1107         1124          204         1459          211         2660 
TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 
        2172         1935         1785         1834         1862         1871 
TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
         205         1746         1794          433         1487         1502 
TCGA-BP-4973 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4982 TCGA-BP-4983 
        1384         1433         1632          454         1014         1413 
TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 
         785         1124          118         1413          501          177 
TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 
        1308         1371          932         1266          563         1177 
TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5169 TCGA-BP-5170 
        1126          840         1140         1071          193         2412 
TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 
        2257          932          293         2263         1495         1165 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 
        1133         1132          693          406          822         1011 
TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5199 TCGA-BP-5200 
         967          714          408          749         1355         1063 
TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4639 
         951           29         1820         1416         1924         2308 
TCGA-CJ-4640 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
        1998         1628         1793          646         2554         1498 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 
        2423         1435         2259         2283         2353         1955 
TCGA-CJ-4878 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4889 
        2186         1883         1759         2125         1952         1946 
TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4899 TCGA-CJ-4901 
        2085         1521          750          841         1528         1450 
TCGA-CJ-4902 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4916 
        1520         1792         1496         1531         1657         1373 
TCGA-CJ-5671 TCGA-CJ-5675 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
        1943         2430          552         1883         1889         2231 
TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CW-5581 TCGA-CW-5583 
        2038         1855         1906         2548         2799         2489 
TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6088 TCGA-CW-6093 
        2609         2226         2378         2271         3222         3146 
TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-4863 
         774         1404           18         1787         1843         1928 
TCGA-CZ-4864 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5456 TCGA-CZ-5458 
        2830         1929         1789           25         1712         1732 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5468 
        1683         1430          662         1740          685           59 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 
         386         2439         2067         1997          373          435 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 
         693         1905         1329         1398         1470          370 
TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5905 
         355         1130          723         1729          551          119 
TCGA-EU-5906 TCGA-GK-A6C7 
         206           61 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               36                 3 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             2746              3668 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           1229.5            1307.5 
[1] "36.0 - 2746.0 (1229.5)" "3.0 - 3668.0 (1307.5)" 
[1] "hr=" "1.5"
D48V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  4Q LOSS MUTATED        15        6        24       20
  4Q LOSS WILD-TYPE     229       50       102       59
D48V3, multiclass
           clus
vv          4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  STAGE I                15               229
  STAGE II                6                50
  STAGE III              24               102
  STAGE IV               20                59
[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"
                   vv
clus                 T1  T2  T3  T4
  4Q LOSS MUTATED    16   8  36   5
  4Q LOSS WILD-TYPE 234  59 141   6
D48V4, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  T1              16               234
  T2               8                59
  T3              36               141
  T4               5                 6
[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"
D48V5, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED    27   3
  4Q LOSS WILD-TYPE 203  15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     27    3
  4Q LOSS WILD-TYPE  203   15
   clus
vv  4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  0              27               203
  1               3                15
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  4Q LOSS MUTATED    46  19   0
  4Q LOSS WILD-TYPE 371  59   9
D48V6, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  M0              46               371
  M1              19                59
  MX               0                 9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V7, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED    19  46
  4Q LOSS WILD-TYPE 159 281
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     19   46
  4Q LOSS WILD-TYPE  159  281
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE              19               159
  MALE                46               281
[1] 2 2
[1] FALSE
D48V8, continuous
D48V9, continuous
[1] "Remove cluster labels:" "4Q LOSS MUTATED"       
clus
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                1                 7 
       TCGA-A3-A8CQ        TCGA-B2-A4SR        TCGA-B8-4621        TCGA-B8-5164 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-B8-A54F        TCGA-B8-A54G        TCGA-G6-A5PC 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4Q LOSS MUTATED       1                         1    61
  4Q LOSS WILD-TYPE     7                        32   396
D48V10, multiclass
                           clus
vv                          4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  ASIAN                                   1                 7
  BLACK OR AFRICAN AMERICAN               1                32
  WHITE                                  61               396
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V11, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED     4  43
  4Q LOSS WILD-TYPE  20 287
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      4   43
  4Q LOSS WILD-TYPE   20  287
                        clus
vv                       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   4                20
  NOT HISPANIC OR LATINO              43               287
[1] 2 2
[1] FALSE

Clustering(49) Variable = 5P LOSS MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                 0   1
  5P LOSS MUTATED     2   1
  5P LOSS WILD-TYPE 336  25
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                3               361 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                1                25 
$`5P LOSS MUTATED`
TCGA-AK-3433 TCGA-CJ-4901 TCGA-CZ-5469 
        2192         1450          946 

$`5P LOSS WILD-TYPE`
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 
        1120         1436           16          735         1493         1491 
TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 
        1130         1508         1478         1106         1186          751 
TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3347 
        1137         1485          665         1043          945         1610 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 
        1385          910         2688         1307         2504         1559 
TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 
         319          873         2270         2274          735         1621 
TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 
        1314         1070          630          567          574          861 
TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A8CQ TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 
        1993          617            3         3343         2566         2223 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
        2017          480         1853         2087         2044         1745 
TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 
        1423         1471         1280         1217         1779         1481 
TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
        1397          874         1143         1168          951          853 
TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4699 TCGA-B0-4706 TCGA-B0-4710 
         369         1238           43          110           26           96 
TCGA-B0-4718 TCGA-B0-4813 TCGA-B0-4819 TCGA-B0-5097 TCGA-B0-5108 TCGA-B0-5110 
         616           18          183          665          911         1092 
TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 
         359          797          657          535           59          493 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 
         554          652         1132          449         2408         3431 
TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 
        1487         3076         1420         1727         1835         2583 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
        2741         1732         1605         1203         3668         2414 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 
        3117         1459         2931         2722         1865         2963 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 
         992         1092           51          374          648          952 
TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 
         358          315          417          656          507          291 
TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
         175            7           38           16          141          166 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
          11            7          511          826          838          762 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 
         750          523          777          788          700          636 
TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
         722           36          822           26          737          522 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
         505          194          434           15         1046          435 
TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J 
         830          519           53          256          150           66 
TCGA-B8-A7U6 TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
         110         3377         2881         2746         3074         2839 
TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4173 TCGA-BP-4174 
        3037           13         2718          701         1893         1879 
TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 
        1955         1670         2964         1625          845         1888 
TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4338 TCGA-BP-4344 TCGA-BP-4347 
        1133          645          461         2859         1666         1367 
TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 
         372          970          374         2208         2372         2361 
TCGA-BP-4761 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4774 
         182         2184         1462          400         1876         1885 
TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 
        1843          411         1731         2080          354         1854 
TCGA-BP-4789 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 
        1489          620         1107         1124          204         1459 
TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
         211         2660         2172         1935         1785         1834 
TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 
        1862         1871          205         1746         1794          433 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 
        1487         1502         1384         1433         1632          454 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 
        1014         1413          785         1124          118         1413 
TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 
         501          177         1308         1371          932         1266 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 
         563         1177         1126          840         1140         1071 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5177 TCGA-BP-5180 
         193         2412         2257          932          293         2263 
TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
        1495         1165         1291         1133         1132          693 
TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 
         406          822         1011          967          714          408 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 
         749         1018          603         1355         1063          951 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4639 TCGA-CJ-4640 
          29         1820         1416         1924         2308         1998 
TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
        1628         1793          646         2554         1498         2423 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
        1435         2259         2283         2353         1955         2186 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4889 
        2014         1883         1759         2125         1952         1946 
TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4897 TCGA-CJ-4899 
        2085         1521          750          841         1808         1528 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 
        1520         1560         1792         1496         1499         1531 
TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-5671 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5681 
        1657         1373         1943         2430         2575          552 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6031 
        1883         1889         2231         2038         1855         1906 
TCGA-CJ-6032 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 
        2548         2799         2489         2609         2226         2017 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CZ-4853 
        2378         2271         3222         2552         3146          774 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-4863 
        1404           18         1943         1787         1843         1928 
TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5456 
        2830         1868         1929         1789           25         1712 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5463 
        1683         1732         1683         1430          330          662 
TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5470 TCGA-CZ-5982 
        1740         1446          685           59          386         2439 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
        2067         1997          373          435          693         1905 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 
        1329         1398         1470          370          355         1130 
TCGA-DV-5574 TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
         723         1729          551          119          206          127 
TCGA-GK-A6C7 
          61 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
              946                 3 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             2192              3668 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             1450              1291 
[1] "946.0 - 2192.0 (1450.0)" "3.0 - 3668.0 (1291.0)"  
[1] "hr=" "4"  
D49V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  5P LOSS MUTATED         0        2         1        4
  5P LOSS WILD-TYPE     244       54       125       75
D49V3, multiclass
           clus
vv          5P LOSS MUTATED 5P LOSS WILD-TYPE
  STAGE I                 0               244
  STAGE II                2                54
  STAGE III               1               125
  STAGE IV                4                75
[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"
                   vv
clus                 T1  T2  T3  T4
  5P LOSS MUTATED     0   3   2   2
  5P LOSS WILD-TYPE 250  64 175   9
D49V4, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  T1               0               250
  T2               3                64
  T3               2               175
  T4               2                 9
[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"
D49V5, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     6   0
  5P LOSS WILD-TYPE 224  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      6    0
  5P LOSS WILD-TYPE  224   18
   clus
vv  5P LOSS MUTATED 5P LOSS WILD-TYPE
  0               6               224
  1               0                18
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  5P LOSS MUTATED     4   3   0
  5P LOSS WILD-TYPE 413  75   9
D49V6, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  M0               4               413
  M1               3                75
  MX               0                 9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V7, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     4   3
  5P LOSS WILD-TYPE 174 324
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      4    3
  5P LOSS WILD-TYPE  174  324
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE               4               174
  MALE                 3               324
[1] 2 2
[1] FALSE
D49V8, continuous
[1] "Remove cluster labels:" "5P LOSS MUTATED"       
clus
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                1                36 
       TCGA-A3-A8CQ        TCGA-AK-3426        TCGA-AK-3430        TCGA-B0-4838 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-B2-5639        TCGA-B4-5377        TCGA-B4-5378        TCGA-B4-5832 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-B4-5834        TCGA-B4-5835        TCGA-B4-5836        TCGA-B4-5838 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-B4-5843        TCGA-B4-5844        TCGA-CZ-4854        TCGA-CZ-4856 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CZ-4858        TCGA-CZ-4860        TCGA-CZ-4861        TCGA-CZ-4862 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CZ-5456        TCGA-CZ-5457        TCGA-CZ-5465        TCGA-CZ-5982 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DV-5565        TCGA-DV-5566        TCGA-DV-5567        TCGA-DV-5568 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DV-5569        TCGA-DV-5573        TCGA-DV-5574        TCGA-DV-5575 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DV-5576        TCGA-EU-5904        TCGA-EU-5905        TCGA-EU-5907 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
D49V9, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5P LOSS MUTATED       0                         0     7
  5P LOSS WILD-TYPE     8                        33   450
D49V10, multiclass
                           clus
vv                          5P LOSS MUTATED 5P LOSS WILD-TYPE
  ASIAN                                   0                 8
  BLACK OR AFRICAN AMERICAN               0                33
  WHITE                                   7               450
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V11, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     0   6
  5P LOSS WILD-TYPE  24 324
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      0    6
  5P LOSS WILD-TYPE   24  324
                        clus
vv                       5P LOSS MUTATED 5P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                24
  NOT HISPANIC OR LATINO               6               324
[1] 2 2
[1] FALSE

Clustering(50) Variable = 5Q LOSS MUTATION ANALYSIS
D50V1, survival
                   sevent
clus2                 0   1
  5Q LOSS MUTATED     2   1
  5Q LOSS WILD-TYPE 336  25
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                3               361 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                1                25 
$`5Q LOSS MUTATED`
TCGA-AK-3433 TCGA-CJ-4901 TCGA-CZ-5469 
        2192         1450          946 

$`5Q LOSS WILD-TYPE`
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 
        1120         1436           16          735         1493         1491 
TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 
        1130         1508         1478         1106         1186          751 
TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3347 
        1137         1485          665         1043          945         1610 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 
        1385          910         2688         1307         2504         1559 
TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 
         319          873         2270         2274          735         1621 
TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 
        1314         1070          630          567          574          861 
TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A8CQ TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 
        1993          617            3         3343         2566         2223 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
        2017          480         1853         2087         2044         1745 
TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 
        1423         1471         1280         1217         1779         1481 
TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
        1397          874         1143         1168          951          853 
TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4699 TCGA-B0-4706 TCGA-B0-4710 
         369         1238           43          110           26           96 
TCGA-B0-4718 TCGA-B0-4813 TCGA-B0-4819 TCGA-B0-5097 TCGA-B0-5108 TCGA-B0-5110 
         616           18          183          665          911         1092 
TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 
         359          797          657          535           59          493 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 
         554          652         1132          449         2408         3431 
TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 
        1487         3076         1420         1727         1835         2583 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
        2741         1732         1605         1203         3668         2414 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 
        3117         1459         2931         2722         1865         2963 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 
         992         1092           51          374          648          952 
TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 
         358          315          417          656          507          291 
TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
         175            7           38           16          141          166 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
          11            7          511          826          838          762 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 
         750          523          777          788          700          636 
TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
         722           36          822           26          737          522 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
         505          194          434           15         1046          435 
TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J 
         830          519           53          256          150           66 
TCGA-B8-A7U6 TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
         110         3377         2881         2746         3074         2839 
TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4173 TCGA-BP-4174 
        3037           13         2718          701         1893         1879 
TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 
        1955         1670         2964         1625          845         1888 
TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4338 TCGA-BP-4344 TCGA-BP-4347 
        1133          645          461         2859         1666         1367 
TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 
         372          970          374         2208         2372         2361 
TCGA-BP-4761 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4774 
         182         2184         1462          400         1876         1885 
TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 
        1843          411         1731         2080          354         1854 
TCGA-BP-4789 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 
        1489          620         1107         1124          204         1459 
TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
         211         2660         2172         1935         1785         1834 
TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 
        1862         1871          205         1746         1794          433 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 
        1487         1502         1384         1433         1632          454 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 
        1014         1413          785         1124          118         1413 
TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 
         501          177         1308         1371          932         1266 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 
         563         1177         1126          840         1140         1071 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5177 TCGA-BP-5180 
         193         2412         2257          932          293         2263 
TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
        1495         1165         1291         1133         1132          693 
TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 
         406          822         1011          967          714          408 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 
         749         1018          603         1355         1063          951 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4639 TCGA-CJ-4640 
          29         1820         1416         1924         2308         1998 
TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
        1628         1793          646         2554         1498         2423 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
        1435         2259         2283         2353         1955         2186 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4889 
        2014         1883         1759         2125         1952         1946 
TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4897 TCGA-CJ-4899 
        2085         1521          750          841         1808         1528 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 
        1520         1560         1792         1496         1499         1531 
TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-5671 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5681 
        1657         1373         1943         2430         2575          552 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6031 
        1883         1889         2231         2038         1855         1906 
TCGA-CJ-6032 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 
        2548         2799         2489         2609         2226         2017 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CZ-4853 
        2378         2271         3222         2552         3146          774 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-4863 
        1404           18         1943         1787         1843         1928 
TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5456 
        2830         1868         1929         1789           25         1712 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5463 
        1683         1732         1683         1430          330          662 
TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5470 TCGA-CZ-5982 
        1740         1446          685           59          386         2439 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
        2067         1997          373          435          693         1905 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 
        1329         1398         1470          370          355         1130 
TCGA-DV-5574 TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
         723         1729          551          119          206          127 
TCGA-GK-A6C7 
          61 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              946                 3 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             2192              3668 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             1450              1291 
[1] "946.0 - 2192.0 (1450.0)" "3.0 - 3668.0 (1291.0)"  
[1] "hr=" "4"  
D50V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  5Q LOSS MUTATED         0        2         1        3
  5Q LOSS WILD-TYPE     244       54       125       76
D50V3, multiclass
           clus
vv          5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  STAGE I                 0               244
  STAGE II                2                54
  STAGE III               1               125
  STAGE IV                3                76
[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"
                   vv
clus                 T1  T2  T3  T4
  5Q LOSS MUTATED     0   2   2   2
  5Q LOSS WILD-TYPE 250  65 175   9
D50V4, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  T1               0               250
  T2               2                65
  T3               2               175
  T4               2                 9
[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"
D50V5, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED     5   0
  5Q LOSS WILD-TYPE 225  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      5    0
  5Q LOSS WILD-TYPE  225   18
   clus
vv  5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  0               5               225
  1               0                18
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  5Q LOSS MUTATED     4   2   0
  5Q LOSS WILD-TYPE 413  76   9
D50V6, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  M0               4               413
  M1               2                76
  MX               0                 9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V7, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED     3   3
  5Q LOSS WILD-TYPE 175 324
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      3    3
  5Q LOSS WILD-TYPE  175  324
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE               3               175
  MALE                 3               324
[1] 2 2
[1] FALSE
D50V8, continuous
[1] "Remove cluster labels:" "5Q LOSS MUTATED"       
clus
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                1                36 
       TCGA-A3-A8CQ        TCGA-AK-3426        TCGA-AK-3430        TCGA-B0-4838 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-B2-5639        TCGA-B4-5377        TCGA-B4-5378        TCGA-B4-5832 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-B4-5834        TCGA-B4-5835        TCGA-B4-5836        TCGA-B4-5838 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-B4-5843        TCGA-B4-5844        TCGA-CZ-4854        TCGA-CZ-4856 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CZ-4858        TCGA-CZ-4860        TCGA-CZ-4861        TCGA-CZ-4862 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CZ-5456        TCGA-CZ-5457        TCGA-CZ-5465        TCGA-CZ-5982 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DV-5565        TCGA-DV-5566        TCGA-DV-5567        TCGA-DV-5568 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DV-5569        TCGA-DV-5573        TCGA-DV-5574        TCGA-DV-5575 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DV-5576        TCGA-EU-5904        TCGA-EU-5905        TCGA-EU-5907 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
D50V9, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5Q LOSS MUTATED       0                         0     6
  5Q LOSS WILD-TYPE     8                        33   451
D50V10, multiclass
                           clus
vv                          5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  ASIAN                                   0                 8
  BLACK OR AFRICAN AMERICAN               0                33
  WHITE                                   6               451
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V11, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED     0   5
  5Q LOSS WILD-TYPE  24 325
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      0    5
  5Q LOSS WILD-TYPE   24  325
                        clus
vv                       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                24
  NOT HISPANIC OR LATINO               5               325
[1] 2 2
[1] FALSE

Clustering(51) Variable = 6P LOSS MUTATION ANALYSIS
D51V1, survival
                   sevent
clus2                 0   1
  6P LOSS MUTATED    64   8
  6P LOSS WILD-TYPE 274  18
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               72               292 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                8                18 
$`6P LOSS MUTATED`
TCGA-A3-3306 TCGA-A3-3316 TCGA-A3-3319 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3347 
        1120         1493         1130          665         1043         1610 
TCGA-A3-3374 TCGA-A3-3380 TCGA-A3-3382 TCGA-AK-3430 TCGA-AK-3433 TCGA-AK-3434 
        1314          567          574          480         2192         2087 
TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3447 TCGA-AK-3458 TCGA-AK-3465 TCGA-AS-3777 
        2044         1745         1217         1168          369         1238 
TCGA-B0-4699 TCGA-B0-4813 TCGA-B0-5108 TCGA-B0-5117 TCGA-B0-5702 TCGA-B2-3923 
         110           18          911          535         1605          992 
TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5838 TCGA-B8-4620 TCGA-B8-5158 TCGA-BP-4167 
         291            7          166          777          636         2718 
TCGA-BP-4176 TCGA-BP-4334 TCGA-BP-4761 TCGA-BP-4768 TCGA-BP-4775 TCGA-BP-4797 
        1955          645          182          400         1843         1107 
TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4962 TCGA-BP-4968 TCGA-BP-4983 TCGA-BP-4986 
        2660         2172         1785         1746         1413          785 
TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-5169 TCGA-BP-5175 TCGA-BP-5180 TCGA-BP-5185 
         501         1308          193          932         2263         1132 
TCGA-BP-5191 TCGA-BP-5201 TCGA-CJ-4635 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4881 
         967          951         1416         2423         1435         2014 
TCGA-CJ-4897 TCGA-CJ-4901 TCGA-CJ-4904 TCGA-CJ-4907 TCGA-CJ-5676 TCGA-CJ-6027 
        1808         1450         1792         1499         2575         1855 
TCGA-CW-5588 TCGA-CZ-4853 TCGA-CZ-4858 TCGA-CZ-4866 TCGA-CZ-5452 TCGA-CZ-5456 
        2017          774         1943         1868         1789         1712 
TCGA-CZ-5465 TCGA-CZ-5468 TCGA-CZ-5984 TCGA-CZ-5987 TCGA-DV-5568 TCGA-EU-5907 
        1446           59         2067          435          370          127 

$`6P LOSS WILD-TYPE`
TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3320 TCGA-A3-3322 
        1436           16          735         1491         1508         1478 
TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3343 
        1106         1186          751         1137         1485          945 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 
        1385          910         2688         1307         2504         1559 
TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 
         319          873         2270         2274          735         1621 
TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A8CQ 
        1070          630          861         1993          617            3 
TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3431 TCGA-AK-3443 
        3343         2566         2223         2017         1853         1423 
TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 
        1471         1280         1779         1481         1397          874 
TCGA-AK-3456 TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4706 TCGA-B0-4710 
        1143          951          853           43           26           96 
TCGA-B0-4718 TCGA-B0-4819 TCGA-B0-5097 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 
         616          183          665         1092          359          797 
TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
         657           59          493          554          652         1132 
TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 
         449         2408         3431         1487         3076         1420 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5703 
        1727         1835         2583         2741         1732         1203 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
        3668         2414         3117         1459         2931         2722 
TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 
        1865         2963         1092           51          374          648 
TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR 
         952          358          315          417          656          507 
TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 
         175           38           16          141           11            7 
TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 
         511          826          838          762          750          523 
TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 
         788          700          722           36          822           26 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 
         737          522          505          194          434           15 
TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H 
        1046          435          830          519           53          256 
TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4161 
         150           66          110         3377         2881         2746 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4169 TCGA-BP-4173 
        3074         2839         3037           13          701         1893 
TCGA-BP-4174 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 
        1879         1670         2964         1625          845         1888 
TCGA-BP-4332 TCGA-BP-4335 TCGA-BP-4338 TCGA-BP-4344 TCGA-BP-4347 TCGA-BP-4349 
        1133          461         2859         1666         1367          372 
TCGA-BP-4351 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4765 
         970          374         2208         2372         2361         2184 
TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 
        1462         1876         1885          411         1731         2080 
TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4795 TCGA-BP-4801 TCGA-BP-4803 
         354         1854         1489          620         1124          204 
TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4961 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 
        1459          211         1935         1834         1862         1871 
TCGA-BP-4967 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 
         205         1794          433         1487         1502         1384 
TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4982 TCGA-BP-4987 TCGA-BP-4989 
        1433         1632          454         1014         1124          118 
TCGA-BP-4991 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 
        1413          177         1371          932         1266          563 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5170 
        1177         1126          840         1140         1071         2412 
TCGA-BP-5174 TCGA-BP-5177 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
        2257          293         1495         1165         1291         1133 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 
         693          406          822         1011          714          408 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5202 
         749         1018          603         1355         1063           29 
TCGA-CJ-4634 TCGA-CJ-4636 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4642 TCGA-CJ-4643 
        1820         1924         2308         1998         1628         1793 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 
         646         2554         1498         2259         2283         2353 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 
        1955         2186         1883         1759         2125         1952 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4899 
        1946         2085         1521          750          841         1528 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4916 
        1520         1560         1496         1531         1657         1373 
TCGA-CJ-5671 TCGA-CJ-5675 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
        1943         2430          552         1883         1889         2231 
TCGA-CJ-5686 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 
        2038         1906         2548         2799         2489         2609 
TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 
        2226         2378         2271         3222         2552         3146 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 
        1404           18         1787         1843         1928         2830 
TCGA-CZ-5451 TCGA-CZ-5453 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
        1929           25         1683         1732         1683         1430 
TCGA-CZ-5461 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5469 TCGA-CZ-5470 
         330          662         1740          685          946          386 
TCGA-CZ-5982 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 
        2439         1997          373          693         1905         1329 
TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 
        1398         1470          355         1130          723         1729 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-GK-A6C7 
         551          119          206           61 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                7                 3 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             2718              3668 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
           1227.5            1318.0 
[1] "7.0 - 2718.0 (1227.5)" "3.0 - 3668.0 (1318.0)"
[1] "hr=" "1.9"
D51V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  6P LOSS MUTATED        36       13        28       21
  6P LOSS WILD-TYPE     208       43        98       58
D51V3, multiclass
           clus
vv          6P LOSS MUTATED 6P LOSS WILD-TYPE
  STAGE I                36               208
  STAGE II               13                43
  STAGE III              28                98
  STAGE IV               21                58
[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"
                   vv
clus                 T1  T2  T3  T4
  6P LOSS MUTATED    37  15  42   4
  6P LOSS WILD-TYPE 213  52 135   7
D51V4, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  T1              37               213
  T2              15                52
  T3              42               135
  T4               4                 7
[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"
D51V5, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    35   8
  6P LOSS WILD-TYPE 195  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     35    8
  6P LOSS WILD-TYPE  195   10
   clus
vv  6P LOSS MUTATED 6P LOSS WILD-TYPE
  0              35               195
  1               8                10
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  6P LOSS MUTATED    79  19   0
  6P LOSS WILD-TYPE 338  59   9
D51V6, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  M0              79               338
  M1              19                59
  MX               0                 9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V7, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    21  77
  6P LOSS WILD-TYPE 157 250
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     21   77
  6P LOSS WILD-TYPE  157  250
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE              21               157
  MALE                77               250
[1] 2 2
[1] FALSE
D51V8, continuous
D51V9, continuous
[1] "Remove cluster labels:" "6P LOSS MUTATED"       
clus
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                1                 7 
       TCGA-A3-A8CQ        TCGA-B2-A4SR        TCGA-B8-4621        TCGA-B8-5164 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-B8-A54F        TCGA-B8-A54G        TCGA-G6-A5PC 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6P LOSS MUTATED       1                         2    93
  6P LOSS WILD-TYPE     7                        31   364
D51V10, multiclass
                           clus
vv                          6P LOSS MUTATED 6P LOSS WILD-TYPE
  ASIAN                                   1                 7
  BLACK OR AFRICAN AMERICAN               2                31
  WHITE                                  93               364
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V11, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     5  63
  6P LOSS WILD-TYPE  19 267
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      5   63
  6P LOSS WILD-TYPE   19  267
                        clus
vv                       6P LOSS MUTATED 6P LOSS WILD-TYPE
  HISPANIC OR LATINO                   5                19
  NOT HISPANIC OR LATINO              63               267
[1] 2 2
[1] FALSE

Clustering(52) Variable = 6Q LOSS MUTATION ANALYSIS
D52V1, survival
                   sevent
clus2                 0   1
  6Q LOSS MUTATED    89   6
  6Q LOSS WILD-TYPE 249  20
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               95               269 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                6                20 
$`6Q LOSS MUTATED`
TCGA-A3-3306 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3335 
        1120         1493         1491         1130         1508          665 
TCGA-A3-3336 TCGA-A3-3347 TCGA-A3-3374 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-A8CQ 
        1043         1610         1314          567          574            3 
TCGA-AK-3430 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3447 
         480         2192         2087         2044         1745         1217 
TCGA-AK-3458 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4699 TCGA-B0-5108 TCGA-B0-5117 
        1168          369         1238          110          911          535 
TCGA-B0-5119 TCGA-B0-5402 TCGA-B0-5702 TCGA-B2-3923 TCGA-B2-5641 TCGA-B4-5377 
          59          449         1605          992          656          291 
TCGA-B4-5832 TCGA-B4-5835 TCGA-B4-5838 TCGA-B8-4148 TCGA-B8-4620 TCGA-B8-5158 
           7           16          166          826          777          636 
TCGA-B8-A54G TCGA-BP-4167 TCGA-BP-4176 TCGA-BP-4325 TCGA-BP-4334 TCGA-BP-4761 
          53         2718         1955         2964          645          182 
TCGA-BP-4768 TCGA-BP-4775 TCGA-BP-4777 TCGA-BP-4797 TCGA-BP-4959 TCGA-BP-4960 
         400         1843         1731         1107         2660         2172 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4968 TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4987 
        1785         1834         1746         1413          785         1124 
TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-5000 TCGA-BP-5169 TCGA-BP-5175 TCGA-BP-5180 
         501         1308          563          193          932         2263 
TCGA-BP-5185 TCGA-BP-5191 TCGA-BP-5201 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4643 
        1132          967          951         1820         1416         1793 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4881 TCGA-CJ-4893 TCGA-CJ-4897 TCGA-CJ-4901 
        2423         1435         2014          750         1808         1450 
TCGA-CJ-4904 TCGA-CJ-4907 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-6027 TCGA-CJ-6032 
        1792         1499         2430         2575         1855         2548 
TCGA-CW-5585 TCGA-CW-5588 TCGA-CZ-4853 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4866 
        2609         2017          774         1943         1787         1868 
TCGA-CZ-5452 TCGA-CZ-5456 TCGA-CZ-5460 TCGA-CZ-5465 TCGA-CZ-5982 TCGA-CZ-5984 
        1789         1712         1430         1446         2439         2067 
TCGA-CZ-5987 TCGA-DV-5568 TCGA-DV-5573 TCGA-DV-5575 TCGA-EU-5907 
         435          370         1130         1729          127 

$`6Q LOSS WILD-TYPE`
TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 
        1436           16          735         1478         1106         1186 
TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3343 TCGA-A3-3349 TCGA-A3-3351 
         751         1137         1485          945         1385          910 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
        2688         1307         2504         1559          319          873 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 
        2270         2274          735         1621         1070          630 
TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 
         861         1993          617         3343         2566         2223 
TCGA-AK-3429 TCGA-AK-3431 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3450 
        2017         1853         1423         1471         1280         1779 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3456 TCGA-AK-3460 TCGA-AK-3461 
        1481         1397          874         1143          951          853 
TCGA-AS-3778 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4718 TCGA-B0-4813 TCGA-B0-4819 
          43           26           96          616           18          183 
TCGA-B0-5097 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5120 
         665         1092          359          797          657          493 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 
         554          652         1132         2408         3431         1487 
TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 
        3076         1420         1727         1835         2583         2741 
TCGA-B0-5701 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 
        1732         1203         3668         2414         3117         1459 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3924 TCGA-B2-4098 
        2931         2722         1865         2963         1092           51 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 
         374          648          952          358          315          417 
TCGA-B2-A4SR TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 
         507          175           38          141           11            7 
TCGA-B8-4146 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4621 
         511          838          762          750          523          788 
TCGA-B8-4622 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
         700          722           36          822           26          737 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
         522          505          194          434           15         1046 
TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J 
         435          830          519          256          150           66 
TCGA-B8-A7U6 TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
         110         3377         2881         2746         3074         2839 
TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4169 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4177 
        3037           13          701         1893         1879         1670 
TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4335 TCGA-BP-4338 
        1625          845         1888         1133          461         2859 
TCGA-BP-4344 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4756 TCGA-BP-4758 
        1666         1367          372          970          374         2208 
TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4774 
        2372         2361         2184         1462         1876         1885 
TCGA-BP-4776 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4795 
         411         2080          354         1854         1489          620 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4961 TCGA-BP-4964 
        1124          204         1459          211         1935         1862 
TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
        1871          205         1794          433         1487         1502 
TCGA-BP-4973 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4982 TCGA-BP-4989 
        1384         1433         1632          454         1014          118 
TCGA-BP-4991 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5001 
        1413          177         1371          932         1266         1177 
TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5170 TCGA-BP-5174 
        1126          840         1140         1071         2412         2257 
TCGA-BP-5177 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 
         293         1495         1165         1291         1133          693 
TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
         406          822         1011          714          408          749 
TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4636 
        1018          603         1355         1063           29         1924 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4642 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
        2308         1998         1628          646         2554         1498 
TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4882 
        2259         2283         2353         1955         2186         1883 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 
        1759         2125         1952         1946         2085         1521 
TCGA-CJ-4894 TCGA-CJ-4899 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4908 
         841         1528         1520         1560         1496         1531 
TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-5671 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
        1657         1373         1943          552         1883         1889 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6031 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5587 
        2231         2038         1906         2799         2489         2226 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CZ-4854 
        2378         2271         3222         2552         3146         1404 
TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-5451 TCGA-CZ-5453 
          18         1843         1928         2830         1929           25 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5461 TCGA-CZ-5463 TCGA-CZ-5464 
        1683         1732         1683          330          662         1740 
TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5985 TCGA-CZ-5986 
         685           59          946          386         1997          373 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5569 
         693         1905         1329         1398         1470          355 
TCGA-DV-5574 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-GK-A6C7 
         723          551          119          206           61 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                3                 7 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             2964              3668 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             1314              1280 
[1] "3.0 - 2964.0 (1314.0)" "7.0 - 3668.0 (1280.0)"
[1] "hr=" "1.2"
D52V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  6Q LOSS MUTATED        54       17        30       24
  6Q LOSS WILD-TYPE     190       39        96       55
D52V3, multiclass
           clus
vv          6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  STAGE I                54               190
  STAGE II               17                39
  STAGE III              30                96
  STAGE IV               24                55
[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"
                   vv
clus                 T1  T2  T3  T4
  6Q LOSS MUTATED    55  19  46   5
  6Q LOSS WILD-TYPE 195  48 131   6
D52V4, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  T1              55               195
  T2              19                48
  T3              46               131
  T4               5                 6
[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"
D52V5, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    44  10
  6Q LOSS WILD-TYPE 186   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     44   10
  6Q LOSS WILD-TYPE  186    8
   clus
vv  6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  0              44               186
  1              10                 8
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  6Q LOSS MUTATED   102  21   2
  6Q LOSS WILD-TYPE 315  57   7
D52V6, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  M0             102               315
  M1              21                57
  MX               2                 7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V7, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    35  90
  6Q LOSS WILD-TYPE 143 237
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     35   90
  6Q LOSS WILD-TYPE  143  237
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE              35               143
  MALE                90               237
[1] 2 2
[1] FALSE
D52V8, continuous
D52V9, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6Q LOSS MUTATED       2                         4   116
  6Q LOSS WILD-TYPE     6                        29   341
D52V10, multiclass
                           clus
vv                          6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  ASIAN                                   2                 6
  BLACK OR AFRICAN AMERICAN               4                29
  WHITE                                 116               341
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V11, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED     7  81
  6Q LOSS WILD-TYPE  17 249
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      7   81
  6Q LOSS WILD-TYPE   17  249
                        clus
vv                       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   7                17
  NOT HISPANIC OR LATINO              81               249
[1] 2 2
[1] FALSE

Clustering(53) Variable = 7Q LOSS MUTATION ANALYSIS
D53V1, survival
                   sevent
clus2                 0   1
  7Q LOSS MUTATED     2   0
  7Q LOSS WILD-TYPE 336  26
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                2               362 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                0                26 
$`7Q LOSS MUTATED`
TCGA-BP-4761 TCGA-CJ-4912 
         182         1657 

$`7Q LOSS WILD-TYPE`
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 
        1120         1436           16          735         1493         1491 
TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 
        1130         1508         1478         1106         1186          751 
TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3347 
        1137         1485          665         1043          945         1610 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 
        1385          910         2688         1307         2504         1559 
TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 
         319          873         2270         2274          735         1621 
TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 
        1314         1070          630          567          574          861 
TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A8CQ TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 
        1993          617            3         3343         2566         2223 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 
        2017          480         1853         2192         2087         2044 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 
        1745         1423         1471         1280         1217         1779 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
        1481         1397          874         1143         1168          951 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4699 TCGA-B0-4706 
         853          369         1238           43          110           26 
TCGA-B0-4710 TCGA-B0-4718 TCGA-B0-4813 TCGA-B0-4819 TCGA-B0-5097 TCGA-B0-5108 
          96          616           18          183          665          911 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 
        1092          359          797          657          535           59 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 
         493          554          652         1132          449         2408 
TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 
        3431         1487         3076         1420         1727         1835 
TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 
        2583         2741         1732         1605         1203         3668 
TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
        2414         3117         1459         2931         2722         1865 
TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 
        2963          992         1092           51          374          648 
TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR 
         952          358          315          417          656          507 
TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
         291          175            7           38           16          141 
TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
         166           11            7          511          826          838 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 
         762          750          523          777          788          700 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
         636          722           36          822           26          737 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
         522          505          194          434           15         1046 
TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I 
         435          830          519           53          256          150 
TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 
          66          110         3377         2881         2746         3074 
TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4173 
        2839         3037           13         2718          701         1893 
TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 
        1879         1955         1670         2964         1625          845 
TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4338 TCGA-BP-4344 
        1888         1133          645          461         2859         1666 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 
        1367          372          970          374         2208         2372 
TCGA-BP-4760 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4774 
        2361         2184         1462          400         1876         1885 
TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 
        1843          411         1731         2080          354         1854 
TCGA-BP-4789 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 
        1489          620         1107         1124          204         1459 
TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
         211         2660         2172         1935         1785         1834 
TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 
        1862         1871          205         1746         1794          433 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 
        1487         1502         1384         1433         1632          454 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 
        1014         1413          785         1124          118         1413 
TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 
         501          177         1308         1371          932         1266 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 
         563         1177         1126          840         1140         1071 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5177 TCGA-BP-5180 
         193         2412         2257          932          293         2263 
TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
        1495         1165         1291         1133         1132          693 
TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 
         406          822         1011          967          714          408 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 
         749         1018          603         1355         1063          951 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4639 TCGA-CJ-4640 
          29         1820         1416         1924         2308         1998 
TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
        1628         1793          646         2554         1498         2423 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
        1435         2259         2283         2353         1955         2186 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4889 
        2014         1883         1759         2125         1952         1946 
TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4897 TCGA-CJ-4899 
        2085         1521          750          841         1808         1528 
TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 
        1450         1520         1560         1792         1496         1499 
TCGA-CJ-4908 TCGA-CJ-4916 TCGA-CJ-5671 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5681 
        1531         1373         1943         2430         2575          552 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6031 
        1883         1889         2231         2038         1855         1906 
TCGA-CJ-6032 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 
        2548         2799         2489         2609         2226         2017 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CZ-4853 
        2378         2271         3222         2552         3146          774 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-4863 
        1404           18         1943         1787         1843         1928 
TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5456 
        2830         1868         1929         1789           25         1712 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5463 
        1683         1732         1683         1430          330          662 
TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 
        1740         1446          685           59          946          386 
TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 
        2439         2067         1997          373          435          693 
TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 
        1905         1329         1398         1470          370          355 
TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 
        1130          723         1729          551          119          206 
TCGA-EU-5907 TCGA-GK-A6C7 
         127           61 

  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
              182                 3 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
             1657              3668 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            919.5            1299.0 
[1] "182.0 - 1657.0 (919.5)" "3.0 - 3668.0 (1299.0)" 
[1] "Remove cluster labels:" "7Q LOSS MUTATED"       
D53V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  7Q LOSS MUTATED         0        1         1        1
  7Q LOSS WILD-TYPE     244       55       125       78
D53V3, multiclass
           clus
vv          7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  STAGE I                 0               244
  STAGE II                1                55
  STAGE III               1               125
  STAGE IV                1                78
[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"
                   vv
clus                 T1  T2  T3  T4
  7Q LOSS MUTATED     0   1   1   1
  7Q LOSS WILD-TYPE 250  66 176  10
D53V4, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  T1               0               250
  T2               1                66
  T3               1               176
  T4               1                10
[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"
D53V5, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     0   1
  7Q LOSS WILD-TYPE 230  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      0    1
  7Q LOSS WILD-TYPE  230   17
   clus
vv  7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  0               0               230
  1               1                17
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  7Q LOSS MUTATED     3   0   0
  7Q LOSS WILD-TYPE 414  78   9
D53V6, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  M0               3               414
  M1               0                78
  MX               0                 9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V7, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     0   3
  7Q LOSS WILD-TYPE 178 324
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      0    3
  7Q LOSS WILD-TYPE  178  324
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  FEMALE               0               178
  MALE                 3               324
[1] 2 2
[1] FALSE
D53V8, continuous
D53V9, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7Q LOSS MUTATED       0                         0     3
  7Q LOSS WILD-TYPE     8                        33   454
D53V10, multiclass
                           clus
vv                          7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  ASIAN                                   0                 8
  BLACK OR AFRICAN AMERICAN               0                33
  WHITE                                   3               454
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V11, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     1   1
  7Q LOSS WILD-TYPE  23 329
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      1    1
  7Q LOSS WILD-TYPE   23  329
                        clus
vv                       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                23
  NOT HISPANIC OR LATINO               1               329
[1] 2 2
[1] FALSE

Clustering(54) Variable = 8P LOSS MUTATION ANALYSIS
D54V1, survival
                   sevent
clus2                 0   1
  8P LOSS MUTATED    86   8
  8P LOSS WILD-TYPE 252  18
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               94               270 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                8                18 
$`8P LOSS MUTATED`
TCGA-A3-3319 TCGA-A3-3325 TCGA-A3-3336 TCGA-A3-3365 TCGA-A3-3372 TCGA-A3-3373 
        1130          751         1043          873          735         1621 
TCGA-A3-3382 TCGA-AK-3425 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3447 
         574         3343         2087         2044         1745         1217 
TCGA-AK-3458 TCGA-AS-3777 TCGA-B0-4699 TCGA-B0-4718 TCGA-B0-4813 TCGA-B0-4819 
        1168         1238          110          616           18          183 
TCGA-B0-5108 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-A4SR 
         911         1420         1727         2722         1865          507 
TCGA-B4-5377 TCGA-B4-5838 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-5158 TCGA-B8-5163 
         291          166          826          838          636          822 
TCGA-B8-5164 TCGA-B8-5545 TCGA-B8-5549 TCGA-B8-5551 TCGA-B8-A54I TCGA-BP-4174 
          26          522          194           15          150         1879 
TCGA-BP-4176 TCGA-BP-4326 TCGA-BP-4338 TCGA-BP-4347 TCGA-BP-4351 TCGA-BP-4775 
        1955         1625         2859         1367          970         1843 
TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4965 
        2080          354          211         2660         2172         1871 
TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4973 TCGA-BP-4986 TCGA-BP-4994 
         205         1746          433         1384          785         1308 
TCGA-BP-4998 TCGA-BP-5004 TCGA-BP-5175 TCGA-BP-5177 TCGA-BP-5182 TCGA-BP-5200 
         932         1126          932          293         1165         1063 
TCGA-BP-5201 TCGA-CJ-4640 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4870 
         951         1998         1628         1793          646         1498 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4889 
        1955         2186         2014         1759         2125         1946 
TCGA-CJ-4894 TCGA-CJ-4897 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4907 TCGA-CJ-4912 
         841         1808         1560         1792         1499         1657 
TCGA-CJ-6027 TCGA-CW-6088 TCGA-CW-6090 TCGA-CZ-4854 TCGA-CZ-4862 TCGA-CZ-5453 
        1855         3222         2552         1404         1843           25 
TCGA-CZ-5457 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5986 
        1683          662         1446          685           59          373 
TCGA-CZ-5988 TCGA-DV-5565 TCGA-DV-5574 TCGA-DV-5575 
         693         1329          723         1729 

$`8P LOSS WILD-TYPE`
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 
        1120         1436           16          735         1493         1491 
TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3326 TCGA-A3-3331 
        1508         1478         1106         1186         1137         1485 
TCGA-A3-3335 TCGA-A3-3343 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 
         665          945         1610         1385          910         2688 
TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3367 TCGA-A3-3370 
        1307         2504         1559          319         2270         2274 
TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 
        1314         1070          630          567          861         1993 
TCGA-A3-3387 TCGA-A3-A8CQ TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 
         617            3         2566         2223         2017          480 
TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3450 
        1853         2192         1423         1471         1280         1779 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3456 TCGA-AK-3460 TCGA-AK-3461 
        1481         1397          874         1143          951          853 
TCGA-AK-3465 TCGA-AS-3778 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-5097 TCGA-B0-5110 
         369           43           26           96          665         1092 
TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 
         359          797          657          535           59          493 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 
         554          652         1132          449         2408         3431 
TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 
        1487         3076         1835         2583         2741         1732 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 
        1605         1203         3668         2414         3117         1459 
TCGA-B0-5711 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
        2931         2963          992         1092           51          374 
TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 
         648          952          358          315          417          656 
TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5843 
         175            7           38           16          141           11 
TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 
           7          511          762          750          523          777 
TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5165 TCGA-B8-5546 
         788          700          722           36          737          505 
TCGA-B8-5550 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G 
         434         1046          435          830          519           53 
TCGA-B8-A54H TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4161 
         256           66          110         3377         2881         2746 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 
        3074         2839         3037           13         2718          701 
TCGA-BP-4173 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 
        1893         1670         2964          845         1888         1133 
TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4344 TCGA-BP-4349 TCGA-BP-4756 TCGA-BP-4758 
         645          461         1666          372          374         2208 
TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 
        2372         2361          182         2184         1462          400 
TCGA-BP-4769 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4784 TCGA-BP-4789 
        1876         1885          411         1731         1854         1489 
TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4961 
         620         1107         1124          204         1459         1935 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4969 TCGA-BP-4971 TCGA-BP-4972 
        1785         1834         1862         1794         1487         1502 
TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4987 
        1433         1632          454         1014         1413         1124 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 
         118         1413          501          177         1371         1266 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5169 
         563         1177          840         1140         1071          193 
TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5183 TCGA-BP-5184 
        2412         2257         2263         1495         1291         1133 
TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 
        1132          693          406          822         1011          967 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 
         714          408          749         1018          603         1355 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4639 TCGA-CJ-4869 
          29         1820         1416         1924         2308         2554 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4882 
        2423         1435         2259         2283         2353         1883 
TCGA-CJ-4886 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4899 TCGA-CJ-4901 
        1952         2085         1521          750         1528         1450 
TCGA-CJ-4902 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4916 TCGA-CJ-5671 TCGA-CJ-5675 
        1520         1496         1531         1373         1943         2430 
TCGA-CJ-5676 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 
        2575          552         1883         1889         2231         2038 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5587 
        1906         2548         2799         2489         2609         2226 
TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4856 
        2017         2378         2271         3146          774           18 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 
        1943         1787         1928         2830         1868         1929 
TCGA-CZ-5452 TCGA-CZ-5456 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 
        1789         1712         1732         1683         1430          330 
TCGA-CZ-5464 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
        1740          946          386         2439         2067         1997 
TCGA-CZ-5987 TCGA-CZ-5989 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 
         435         1905         1398         1470          370          355 
TCGA-DV-5573 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-GK-A6C7 
        1130          551          119          206          127           61 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               15                 3 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             3343              3668 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           1227.5            1310.5 
[1] "15.0 - 3343.0 (1227.5)" "3.0 - 3668.0 (1310.5)" 
[1] "hr=" "1.3"
D54V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  8P LOSS MUTATED        57       14        39       24
  8P LOSS WILD-TYPE     187       42        87       55
D54V3, multiclass
           clus
vv          8P LOSS MUTATED 8P LOSS WILD-TYPE
  STAGE I                57               187
  STAGE II               14                42
  STAGE III              39                87
  STAGE IV               24                55
[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"
                   vv
clus                 T1  T2  T3  T4
  8P LOSS MUTATED    59  16  56   3
  8P LOSS WILD-TYPE 191  51 121   8
D54V4, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  T1              59               191
  T2              16                51
  T3              56               121
  T4               3                 8
[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"
D54V5, binary
                   cls
clus                  0   1
  8P LOSS MUTATED    55   5
  8P LOSS WILD-TYPE 175  13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     55    5
  8P LOSS WILD-TYPE  175   13
   clus
vv  8P LOSS MUTATED 8P LOSS WILD-TYPE
  0              55               175
  1               5                13
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  8P LOSS MUTATED   108  25   1
  8P LOSS WILD-TYPE 309  53   8
D54V6, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  M0             108               309
  M1              25                53
  MX               1                 8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V7, binary
                   cls
clus                  0   1
  8P LOSS MUTATED    38  96
  8P LOSS WILD-TYPE 140 231
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     38   96
  8P LOSS WILD-TYPE  140  231
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE              38               140
  MALE                96               231
[1] 2 2
[1] FALSE
D54V8, continuous
D54V9, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8P LOSS MUTATED       3                         6   123
  8P LOSS WILD-TYPE     5                        27   334
D54V10, multiclass
                           clus
vv                          8P LOSS MUTATED 8P LOSS WILD-TYPE
  ASIAN                                   3                 5
  BLACK OR AFRICAN AMERICAN               6                27
  WHITE                                 123               334
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V11, binary
                   cls
clus                  0   1
  8P LOSS MUTATED    11  79
  8P LOSS WILD-TYPE  13 251
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     11   79
  8P LOSS WILD-TYPE   13  251
                        clus
vv                       8P LOSS MUTATED 8P LOSS WILD-TYPE
  HISPANIC OR LATINO                  11                13
  NOT HISPANIC OR LATINO              79               251
[1] 2 2
[1] FALSE

Clustering(55) Variable = 8Q LOSS MUTATION ANALYSIS
D55V1, survival
                   sevent
clus2                 0   1
  8Q LOSS MUTATED    44   3
  8Q LOSS WILD-TYPE 294  23
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               47               317 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                3                23 
$`8Q LOSS MUTATED`
TCGA-A3-3365 TCGA-A3-3372 TCGA-A3-3373 TCGA-AK-3440 TCGA-AK-3458 TCGA-AS-3777 
         873          735         1621         1745         1168         1238 
TCGA-B0-4699 TCGA-B0-4718 TCGA-B0-4813 TCGA-B0-5696 TCGA-B4-5838 TCGA-B8-5164 
         110          616           18         1727          166           26 
TCGA-B8-5545 TCGA-B8-5549 TCGA-BP-4347 TCGA-BP-4351 TCGA-BP-4775 TCGA-BP-4781 
         522          194         1367          970         1843         2080 
TCGA-BP-4960 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4973 TCGA-BP-4994 TCGA-BP-5004 
        2172          205         1746         1384         1308         1126 
TCGA-BP-5177 TCGA-BP-5200 TCGA-BP-5201 TCGA-CJ-4640 TCGA-CJ-4642 TCGA-CJ-4876 
         293         1063          951         1998         1628         1955 
TCGA-CJ-4885 TCGA-CJ-4889 TCGA-CJ-4894 TCGA-CJ-4897 TCGA-CJ-4903 TCGA-CJ-4904 
        2125         1946          841         1808         1560         1792 
TCGA-CJ-4907 TCGA-CW-6088 TCGA-CW-6090 TCGA-CZ-4862 TCGA-CZ-5453 TCGA-CZ-5457 
        1499         3222         2552         1843           25         1683 
TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5986 TCGA-CZ-5988 TCGA-DV-5575 
         662         1446          373          693         1729 

$`8Q LOSS WILD-TYPE`
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 
        1120         1436           16          735         1493         1491 
TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 
        1130         1508         1478         1106         1186          751 
TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3347 
        1137         1485          665         1043          945         1610 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 
        1385          910         2688         1307         2504         1559 
TCGA-A3-3363 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 
         319         2270         2274         1314         1070          630 
TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A8CQ 
         567          574          861         1993          617            3 
TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 
        3343         2566         2223         2017          480         1853 
TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 
        2192         2087         2044         1423         1471         1280 
TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3456 
        1217         1779         1481         1397          874         1143 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3778 TCGA-B0-4706 TCGA-B0-4710 
         951          853          369           43           26           96 
TCGA-B0-4819 TCGA-B0-5097 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 
         183          665          911         1092          359          797 
TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
         657          535           59          493          554          652 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 
        1132          449         2408         3431         1487         3076 
TCGA-B0-5695 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
        1420         1835         2583         2741         1732         1605 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
        1203         3668         2414         3117         1459         2931 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
        2722         1865         2963          992         1092           51 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 
         374          648          952          358          315          417 
TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 
         656          507          291          175            7           38 
TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 
          16          141           11            7          511          826 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 
         838          762          750          523          777          788 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5165 
         700          636          722           36          822          737 
TCGA-B8-5546 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D 
         505          434           15         1046          435          830 
TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 
         519           53          256          150           66          110 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 
        3377         2881         2746         3074         2839         3037 
TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 
          13         2718          701         1893         1879         1955 
TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 
        1670         2964         1625          845         1888         1133 
TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4338 TCGA-BP-4344 TCGA-BP-4349 TCGA-BP-4756 
         645          461         2859         1666          372          374 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4765 TCGA-BP-4766 
        2208         2372         2361          182         2184         1462 
TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4782 
         400         1876         1885          411         1731          354 
TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4801 TCGA-BP-4803 
        1854         1489          620         1107         1124          204 
TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
        1459          211         2660         1935         1785         1834 
TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
        1862         1871         1794          433         1487         1502 
TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4986 
        1433         1632          454         1014         1413          785 
TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 
        1124          118         1413          501          177         1371 
TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5006 TCGA-BP-5007 
         932         1266          563         1177          840         1140 
TCGA-BP-5008 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5180 
        1071          193         2412         2257          932         2263 
TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
        1495         1165         1291         1133         1132          693 
TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 
         406          822         1011          967          714          408 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5202 TCGA-CJ-4634 
         749         1018          603         1355           29         1820 
TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4639 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 
        1416         1924         2308         1793          646         2554 
TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 
        1498         2423         1435         2259         2283         2353 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4886 TCGA-CJ-4890 
        2186         2014         1883         1759         1952         2085 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4899 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4905 
        1521          750         1528         1450         1520         1496 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-5671 TCGA-CJ-5675 TCGA-CJ-5676 
        1531         1657         1373         1943         2430         2575 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 
         552         1883         1889         2231         2038         1855 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5587 
        1906         2548         2799         2489         2609         2226 
TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4854 
        2017         2378         2271         3146          774         1404 
TCGA-CZ-4856 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 
          18         1943         1787         1928         2830         1868 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5456 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
        1929         1789         1712         1732         1683         1430 
TCGA-CZ-5461 TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 
         330         1740          685           59          946          386 
TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5987 TCGA-CZ-5989 TCGA-DV-5565 
        2439         2067         1997          435         1905         1329 
TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 
        1398         1470          370          355         1130          723 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-GK-A6C7 
         551          119          206          127           61 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               18                 3 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             3222              3668 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             1367              1280 
[1] "18.0 - 3222.0 (1367.0)" "3.0 - 3668.0 (1280.0)" 
[1] "hr=" "1.1"
D55V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  8Q LOSS MUTATED        26        7        20        9
  8Q LOSS WILD-TYPE     218       49       106       70
D55V3, multiclass
           clus
vv          8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  STAGE I                26               218
  STAGE II                7                49
  STAGE III              20               106
  STAGE IV                9                70
[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"
                   vv
clus                 T1  T2  T3  T4
  8Q LOSS MUTATED    26   7  27   2
  8Q LOSS WILD-TYPE 224  60 150   9
D55V4, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  T1              26               224
  T2               7                60
  T3              27               150
  T4               2                 9
[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"
D55V5, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    25   3
  8Q LOSS WILD-TYPE 205  15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     25    3
  8Q LOSS WILD-TYPE  205   15
   clus
vv  8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  0              25               205
  1               3                15
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  8Q LOSS MUTATED    53   9   0
  8Q LOSS WILD-TYPE 364  69   9
D55V6, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  M0              53               364
  M1               9                69
  MX               0                 9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V7, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    14  48
  8Q LOSS WILD-TYPE 164 279
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     14   48
  8Q LOSS WILD-TYPE  164  279
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE              14               164
  MALE                48               279
[1] 2 2
[1] FALSE
D55V8, continuous
D55V9, continuous
[1] "Remove cluster labels:" "8Q LOSS MUTATED"       
clus
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                1                 7 
       TCGA-A3-A8CQ        TCGA-B2-A4SR        TCGA-B8-4621        TCGA-B8-5158 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-B8-A54F        TCGA-B8-A54G        TCGA-G6-A5PC 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8Q LOSS MUTATED       1                         1    59
  8Q LOSS WILD-TYPE     7                        32   398
D55V10, multiclass
                           clus
vv                          8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  ASIAN                                   1                 7
  BLACK OR AFRICAN AMERICAN               1                32
  WHITE                                  59               398
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V11, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     6  33
  8Q LOSS WILD-TYPE  18 297
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      6   33
  8Q LOSS WILD-TYPE   18  297
                        clus
vv                       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   6                18
  NOT HISPANIC OR LATINO              33               297
[1] 2 2
[1] FALSE

Clustering(56) Variable = 9P LOSS MUTATION ANALYSIS
D56V1, survival
                   sevent
clus2                 0   1
  9P LOSS MUTATED    75   9
  9P LOSS WILD-TYPE 263  17
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               84               280 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                9                17 
$`9P LOSS MUTATED`
TCGA-A3-3306 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3325 TCGA-A3-3347 
        1120         1493         1491         1130          751         1610 
TCGA-A3-3372 TCGA-A3-3382 TCGA-AK-3425 TCGA-AK-3436 TCGA-AK-3445 TCGA-AK-3450 
         735          574         3343         2044         1280         1779 
TCGA-AS-3777 TCGA-B0-4710 TCGA-B0-4819 TCGA-B0-5097 TCGA-B0-5113 TCGA-B0-5116 
        1238           96          183          665          359          657 
TCGA-B0-5121 TCGA-B0-5402 TCGA-B0-5701 TCGA-B2-5633 TCGA-B2-5641 TCGA-B4-5832 
         554          449         1732          358          656            7 
TCGA-B4-5838 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5549 TCGA-B8-5551 
         166          777          700          636          194           15 
TCGA-BP-4161 TCGA-BP-4167 TCGA-BP-4176 TCGA-BP-4351 TCGA-BP-4766 TCGA-BP-4768 
        2746         2718         1955          970         1462          400 
TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4797 TCGA-BP-4803 TCGA-BP-4960 TCGA-BP-4962 
        2080          354         1107          204         2172         1785 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4973 TCGA-BP-4986 TCGA-BP-4994 TCGA-BP-4995 
        1834         1862         1384          785         1308         1371 
TCGA-BP-5000 TCGA-BP-5169 TCGA-BP-5175 TCGA-BP-5180 TCGA-BP-5183 TCGA-BP-5189 
         563          193          932         2263         1291          822 
TCGA-BP-5191 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5201 TCGA-CJ-4635 TCGA-CJ-4871 
         967         1018          603          951         1416         2423 
TCGA-CJ-4881 TCGA-CJ-4890 TCGA-CJ-4901 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 
        2014         2085         1450         1499         1531         1657 
TCGA-CJ-5671 TCGA-CJ-5676 TCGA-CJ-5682 TCGA-CJ-6027 TCGA-CJ-6031 TCGA-CW-5588 
        1943         2575         1883         1855         1906         2017 
TCGA-CW-6090 TCGA-CZ-4854 TCGA-CZ-4858 TCGA-CZ-5456 TCGA-CZ-5461 TCGA-CZ-5465 
        2552         1404         1943         1712          330         1446 
TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5987 
         685           59          946         2067         1997          435 

$`9P LOSS WILD-TYPE`
TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 
        1436           16          735         1508         1478         1106 
TCGA-A3-3324 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 
        1186         1137         1485          665         1043          945 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 
        1385          910         2688         1307         2504         1559 
TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 
         319          873         2270         2274         1621         1314 
TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 
        1070          630          567          861         1993          617 
TCGA-A3-A8CQ TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 
           3         2566         2223         2017          480         1853 
TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3447 
        2192         2087         1745         1423         1471         1217 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
        1481         1397          874         1143         1168          951 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3778 TCGA-B0-4699 TCGA-B0-4706 TCGA-B0-4718 
         853          369           43          110           26          616 
TCGA-B0-4813 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5115 TCGA-B0-5117 TCGA-B0-5119 
          18          911         1092          797          535           59 
TCGA-B0-5120 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 
         493          652         1132         2408         3431         1487 
TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 
        3076         1420         1727         1835         2583         2741 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 
        1605         1203         3668         2414         3117         1459 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 
        2931         2722         1865         2963          992         1092 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5635 TCGA-B2-5639 
          51          374          648          952          315          417 
TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
         507          291          175           38           16          141 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
          11            7          511          826          838          762 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4621 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 
         750          523          788          722           36          822 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5550 TCGA-B8-5552 
          26          737          522          505          434         1046 
TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I 
         435          830          519           53          256          150 
TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4162 TCGA-BP-4163 
          66          110         3377         2881         3074         2839 
TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4169 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4177 
        3037           13          701         1893         1879         1670 
TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 
        2964         1625          845         1888         1133          645 
TCGA-BP-4335 TCGA-BP-4338 TCGA-BP-4344 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4756 
         461         2859         1666         1367          372          374 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4765 TCGA-BP-4769 
        2208         2372         2361          182         2184         1876 
TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4784 TCGA-BP-4789 
        1885         1843          411         1731         1854         1489 
TCGA-BP-4795 TCGA-BP-4801 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4961 
         620         1124         1459          211         2660         1935 
TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 
        1871          205         1746         1794          433         1487 
TCGA-BP-4972 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4982 TCGA-BP-4983 
        1502         1433         1632          454         1014         1413 
TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4998 
        1124          118         1413          501          177          932 
TCGA-BP-4999 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 
        1266         1177         1126          840         1140         1071 
TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5177 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5184 
        2412         2257          293         1495         1165         1133 
TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 
        1132          693          406         1011          714          408 
TCGA-BP-5195 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4636 
         749         1355         1063           29         1820         1924 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 
        2308         1998         1628         1793          646         2554 
TCGA-CJ-4870 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 
        1498         1435         2259         2283         2353         1955 
TCGA-CJ-4878 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4889 
        2186         1883         1759         2125         1952         1946 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4902 
        1521          750          841         1808         1528         1520 
TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4916 TCGA-CJ-5675 TCGA-CJ-5681 
        1560         1792         1496         1373         2430          552 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6032 TCGA-CW-5581 TCGA-CW-5583 
        1889         2231         2038         2548         2799         2489 
TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6088 TCGA-CW-6093 
        2609         2226         2378         2271         3222         3146 
TCGA-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 
         774           18         1787         1843         1928         2830 
TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5457 TCGA-CZ-5458 
        1868         1929         1789           25         1683         1732 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5470 TCGA-CZ-5982 
        1683         1430          662         1740          386         2439 
TCGA-CZ-5986 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 
         373          693         1905         1329         1398         1470 
TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-EU-5904 
         370          355         1130          723         1729          551 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-GK-A6C7 
         119          206          127           61 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                7                 3 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             3343              3668 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           1285.5            1310.5 
[1] "7.0 - 3343.0 (1285.5)" "3.0 - 3668.0 (1310.5)"
[1] "hr=" "1.8"
D56V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  9P LOSS MUTATED        48       11        50       35
  9P LOSS WILD-TYPE     196       45        76       44
D56V3, multiclass
           clus
vv          9P LOSS MUTATED 9P LOSS WILD-TYPE
  STAGE I                48               196
  STAGE II               11                45
  STAGE III              50                76
  STAGE IV               35                44
[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"
                   vv
clus                 T1  T2  T3  T4
  9P LOSS MUTATED    52  15  72   5
  9P LOSS WILD-TYPE 198  52 105   6
D56V4, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  T1              52               198
  T2              15                52
  T3              72               105
  T4               5                 6
[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"
D56V5, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    59   8
  9P LOSS WILD-TYPE 171  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     59    8
  9P LOSS WILD-TYPE  171   10
   clus
vv  9P LOSS MUTATED 9P LOSS WILD-TYPE
  0              59               171
  1               8                10
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  9P LOSS MUTATED   109  35   0
  9P LOSS WILD-TYPE 308  43   9
D56V6, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  M0             109               308
  M1              35                43
  MX               0                 9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V7, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    34 110
  9P LOSS WILD-TYPE 144 217
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     34  110
  9P LOSS WILD-TYPE  144  217
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE              34               144
  MALE               110               217
[1] 2 2
[1] FALSE
D56V8, continuous
D56V9, continuous
[1] "Remove cluster labels:" "9P LOSS MUTATED"       
clus
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                2                 6 
       TCGA-A3-A8CQ        TCGA-B2-A4SR        TCGA-B8-4621        TCGA-B8-5164 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-B8-A54F        TCGA-B8-A54G 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9P LOSS MUTATED       1                         5   134
  9P LOSS WILD-TYPE     7                        28   323
D56V10, multiclass
                           clus
vv                          9P LOSS MUTATED 9P LOSS WILD-TYPE
  ASIAN                                   1                 7
  BLACK OR AFRICAN AMERICAN               5                28
  WHITE                                 134               323
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V11, binary
                   cls
clus                  0   1
  9P LOSS MUTATED     6  95
  9P LOSS WILD-TYPE  18 235
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      6   95
  9P LOSS WILD-TYPE   18  235
                        clus
vv                       9P LOSS MUTATED 9P LOSS WILD-TYPE
  HISPANIC OR LATINO                   6                18
  NOT HISPANIC OR LATINO              95               235
[1] 2 2
[1] FALSE

Clustering(57) Variable = 9Q LOSS MUTATION ANALYSIS
D57V1, survival
                   sevent
clus2                 0   1
  9Q LOSS MUTATED    78   8
  9Q LOSS WILD-TYPE 260  18
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               86               278 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                8                18 
$`9Q LOSS MUTATED`
TCGA-A3-3306 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3325 TCGA-A3-3347 
        1120         1493         1491         1130          751         1610 
TCGA-A3-3372 TCGA-A3-3382 TCGA-AK-3425 TCGA-AK-3436 TCGA-AK-3445 TCGA-AK-3450 
         735          574         3343         2044         1280         1779 
TCGA-AK-3456 TCGA-AS-3777 TCGA-B0-4710 TCGA-B0-4819 TCGA-B0-5097 TCGA-B0-5113 
        1143         1238           96          183          665          359 
TCGA-B0-5116 TCGA-B0-5402 TCGA-B0-5696 TCGA-B0-5701 TCGA-B2-5633 TCGA-B2-5641 
         657          449         1727         1732          358          656 
TCGA-B4-5832 TCGA-B4-5838 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5549 
           7          166          777          700          636          194 
TCGA-B8-5551 TCGA-BP-4161 TCGA-BP-4167 TCGA-BP-4176 TCGA-BP-4351 TCGA-BP-4768 
          15         2746         2718         1955          970          400 
TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4797 TCGA-BP-4803 TCGA-BP-4960 TCGA-BP-4962 
        2080          354         1107          204         2172         1785 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4973 TCGA-BP-4986 TCGA-BP-4994 TCGA-BP-4995 
        1834         1862         1384          785         1308         1371 
TCGA-BP-5000 TCGA-BP-5169 TCGA-BP-5175 TCGA-BP-5180 TCGA-BP-5183 TCGA-BP-5189 
         563          193          932         2263         1291          822 
TCGA-BP-5191 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5201 TCGA-CJ-4635 TCGA-CJ-4868 
         967         1018          603          951         1416          646 
TCGA-CJ-4871 TCGA-CJ-4873 TCGA-CJ-4876 TCGA-CJ-4881 TCGA-CJ-4890 TCGA-CJ-4901 
        2423         2259         1955         2014         2085         1450 
TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-5671 TCGA-CJ-5676 TCGA-CJ-5682 
        1499         1531         1657         1943         2575         1883 
TCGA-CJ-6027 TCGA-CJ-6031 TCGA-CW-5588 TCGA-CW-6090 TCGA-CZ-4858 TCGA-CZ-5452 
        1855         1906         2017         2552         1943         1789 
TCGA-CZ-5456 TCGA-CZ-5461 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5469 TCGA-CZ-5984 
        1712          330         1446          685          946         2067 
TCGA-CZ-5985 TCGA-CZ-5987 
        1997          435 

$`9Q LOSS WILD-TYPE`
TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 
        1436           16          735         1508         1478         1106 
TCGA-A3-3324 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 
        1186         1137         1485          665         1043          945 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 
        1385          910         2688         1307         2504         1559 
TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 
         319          873         2270         2274         1621         1314 
TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 
        1070          630          567          861         1993          617 
TCGA-A3-A8CQ TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 
           3         2566         2223         2017          480         1853 
TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3447 
        2192         2087         1745         1423         1471         1217 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
        1481         1397          874         1168          951          853 
TCGA-AK-3465 TCGA-AS-3778 TCGA-B0-4699 TCGA-B0-4706 TCGA-B0-4718 TCGA-B0-4813 
         369           43          110           26          616           18 
TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5115 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 
         911         1092          797          535           59          493 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 
         554          652         1132         2408         3431         1487 
TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5702 
        3076         1420         1835         2583         2741         1605 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
        1203         3668         2414         3117         1459         2931 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
        2722         1865         2963          992         1092           51 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-A4SR 
         374          648          952          315          417          507 
TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5843 
         291          175           38           16          141           11 
TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
           7          511          826          838          762          750 
TCGA-B8-4619 TCGA-B8-4621 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 
         523          788          722           36          822           26 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5550 TCGA-B8-5552 TCGA-B8-5553 
         737          522          505          434         1046          435 
TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J 
         830          519           53          256          150           66 
TCGA-B8-A7U6 TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 
         110         3377         2881         3074         2839         3037 
TCGA-BP-4166 TCGA-BP-4169 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4177 TCGA-BP-4325 
          13          701         1893         1879         1670         2964 
TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 
        1625          845         1888         1133          645          461 
TCGA-BP-4338 TCGA-BP-4344 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4756 TCGA-BP-4758 
        2859         1666         1367          372          374         2208 
TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 
        2372         2361          182         2184         1462         1876 
TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4784 TCGA-BP-4789 
        1885         1843          411         1731         1854         1489 
TCGA-BP-4795 TCGA-BP-4801 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4961 
         620         1124         1459          211         2660         1935 
TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 
        1871          205         1746         1794          433         1487 
TCGA-BP-4972 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4982 TCGA-BP-4983 
        1502         1433         1632          454         1014         1413 
TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4998 
        1124          118         1413          501          177          932 
TCGA-BP-4999 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 
        1266         1177         1126          840         1140         1071 
TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5177 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5184 
        2412         2257          293         1495         1165         1133 
TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 
        1132          693          406         1011          714          408 
TCGA-BP-5195 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4636 
         749         1355         1063           29         1820         1924 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4869 TCGA-CJ-4870 
        2308         1998         1628         1793         2554         1498 
TCGA-CJ-4872 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4878 TCGA-CJ-4882 TCGA-CJ-4884 
        1435         2283         2353         2186         1883         1759 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4889 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 
        2125         1952         1946         1521          750          841 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 
        1808         1528         1520         1560         1792         1496 
TCGA-CJ-4916 TCGA-CJ-5675 TCGA-CJ-5681 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 
        1373         2430          552         1889         2231         2038 
TCGA-CJ-6032 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 
        2548         2799         2489         2609         2226         2378 
TCGA-CW-5591 TCGA-CW-6088 TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 
        2271         3222         3146          774         1404           18 
TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 
        1787         1843         1928         2830         1868         1929 
TCGA-CZ-5453 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5463 
          25         1683         1732         1683         1430          662 
TCGA-CZ-5464 TCGA-CZ-5468 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5986 TCGA-CZ-5988 
        1740           59          386         2439          373          693 
TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 
        1905         1329         1398         1470          370          355 
TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 
        1130          723         1729          551          119          206 
TCGA-EU-5907 TCGA-GK-A6C7 
         127           61 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                7                 3 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             3343              3668 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           1299.5            1286.5 
[1] "7.0 - 3343.0 (1299.5)" "3.0 - 3668.0 (1286.5)"
[1] "hr=" "1.4"
D57V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  9Q LOSS MUTATED        45       14        52       34
  9Q LOSS WILD-TYPE     199       42        74       45
D57V3, multiclass
           clus
vv          9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  STAGE I                45               199
  STAGE II               14                42
  STAGE III              52                74
  STAGE IV               34                45
[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"
                   vv
clus                 T1  T2  T3  T4
  9Q LOSS MUTATED    48  18  75   4
  9Q LOSS WILD-TYPE 202  49 102   7
D57V4, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  T1              48               202
  T2              18                49
  T3              75               102
  T4               4                 7
[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"
D57V5, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    62   8
  9Q LOSS WILD-TYPE 168  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     62    8
  9Q LOSS WILD-TYPE  168   10
   clus
vv  9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  0              62               168
  1               8                10
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  9Q LOSS MUTATED   111  34   0
  9Q LOSS WILD-TYPE 306  44   9
D57V6, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  M0             111               306
  M1              34                44
  MX               0                 9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V7, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    34 111
  9Q LOSS WILD-TYPE 144 216
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     34  111
  9Q LOSS WILD-TYPE  144  216
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE              34               144
  MALE               111               216
[1] 2 2
[1] FALSE
D57V8, continuous
D57V9, continuous
[1] "Remove cluster labels:" "9Q LOSS MUTATED"       
clus
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                1                 7 
       TCGA-A3-A8CQ        TCGA-B2-A4SR        TCGA-B8-4621        TCGA-B8-5164 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-B8-A54F        TCGA-B8-A54G        TCGA-G6-A5PC 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9Q LOSS MUTATED       1                         5   135
  9Q LOSS WILD-TYPE     7                        28   322
D57V10, multiclass
                           clus
vv                          9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  ASIAN                                   1                 7
  BLACK OR AFRICAN AMERICAN               5                28
  WHITE                                 135               322
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V11, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED     8  94
  9Q LOSS WILD-TYPE  16 236
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      8   94
  9Q LOSS WILD-TYPE   16  236
                        clus
vv                       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   8                16
  NOT HISPANIC OR LATINO              94               236
[1] 2 2
[1] FALSE

Clustering(58) Variable = 10P LOSS MUTATION ANALYSIS
D58V1, survival
                    sevent
clus2                  0   1
  10P LOSS MUTATED    43   4
  10P LOSS WILD-TYPE 295  22
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                47                317 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 4                 22 
$`10P LOSS MUTATED`
TCGA-A3-3374 TCGA-A3-3380 TCGA-AK-3433 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3458 
        1314          567         2192         1745         1423         1168 
TCGA-AK-3461 TCGA-AK-3465 TCGA-B0-4699 TCGA-B0-4819 TCGA-B0-5117 TCGA-B2-3923 
         853          369          110          183          535          992 
TCGA-B2-5641 TCGA-B4-5835 TCGA-B8-5549 TCGA-B8-5550 TCGA-BP-4161 TCGA-BP-4166 
         656           16          194          434         2746           13 
TCGA-BP-4334 TCGA-BP-4351 TCGA-BP-4775 TCGA-BP-4797 TCGA-BP-4803 TCGA-BP-4960 
         645          970         1843         1107          204         2172 
TCGA-BP-4973 TCGA-BP-4994 TCGA-BP-5169 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5201 
        1384         1308          193         1018          603          951 
TCGA-CJ-4635 TCGA-CJ-4874 TCGA-CJ-4882 TCGA-CJ-4893 TCGA-CJ-4897 TCGA-CJ-4901 
        1416         2283         1883          750         1808         1450 
TCGA-CJ-4907 TCGA-CJ-5676 TCGA-CW-6090 TCGA-CZ-5457 TCGA-CZ-5460 TCGA-CZ-5465 
        1499         2575         2552         1683         1430         1446 
TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-DV-5566 TCGA-EU-5907 
         946          386         2439         1398          127 

$`10P LOSS WILD-TYPE`
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 
        1120         1436           16          735         1493         1491 
TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 
        1130         1508         1478         1106         1186          751 
TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3347 
        1137         1485          665         1043          945         1610 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 
        1385          910         2688         1307         2504         1559 
TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 
         319          873         2270         2274          735         1621 
TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 
        1070          630          574          861         1993          617 
TCGA-A3-A8CQ TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 
           3         3343         2566         2223         2017          480 
TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 
        1853         2087         2044         1471         1280         1217 
TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3456 TCGA-AK-3460 
        1779         1481         1397          874         1143          951 
TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4718 TCGA-B0-4813 
        1238           43           26           96          616           18 
TCGA-B0-5097 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 
         665          911         1092          359          797          657 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
          59          493          554          652         1132          449 
TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5696 
        2408         3431         1487         3076         1420         1727 
TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
        1835         2583         2741         1732         1605         1203 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
        3668         2414         3117         1459         2931         2722 
TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 
        1865         2963         1092           51          374          648 
TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-A4SR TCGA-B4-5377 
         952          358          315          417          507          291 
TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 
         175            7           38          141          166           11 
TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
           7          511          826          838          762          750 
TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 
         523          777          788          700          636          722 
TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
          36          822           26          737          522          505 
TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G 
          15         1046          435          830          519           53 
TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4158 TCGA-BP-4160 
         256          150           66          110         3377         2881 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4173 
        3074         2839         3037         2718          701         1893 
TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 
        1879         1955         1670         2964         1625          845 
TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4335 TCGA-BP-4338 TCGA-BP-4344 TCGA-BP-4347 
        1888         1133          461         2859         1666         1367 
TCGA-BP-4349 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 
         372          374         2208         2372         2361          182 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4774 TCGA-BP-4776 
        2184         1462          400         1876         1885          411 
TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4795 
        1731         2080          354         1854         1489          620 
TCGA-BP-4801 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4961 TCGA-BP-4962 
        1124         1459          211         2660         1935         1785 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 
        1834         1862         1871          205         1746         1794 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 
         433         1487         1502         1433         1632          454 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 
        1014         1413          785         1124          118         1413 
TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 
         501          177         1371          932         1266          563 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5170 
        1177         1126          840         1140         1071         2412 
TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 
        2257          932          293         2263         1495         1165 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 
        1291         1133         1132          693          406          822 
TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5199 
        1011          967          714          408          749         1355 
TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4636 TCGA-CJ-4639 TCGA-CJ-4640 
        1063           29         1820         1924         2308         1998 
TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
        1628         1793          646         2554         1498         2423 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 
        1435         2259         2353         1955         2186         2014 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 
        1759         2125         1952         1946         2085         1521 
TCGA-CJ-4894 TCGA-CJ-4899 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 
         841         1528         1520         1560         1792         1496 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-5671 TCGA-CJ-5675 TCGA-CJ-5681 
        1531         1657         1373         1943         2430          552 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6031 
        1883         1889         2231         2038         1855         1906 
TCGA-CJ-6032 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 
        2548         2799         2489         2609         2226         2017 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6088 TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4854 
        2378         2271         3222         3146          774         1404 
TCGA-CZ-4856 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 
          18         1943         1787         1843         1928         2830 
TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5456 TCGA-CZ-5458 
        1868         1929         1789           25         1712         1732 
TCGA-CZ-5459 TCGA-CZ-5461 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5468 
        1683          330          662         1740          685           59 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
        2067         1997          373          435          693         1905 
TCGA-DV-5565 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 
        1329         1470          370          355         1130          723 
TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-GK-A6C7 
        1729          551          119          206           61 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                13                  3 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              2746               3668 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              1107               1329 
[1] "13.0 - 2746.0 (1107.0)" "3.0 - 3668.0 (1329.0)" 
[1] "hr=" "1.4"
D58V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  10P LOSS MUTATED        23        6        23       13
  10P LOSS WILD-TYPE     221       50       103       66
D58V3, multiclass
           clus
vv          10P LOSS MUTATED 10P LOSS WILD-TYPE
  STAGE I                 23                221
  STAGE II                 6                 50
  STAGE III               23                103
  STAGE IV                13                 66
[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"
                    vv
clus                  T1  T2  T3  T4
  10P LOSS MUTATED    23   7  31   4
  10P LOSS WILD-TYPE 227  60 146   7
D58V4, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  T1               23                227
  T2                7                 60
  T3               31                146
  T4                4                  7
[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"
D58V5, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    30   0
  10P LOSS WILD-TYPE 200  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     30    0
  10P LOSS WILD-TYPE  200   18
   clus
vv  10P LOSS MUTATED 10P LOSS WILD-TYPE
  0               30                200
  1                0                 18
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  10P LOSS MUTATED    53  12   0
  10P LOSS WILD-TYPE 364  66   9
D58V6, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  M0               53                364
  M1               12                 66
  MX                0                  9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V7, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    19  46
  10P LOSS WILD-TYPE 159 281
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     19   46
  10P LOSS WILD-TYPE  159  281
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE               19                159
  MALE                 46                281
[1] 2 2
[1] FALSE
D58V8, continuous
D58V9, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10P LOSS MUTATED       0                         3    59
  10P LOSS WILD-TYPE     8                        30   398
D58V10, multiclass
                           clus
vv                          10P LOSS MUTATED 10P LOSS WILD-TYPE
  ASIAN                                    0                  8
  BLACK OR AFRICAN AMERICAN                3                 30
  WHITE                                   59                398
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V11, binary
                    cls
clus                   0   1
  10P LOSS MUTATED     5  37
  10P LOSS WILD-TYPE  19 293
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      5   37
  10P LOSS WILD-TYPE   19  293
                        clus
vv                       10P LOSS MUTATED 10P LOSS WILD-TYPE
  HISPANIC OR LATINO                    5                 19
  NOT HISPANIC OR LATINO               37                293
[1] 2 2
[1] FALSE

Clustering(59) Variable = 10Q LOSS MUTATION ANALYSIS
D59V1, survival
                    sevent
clus2                  0   1
  10Q LOSS MUTATED    58   5
  10Q LOSS WILD-TYPE 280  21
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                63                301 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 5                 21 
$`10Q LOSS MUTATED`
TCGA-A3-3316 TCGA-A3-3331 TCGA-A3-3374 TCGA-A3-3380 TCGA-AK-3433 TCGA-AK-3440 
        1493         1485         1314          567         2192         1745 
TCGA-AK-3443 TCGA-AK-3458 TCGA-AK-3461 TCGA-AK-3465 TCGA-B0-4699 TCGA-B0-4718 
        1423         1168          853          369          110          616 
TCGA-B0-4819 TCGA-B0-5117 TCGA-B0-5402 TCGA-B0-5703 TCGA-B0-5706 TCGA-B2-3923 
         183          535          449         1203         2414          992 
TCGA-B2-5641 TCGA-B4-5835 TCGA-B4-5838 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-A7U6 
         656           16          166          194          434          110 
TCGA-BP-4161 TCGA-BP-4166 TCGA-BP-4329 TCGA-BP-4334 TCGA-BP-4351 TCGA-BP-4766 
        2746           13          845          645          970         1462 
TCGA-BP-4775 TCGA-BP-4797 TCGA-BP-4803 TCGA-BP-4960 TCGA-BP-4973 TCGA-BP-4994 
        1843         1107          204         2172         1384         1308 
TCGA-BP-5169 TCGA-BP-5180 TCGA-BP-5185 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5201 
         193         2263         1132         1018          603          951 
TCGA-CJ-4635 TCGA-CJ-4642 TCGA-CJ-4872 TCGA-CJ-4874 TCGA-CJ-4882 TCGA-CJ-4893 
        1416         1628         1435         2283         1883          750 
TCGA-CJ-4897 TCGA-CJ-4901 TCGA-CJ-4907 TCGA-CJ-5676 TCGA-CJ-6032 TCGA-CW-6090 
        1808         1450         1499         2575         2548         2552 
TCGA-CZ-5457 TCGA-CZ-5460 TCGA-CZ-5465 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 
        1683         1430         1446          946          386         2439 
TCGA-DV-5565 TCGA-DV-5566 TCGA-EU-5907 
        1329         1398          127 

$`10Q LOSS WILD-TYPE`
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3319 
        1120         1436           16          735         1491         1130 
TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 
        1508         1478         1106         1186          751         1137 
TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 
         665         1043          945         1610         1385          910 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
        2688         1307         2504         1559          319          873 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 
        2270         2274          735         1621         1070          630 
TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A8CQ TCGA-AK-3425 
         574          861         1993          617            3         3343 
TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 
        2566         2223         2017          480         1853         2087 
TCGA-AK-3436 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 
        2044         1471         1280         1217         1779         1481 
TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3456 TCGA-AK-3460 TCGA-AS-3777 TCGA-AS-3778 
        1397          874         1143          951         1238           43 
TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4813 TCGA-B0-5097 TCGA-B0-5108 TCGA-B0-5110 
          26           96           18          665          911         1092 
TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
         359          797          657           59          493          554 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 
         652         1132         2408         3431         1487         3076 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 
        1420         1727         1835         2583         2741         1732 
TCGA-B0-5702 TCGA-B0-5705 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
        1605         3668         3117         1459         2931         2722 
TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 
        1865         2963         1092           51          374          648 
TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-A4SR TCGA-B4-5377 
         952          358          315          417          507          291 
TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 
         175            7           38          141           11            7 
TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 
         511          826          838          762          750          523 
TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 
         777          788          700          636          722           36 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5551 
         822           26          737          522          505           15 
TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H 
        1046          435          830          519           53          256 
TCGA-B8-A54I TCGA-B8-A54J TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4162 TCGA-BP-4163 
         150           66         3377         2881         3074         2839 
TCGA-BP-4165 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 
        3037         2718          701         1893         1879         1955 
TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4335 
        1670         2964         1625         1888         1133          461 
TCGA-BP-4338 TCGA-BP-4344 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4756 TCGA-BP-4758 
        2859         1666         1367          372          374         2208 
TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4765 TCGA-BP-4768 TCGA-BP-4769 
        2372         2361          182         2184          400         1876 
TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 
        1885          411         1731         2080          354         1854 
TCGA-BP-4789 TCGA-BP-4795 TCGA-BP-4801 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 
        1489          620         1124         1459          211         2660 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 
        1935         1785         1834         1862         1871          205 
TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4975 
        1746         1794          433         1487         1502         1433 
TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4987 
        1632          454         1014         1413          785         1124 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 
         118         1413          501          177         1371          932 
TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 
        1266          563         1177         1126          840         1140 
TCGA-BP-5008 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5177 TCGA-BP-5181 
        1071         2412         2257          932          293         1495 
TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 
        1165         1291         1133          693          406          822 
TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5199 
        1011          967          714          408          749         1355 
TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4636 TCGA-CJ-4639 TCGA-CJ-4640 
        1063           29         1820         1924         2308         1998 
TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4873 
        1793          646         2554         1498         2423         2259 
TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4884 TCGA-CJ-4885 
        2353         1955         2186         2014         1759         2125 
TCGA-CJ-4886 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4894 TCGA-CJ-4899 
        1952         1946         2085         1521          841         1528 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 
        1520         1560         1792         1496         1531         1657 
TCGA-CJ-4916 TCGA-CJ-5671 TCGA-CJ-5675 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
        1373         1943         2430          552         1883         1889 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6031 TCGA-CW-5581 TCGA-CW-5583 
        2231         2038         1855         1906         2799         2489 
TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6088 
        2609         2226         2017         2378         2271         3222 
TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4858 TCGA-CZ-4859 
        3146          774         1404           18         1943         1787 
TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 
        1843         1928         2830         1868         1929         1789 
TCGA-CZ-5453 TCGA-CZ-5456 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5461 TCGA-CZ-5463 
          25         1712         1732         1683          330          662 
TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
        1740          685           59         2067         1997          373 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 
         435          693         1905         1470          370          355 
TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 
        1130          723         1729          551          119          206 
TCGA-GK-A6C7 
          61 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                13                  3 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              2746               3668 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              1203               1307 
[1] "13.0 - 2746.0 (1203.0)" "3.0 - 3668.0 (1307.0)" 
[1] "hr=" "1.3"
D59V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  10Q LOSS MUTATED        32       11        27       17
  10Q LOSS WILD-TYPE     212       45        99       62
D59V3, multiclass
           clus
vv          10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  STAGE I                 32                212
  STAGE II                11                 45
  STAGE III               27                 99
  STAGE IV                17                 62
[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"
                    vv
clus                  T1  T2  T3  T4
  10Q LOSS MUTATED    32  12  37   6
  10Q LOSS WILD-TYPE 218  55 140   5
D59V4, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  T1               32                218
  T2               12                 55
  T3               37                140
  T4                6                  5
[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"
D59V5, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    38   1
  10Q LOSS WILD-TYPE 192  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     38    1
  10Q LOSS WILD-TYPE  192   17
   clus
vv  10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  0               38                192
  1                1                 17
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  10Q LOSS MUTATED    71  15   0
  10Q LOSS WILD-TYPE 346  63   9
D59V6, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  M0               71                346
  M1               15                 63
  MX                0                  9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V7, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    24  63
  10Q LOSS WILD-TYPE 154 264
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     24   63
  10Q LOSS WILD-TYPE  154  264
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE               24                154
  MALE                 63                264
[1] 2 2
[1] FALSE
D59V8, continuous
D59V9, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10Q LOSS MUTATED       0                         4    80
  10Q LOSS WILD-TYPE     8                        29   377
D59V10, multiclass
                           clus
vv                          10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  ASIAN                                    0                  8
  BLACK OR AFRICAN AMERICAN                4                 29
  WHITE                                   80                377
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V11, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED     6  52
  10Q LOSS WILD-TYPE  18 278
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      6   52
  10Q LOSS WILD-TYPE   18  278
                        clus
vv                       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    6                 18
  NOT HISPANIC OR LATINO               52                278
[1] 2 2
[1] FALSE

Clustering(60) Variable = 11P LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                  0   1
  11P LOSS MUTATED     9   2
  11P LOSS WILD-TYPE 329  24
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                11                353 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 2                 24 
$`11P LOSS MUTATED`
TCGA-A3-3316 TCGA-AK-3465 TCGA-B0-4819 TCGA-B0-5702 TCGA-B2-5641 TCGA-B4-5838 
        1493          369          183         1605          656          166 
TCGA-BP-4768 TCGA-BP-5201 TCGA-CW-5588 TCGA-CZ-5465 TCGA-CZ-5469 
         400          951         2017         1446          946 

$`11P LOSS WILD-TYPE`
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3319 
        1120         1436           16          735         1491         1130 
TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 
        1508         1478         1106         1186          751         1137 
TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3347 TCGA-A3-3349 
        1485          665         1043          945         1610         1385 
TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 
         910         2688         1307         2504         1559          319 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 
         873         2270         2274          735         1621         1314 
TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 
        1070          630          567          574          861         1993 
TCGA-A3-3387 TCGA-A3-A8CQ TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
         617            3         3343         2566         2223         2017 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
         480         1853         2192         2087         2044         1745 
TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 
        1423         1471         1280         1217         1779         1481 
TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
        1397          874         1143         1168          951          853 
TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4699 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4718 
        1238           43          110           26           96          616 
TCGA-B0-4813 TCGA-B0-5097 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 
          18          665          911         1092          359          797 
TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
         657          535           59          493          554          652 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 
        1132          449         2408         3431         1487         3076 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 
        1420         1727         1835         2583         2741         1732 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
        1203         3668         2414         3117         1459         2931 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
        2722         1865         2963          992         1092           51 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 
         374          648          952          358          315          417 
TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 
         507          291          175            7           38           16 
TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
         141           11            7          511          826          838 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 
         762          750          523          777          788          700 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
         636          722           36          822           26          737 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
         522          505          194          434           15         1046 
TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I 
         435          830          519           53          256          150 
TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 
          66          110         3377         2881         2746         3074 
TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4173 
        2839         3037           13         2718          701         1893 
TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 
        1879         1955         1670         2964         1625          845 
TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4338 TCGA-BP-4344 
        1888         1133          645          461         2859         1666 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 
        1367          372          970          374         2208         2372 
TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4774 
        2361          182         2184         1462         1876         1885 
TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 
        1843          411         1731         2080          354         1854 
TCGA-BP-4789 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 
        1489          620         1107         1124          204         1459 
TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
         211         2660         2172         1935         1785         1834 
TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 
        1862         1871          205         1746         1794          433 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 
        1487         1502         1384         1433         1632          454 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 
        1014         1413          785         1124          118         1413 
TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 
         501          177         1308         1371          932         1266 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 
         563         1177         1126          840         1140         1071 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5177 TCGA-BP-5180 
         193         2412         2257          932          293         2263 
TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
        1495         1165         1291         1133         1132          693 
TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 
         406          822         1011          967          714          408 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5202 
         749         1018          603         1355         1063           29 
TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4642 
        1820         1416         1924         2308         1998         1628 
TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 
        1793          646         2554         1498         2423         1435 
TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 
        2259         2283         2353         1955         2186         2014 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4889 TCGA-CJ-4890 
        1883         1759         2125         1952         1946         2085 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4901 
        1521          750          841         1808         1528         1450 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 
        1520         1560         1792         1496         1499         1531 
TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-5671 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5681 
        1657         1373         1943         2430         2575          552 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6031 
        1883         1889         2231         2038         1855         1906 
TCGA-CJ-6032 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 
        2548         2799         2489         2609         2226         2378 
TCGA-CW-5591 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4854 
        2271         3222         2552         3146          774         1404 
TCGA-CZ-4856 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 
          18         1943         1787         1843         1928         2830 
TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5456 TCGA-CZ-5457 
        1868         1929         1789           25         1712         1683 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5463 TCGA-CZ-5464 
        1732         1683         1430          330          662         1740 
TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
         685           59          386         2439         2067         1997 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
         373          435          693         1905         1329         1398 
TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 
        1470          370          355         1130          723         1729 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-GK-A6C7 
         551          119          206          127           61 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               166                  3 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              2017               3668 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               946               1308 
[1] "166.0 - 2017.0 (946.0)" "3.0 - 3668.0 (1308.0)" 
[1] "hr=" "3.5"
D60V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  11P LOSS MUTATED         6        3         5        4
  11P LOSS WILD-TYPE     238       53       121       75
D60V3, multiclass
           clus
vv          11P LOSS MUTATED 11P LOSS WILD-TYPE
  STAGE I                  6                238
  STAGE II                 3                 53
  STAGE III                5                121
  STAGE IV                 4                 75
[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"
                    vv
clus                  T1  T2  T3  T4
  11P LOSS MUTATED     6   3   9   0
  11P LOSS WILD-TYPE 244  64 168  11
D60V4, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  T1                6                244
  T2                3                 64
  T3                9                168
  T4                0                 11
[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"
D60V5, binary
                    cls
clus                   0   1
  11P LOSS MUTATED     8   2
  11P LOSS WILD-TYPE 222  16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      8    2
  11P LOSS WILD-TYPE  222   16
   clus
vv  11P LOSS MUTATED 11P LOSS WILD-TYPE
  0                8                222
  1                2                 16
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  11P LOSS MUTATED    14   4   0
  11P LOSS WILD-TYPE 403  74   9
D60V6, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  M0               14                403
  M1                4                 74
  MX                0                  9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V7, binary
                    cls
clus                   0   1
  11P LOSS MUTATED     6  12
  11P LOSS WILD-TYPE 172 315
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      6   12
  11P LOSS WILD-TYPE  172  315
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE                6                172
  MALE                 12                315
[1] 2 2
[1] FALSE
D60V8, continuous
D60V9, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11P LOSS MUTATED       0                         1    16
  11P LOSS WILD-TYPE     8                        32   441
D60V10, multiclass
                           clus
vv                          11P LOSS MUTATED 11P LOSS WILD-TYPE
  ASIAN                                    0                  8
  BLACK OR AFRICAN AMERICAN                1                 32
  WHITE                                   16                441
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V11, binary
                    cls
clus                   0   1
  11P LOSS MUTATED     0  13
  11P LOSS WILD-TYPE  24 317
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      0   13
  11P LOSS WILD-TYPE   24  317
                        clus
vv                       11P LOSS MUTATED 11P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 24
  NOT HISPANIC OR LATINO               13                317
[1] 2 2
[1] FALSE

Clustering(61) Variable = 11Q LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                  0   1
  11Q LOSS MUTATED    12   3
  11Q LOSS WILD-TYPE 326  23
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                15                349 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 3                 23 
$`11Q LOSS MUTATED`
TCGA-A3-3316 TCGA-AK-3425 TCGA-AK-3465 TCGA-B0-4819 TCGA-B0-5702 TCGA-B2-5641 
        1493         3343          369          183         1605          656 
TCGA-B4-5832 TCGA-B4-5838 TCGA-BP-4768 TCGA-BP-4986 TCGA-BP-5201 TCGA-CW-5588 
           7          166          400          785          951         2017 
TCGA-CZ-5465 TCGA-CZ-5468 TCGA-CZ-5469 
        1446           59          946 

$`11Q LOSS WILD-TYPE`
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3319 
        1120         1436           16          735         1491         1130 
TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 
        1508         1478         1106         1186          751         1137 
TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3347 TCGA-A3-3349 
        1485          665         1043          945         1610         1385 
TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 
         910         2688         1307         2504         1559          319 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 
         873         2270         2274          735         1621         1314 
TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 
        1070          630          567          574          861         1993 
TCGA-A3-3387 TCGA-A3-A8CQ TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 
         617            3         2566         2223         2017          480 
TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 
        1853         2192         2087         2044         1745         1423 
TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 
        1471         1280         1217         1779         1481         1397 
TCGA-AK-3454 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3777 
         874         1143         1168          951          853         1238 
TCGA-AS-3778 TCGA-B0-4699 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4718 TCGA-B0-4813 
          43          110           26           96          616           18 
TCGA-B0-5097 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 
         665          911         1092          359          797          657 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
         535           59          493          554          652         1132 
TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 
         449         2408         3431         1487         3076         1420 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5703 
        1727         1835         2583         2741         1732         1203 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
        3668         2414         3117         1459         2931         2722 
TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
        1865         2963          992         1092           51          374 
TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-A4SR 
         648          952          358          315          417          507 
TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5843 
         291          175           38           16          141           11 
TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
           7          511          826          838          762          750 
TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 
         523          777          788          700          636          722 
TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
          36          822           26          737          522          505 
TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D 
         194          434           15         1046          435          830 
TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 
         519           53          256          150           66          110 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 
        3377         2881         2746         3074         2839         3037 
TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 
          13         2718          701         1893         1879         1955 
TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 
        1670         2964         1625          845         1888         1133 
TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4338 TCGA-BP-4344 TCGA-BP-4347 TCGA-BP-4349 
         645          461         2859         1666         1367          372 
TCGA-BP-4351 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 
         970          374         2208         2372         2361          182 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 
        2184         1462         1876         1885         1843          411 
TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4795 
        1731         2080          354         1854         1489          620 
TCGA-BP-4797 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 
        1107         1124          204         1459          211         2660 
TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 
        2172         1935         1785         1834         1862         1871 
TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
         205         1746         1794          433         1487         1502 
TCGA-BP-4973 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4982 TCGA-BP-4983 
        1384         1433         1632          454         1014         1413 
TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 
        1124          118         1413          501          177         1308 
TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
        1371          932         1266          563         1177         1126 
TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 
         840         1140         1071          193         2412         2257 
TCGA-BP-5175 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 
         932          293         2263         1495         1165         1291 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 
        1133         1132          693          406          822         1011 
TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 
         967          714          408          749         1018          603 
TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 
        1355         1063           29         1820         1416         1924 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 
        2308         1998         1628         1793          646         2554 
TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 
        1498         2423         1435         2259         2283         2353 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
        1955         2186         2014         1883         1759         2125 
TCGA-CJ-4886 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 
        1952         1946         2085         1521          750          841 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 
        1808         1528         1450         1520         1560         1792 
TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-5671 
        1496         1499         1531         1657         1373         1943 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
        2430         2575          552         1883         1889         2231 
TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CW-5581 TCGA-CW-5583 
        2038         1855         1906         2548         2799         2489 
TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6088 TCGA-CW-6090 
        2609         2226         2378         2271         3222         2552 
TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4858 TCGA-CZ-4859 
        3146          774         1404           18         1943         1787 
TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 
        1843         1928         2830         1868         1929         1789 
TCGA-CZ-5453 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
          25         1712         1683         1732         1683         1430 
TCGA-CZ-5461 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5470 TCGA-CZ-5982 
         330          662         1740          685          386         2439 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
        2067         1997          373          435          693         1905 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 
        1329         1398         1470          370          355         1130 
TCGA-DV-5574 TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
         723         1729          551          119          206          127 
TCGA-GK-A6C7 
          61 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 7                  3 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              3343               3668 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               785               1314 
[1] "7.0 - 3343.0 (785.0)"  "3.0 - 3668.0 (1314.0)"
[1] "hr=" "3.9"
D61V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  11Q LOSS MUTATED         9        3         6        5
  11Q LOSS WILD-TYPE     235       53       120       74
D61V3, multiclass
           clus
vv          11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  STAGE I                  9                235
  STAGE II                 3                 53
  STAGE III                6                120
  STAGE IV                 5                 74
[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"
                    vv
clus                  T1  T2  T3  T4
  11Q LOSS MUTATED     9   3  11   0
  11Q LOSS WILD-TYPE 241  64 166  11
D61V4, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  T1                9                241
  T2                3                 64
  T3               11                166
  T4                0                 11
[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"
D61V5, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    11   2
  11Q LOSS WILD-TYPE 219  16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     11    2
  11Q LOSS WILD-TYPE  219   16
   clus
vv  11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  0               11                219
  1                2                 16
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  11Q LOSS MUTATED    18   5   0
  11Q LOSS WILD-TYPE 399  73   9
D61V6, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  M0               18                399
  M1                5                 73
  MX                0                  9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V7, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED     6  17
  11Q LOSS WILD-TYPE 172 310
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      6   17
  11Q LOSS WILD-TYPE  172  310
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE                6                172
  MALE                 17                310
[1] 2 2
[1] FALSE
D61V8, continuous
D61V9, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11Q LOSS MUTATED       0                         1    21
  11Q LOSS WILD-TYPE     8                        32   436
D61V10, multiclass
                           clus
vv                          11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  ASIAN                                    0                  8
  BLACK OR AFRICAN AMERICAN                1                 32
  WHITE                                   21                436
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V11, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED     1  16
  11Q LOSS WILD-TYPE  23 314
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      1   16
  11Q LOSS WILD-TYPE   23  314
                        clus
vv                       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 23
  NOT HISPANIC OR LATINO               16                314
[1] 2 2
[1] FALSE

Clustering(62) Variable = 12P LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                  0   1
  12P LOSS MUTATED     3   0
  12P LOSS WILD-TYPE 335  26
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 3                361 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 0                 26 
$`12P LOSS MUTATED`
TCGA-BP-4166 TCGA-BP-4775 TCGA-CZ-5457 
          13         1843         1683 

$`12P LOSS WILD-TYPE`
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 
        1120         1436           16          735         1493         1491 
TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 
        1130         1508         1478         1106         1186          751 
TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3347 
        1137         1485          665         1043          945         1610 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 
        1385          910         2688         1307         2504         1559 
TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 
         319          873         2270         2274          735         1621 
TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 
        1314         1070          630          567          574          861 
TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A8CQ TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 
        1993          617            3         3343         2566         2223 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 
        2017          480         1853         2192         2087         2044 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 
        1745         1423         1471         1280         1217         1779 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
        1481         1397          874         1143         1168          951 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4699 TCGA-B0-4706 
         853          369         1238           43          110           26 
TCGA-B0-4710 TCGA-B0-4718 TCGA-B0-4813 TCGA-B0-4819 TCGA-B0-5097 TCGA-B0-5108 
          96          616           18          183          665          911 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 
        1092          359          797          657          535           59 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 
         493          554          652         1132          449         2408 
TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 
        3431         1487         3076         1420         1727         1835 
TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 
        2583         2741         1732         1605         1203         3668 
TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
        2414         3117         1459         2931         2722         1865 
TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 
        2963          992         1092           51          374          648 
TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR 
         952          358          315          417          656          507 
TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
         291          175            7           38           16          141 
TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
         166           11            7          511          826          838 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 
         762          750          523          777          788          700 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
         636          722           36          822           26          737 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
         522          505          194          434           15         1046 
TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I 
         435          830          519           53          256          150 
TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 
          66          110         3377         2881         2746         3074 
TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4173 TCGA-BP-4174 
        2839         3037         2718          701         1893         1879 
TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 
        1955         1670         2964         1625          845         1888 
TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4338 TCGA-BP-4344 TCGA-BP-4347 
        1133          645          461         2859         1666         1367 
TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 
         372          970          374         2208         2372         2361 
TCGA-BP-4761 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4774 
         182         2184         1462          400         1876         1885 
TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4789 
         411         1731         2080          354         1854         1489 
TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 
         620         1107         1124          204         1459          211 
TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 
        2660         2172         1935         1785         1834         1862 
TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 
        1871          205         1746         1794          433         1487 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4982 
        1502         1384         1433         1632          454         1014 
TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
        1413          785         1124          118         1413          501 
TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 
         177         1308         1371          932         1266          563 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5169 
        1177         1126          840         1140         1071          193 
TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5181 
        2412         2257          932          293         2263         1495 
TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 
        1165         1291         1133         1132          693          406 
TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
         822         1011          967          714          408          749 
TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 
        1018          603         1355         1063          951           29 
TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4642 
        1820         1416         1924         2308         1998         1628 
TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 
        1793          646         2554         1498         2423         1435 
TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 
        2259         2283         2353         1955         2186         2014 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4889 TCGA-CJ-4890 
        1883         1759         2125         1952         1946         2085 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4901 
        1521          750          841         1808         1528         1450 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 
        1520         1560         1792         1496         1499         1531 
TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-5671 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5681 
        1657         1373         1943         2430         2575          552 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6031 
        1883         1889         2231         2038         1855         1906 
TCGA-CJ-6032 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 
        2548         2799         2489         2609         2226         2017 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CZ-4853 
        2378         2271         3222         2552         3146          774 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-4863 
        1404           18         1943         1787         1843         1928 
TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5456 
        2830         1868         1929         1789           25         1712 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5463 TCGA-CZ-5464 
        1732         1683         1430          330          662         1740 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 
        1446          685           59          946          386         2439 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
        2067         1997          373          435          693         1905 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 
        1329         1398         1470          370          355         1130 
TCGA-DV-5574 TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
         723         1729          551          119          206          127 
TCGA-GK-A6C7 
          61 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                13                  3 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              1843               3668 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              1683               1291 
[1] "13.0 - 1843.0 (1683.0)" "3.0 - 3668.0 (1291.0)" 
[1] "hr="     "3300000"
D62V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  12P LOSS MUTATED         1        0         2        0
  12P LOSS WILD-TYPE     243       56       124       79
D62V3, multiclass
           clus
vv          12P LOSS MUTATED 12P LOSS WILD-TYPE
  STAGE I                  1                243
  STAGE II                 0                 56
  STAGE III                2                124
  STAGE IV                 0                 79
[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"
                    vv
clus                  T1  T2  T3  T4
  12P LOSS MUTATED     1   0   2   0
  12P LOSS WILD-TYPE 249  67 175  11
D62V4, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  T1                1                249
  T2                0                 67
  T3                2                175
  T4                0                 11
[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"
D62V5, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     1   0
  12P LOSS WILD-TYPE 229  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      1    0
  12P LOSS WILD-TYPE  229   18
   clus
vv  12P LOSS MUTATED 12P LOSS WILD-TYPE
  0                1                229
  1                0                 18
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  12P LOSS MUTATED     3   0   0
  12P LOSS WILD-TYPE 414  78   9
D62V6, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  M0                3                414
  M1                0                 78
  MX                0                  9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V7, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     1   2
  12P LOSS WILD-TYPE 177 325
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      1    2
  12P LOSS WILD-TYPE  177  325
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE                1                177
  MALE                  2                325
[1] 2 2
[1] FALSE
D62V8, continuous
[1] "Remove cluster labels:" "12P LOSS MUTATED"      
clus
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 1                 36 
        TCGA-A3-A8CQ         TCGA-AK-3426         TCGA-AK-3430 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-B0-4838         TCGA-B2-5639         TCGA-B4-5377 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-B4-5378         TCGA-B4-5832         TCGA-B4-5834 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-B4-5835         TCGA-B4-5836         TCGA-B4-5838 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-B4-5843         TCGA-B4-5844         TCGA-CZ-4854 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CZ-4856         TCGA-CZ-4858         TCGA-CZ-4860 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CZ-4861         TCGA-CZ-4862         TCGA-CZ-5456 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CZ-5465         TCGA-CZ-5469         TCGA-CZ-5982 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DV-5565         TCGA-DV-5566         TCGA-DV-5567 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DV-5568         TCGA-DV-5569         TCGA-DV-5573 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DV-5574         TCGA-DV-5575         TCGA-DV-5576 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EU-5904         TCGA-EU-5905         TCGA-EU-5907 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
D62V9, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12P LOSS MUTATED       0                         0     3
  12P LOSS WILD-TYPE     8                        33   454
D62V10, multiclass
                           clus
vv                          12P LOSS MUTATED 12P LOSS WILD-TYPE
  ASIAN                                    0                  8
  BLACK OR AFRICAN AMERICAN                0                 33
  WHITE                                    3                454
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V11, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     0   1
  12P LOSS WILD-TYPE  24 329
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      0    1
  12P LOSS WILD-TYPE   24  329
                        clus
vv                       12P LOSS MUTATED 12P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 24
  NOT HISPANIC OR LATINO                1                329
[1] 2 2
[1] FALSE

Clustering(63) Variable = 12Q LOSS MUTATION ANALYSIS
D63V1, survival
                    sevent
clus2                  0   1
  12Q LOSS MUTATED     3   0
  12Q LOSS WILD-TYPE 335  26
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 3                361 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 0                 26 
$`12Q LOSS MUTATED`
TCGA-BP-4166 TCGA-BP-4775 TCGA-CZ-5457 
          13         1843         1683 

$`12Q LOSS WILD-TYPE`
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 
        1120         1436           16          735         1493         1491 
TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 
        1130         1508         1478         1106         1186          751 
TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3347 
        1137         1485          665         1043          945         1610 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 
        1385          910         2688         1307         2504         1559 
TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 
         319          873         2270         2274          735         1621 
TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 
        1314         1070          630          567          574          861 
TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A8CQ TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 
        1993          617            3         3343         2566         2223 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 
        2017          480         1853         2192         2087         2044 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 
        1745         1423         1471         1280         1217         1779 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
        1481         1397          874         1143         1168          951 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4699 TCGA-B0-4706 
         853          369         1238           43          110           26 
TCGA-B0-4710 TCGA-B0-4718 TCGA-B0-4813 TCGA-B0-4819 TCGA-B0-5097 TCGA-B0-5108 
          96          616           18          183          665          911 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 
        1092          359          797          657          535           59 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 
         493          554          652         1132          449         2408 
TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 
        3431         1487         3076         1420         1727         1835 
TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 
        2583         2741         1732         1605         1203         3668 
TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
        2414         3117         1459         2931         2722         1865 
TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 
        2963          992         1092           51          374          648 
TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR 
         952          358          315          417          656          507 
TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
         291          175            7           38           16          141 
TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
         166           11            7          511          826          838 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 
         762          750          523          777          788          700 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
         636          722           36          822           26          737 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
         522          505          194          434           15         1046 
TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I 
         435          830          519           53          256          150 
TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 
          66          110         3377         2881         2746         3074 
TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4173 TCGA-BP-4174 
        2839         3037         2718          701         1893         1879 
TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 
        1955         1670         2964         1625          845         1888 
TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4338 TCGA-BP-4344 TCGA-BP-4347 
        1133          645          461         2859         1666         1367 
TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 
         372          970          374         2208         2372         2361 
TCGA-BP-4761 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4774 
         182         2184         1462          400         1876         1885 
TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4789 
         411         1731         2080          354         1854         1489 
TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 
         620         1107         1124          204         1459          211 
TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 
        2660         2172         1935         1785         1834         1862 
TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 
        1871          205         1746         1794          433         1487 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4982 
        1502         1384         1433         1632          454         1014 
TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
        1413          785         1124          118         1413          501 
TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 
         177         1308         1371          932         1266          563 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5169 
        1177         1126          840         1140         1071          193 
TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5181 
        2412         2257          932          293         2263         1495 
TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 
        1165         1291         1133         1132          693          406 
TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
         822         1011          967          714          408          749 
TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 
        1018          603         1355         1063          951           29 
TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4642 
        1820         1416         1924         2308         1998         1628 
TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 
        1793          646         2554         1498         2423         1435 
TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 
        2259         2283         2353         1955         2186         2014 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4889 TCGA-CJ-4890 
        1883         1759         2125         1952         1946         2085 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4901 
        1521          750          841         1808         1528         1450 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 
        1520         1560         1792         1496         1499         1531 
TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-5671 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5681 
        1657         1373         1943         2430         2575          552 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6031 
        1883         1889         2231         2038         1855         1906 
TCGA-CJ-6032 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 
        2548         2799         2489         2609         2226         2017 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CZ-4853 
        2378         2271         3222         2552         3146          774 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-4863 
        1404           18         1943         1787         1843         1928 
TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5456 
        2830         1868         1929         1789           25         1712 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5463 TCGA-CZ-5464 
        1732         1683         1430          330          662         1740 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 
        1446          685           59          946          386         2439 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
        2067         1997          373          435          693         1905 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 
        1329         1398         1470          370          355         1130 
TCGA-DV-5574 TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
         723         1729          551          119          206          127 
TCGA-GK-A6C7 
          61 

  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                13                  3 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
              1843               3668 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
              1683               1291 
[1] "13.0 - 1843.0 (1683.0)" "3.0 - 3668.0 (1291.0)" 
[1] "hr="     "3300000"
D63V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  12Q LOSS MUTATED         1        0         3        0
  12Q LOSS WILD-TYPE     243       56       123       79
D63V3, multiclass
           clus
vv          12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  STAGE I                  1                243
  STAGE II                 0                 56
  STAGE III                3                123
  STAGE IV                 0                 79
[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"
                    vv
clus                  T1  T2  T3  T4
  12Q LOSS MUTATED     1   0   3   0
  12Q LOSS WILD-TYPE 249  67 174  11
D63V4, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  T1                1                249
  T2                0                 67
  T3                3                174
  T4                0                 11
[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"
D63V5, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     2   0
  12Q LOSS WILD-TYPE 228  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      2    0
  12Q LOSS WILD-TYPE  228   18
   clus
vv  12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  0                2                228
  1                0                 18
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  12Q LOSS MUTATED     4   0   0
  12Q LOSS WILD-TYPE 413  78   9
D63V6, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  M0                4                413
  M1                0                 78
  MX                0                  9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V7, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     1   3
  12Q LOSS WILD-TYPE 177 324
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      1    3
  12Q LOSS WILD-TYPE  177  324
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FEMALE                1                177
  MALE                  3                324
[1] 2 2
[1] FALSE
D63V8, continuous
[1] "Remove cluster labels:" "12Q LOSS MUTATED"      
clus
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 1                 36 
        TCGA-A3-A8CQ         TCGA-AK-3426         TCGA-AK-3430 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-B0-4838         TCGA-B2-5639         TCGA-B4-5377 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-B4-5378         TCGA-B4-5832         TCGA-B4-5834 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-B4-5835         TCGA-B4-5836         TCGA-B4-5838 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-B4-5843         TCGA-B4-5844         TCGA-CZ-4854 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CZ-4856         TCGA-CZ-4858         TCGA-CZ-4860 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CZ-4861         TCGA-CZ-4862         TCGA-CZ-5456 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CZ-5465         TCGA-CZ-5469         TCGA-CZ-5982 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DV-5565         TCGA-DV-5566         TCGA-DV-5567 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DV-5568         TCGA-DV-5569         TCGA-DV-5573 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DV-5574         TCGA-DV-5575         TCGA-DV-5576 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EU-5904         TCGA-EU-5905         TCGA-EU-5907 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
D63V9, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12Q LOSS MUTATED       0                         0     4
  12Q LOSS WILD-TYPE     8                        33   453
D63V10, multiclass
                           clus
vv                          12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  ASIAN                                    0                  8
  BLACK OR AFRICAN AMERICAN                0                 33
  WHITE                                    4                453
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V11, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     0   2
  12Q LOSS WILD-TYPE  24 328
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      0    2
  12Q LOSS WILD-TYPE   24  328
                        clus
vv                       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 24
  NOT HISPANIC OR LATINO                2                328
[1] 2 2
[1] FALSE

Clustering(64) Variable = 13Q LOSS MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                  0   1
  13Q LOSS MUTATED    36   8
  13Q LOSS WILD-TYPE 302  18
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                44                320 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 8                 18 
$`13Q LOSS MUTATED`
TCGA-A3-3319 TCGA-A3-3347 TCGA-A3-3370 TCGA-A3-3374 TCGA-AK-3433 TCGA-AK-3440 
        1130         1610         2274         1314         2192         1745 
TCGA-AK-3445 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4699 TCGA-B0-4819 TCGA-B0-5113 
        1280          369         1238          110          183          359 
TCGA-B0-5117 TCGA-B0-5696 TCGA-B4-5832 TCGA-B4-5835 TCGA-B4-5838 TCGA-B8-5163 
         535         1727            7           16          166          822 
TCGA-B8-5549 TCGA-BP-4167 TCGA-BP-4334 TCGA-BP-4338 TCGA-BP-4768 TCGA-BP-4964 
         194         2718          645         2859          400         1862 
TCGA-BP-4968 TCGA-BP-4973 TCGA-BP-4994 TCGA-BP-5004 TCGA-BP-5175 TCGA-BP-5191 
        1746         1384         1308         1126          932          967 
TCGA-CJ-4868 TCGA-CJ-4881 TCGA-CJ-4901 TCGA-CW-5588 TCGA-CW-6090 TCGA-CZ-4854 
         646         2014         1450         2017         2552         1404 
TCGA-CZ-4863 TCGA-CZ-4866 TCGA-CZ-5457 TCGA-CZ-5465 TCGA-CZ-5468 TCGA-CZ-5469 
        1928         1868         1683         1446           59          946 
TCGA-CZ-5984 TCGA-DV-5568 
        2067          370 

$`13Q LOSS WILD-TYPE`
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 
        1120         1436           16          735         1493         1491 
TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 
        1508         1478         1106         1186          751         1137 
TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3349 TCGA-A3-3351 
        1485          665         1043          945         1385          910 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
        2688         1307         2504         1559          319          873 
TCGA-A3-3367 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 
        2270          735         1621         1070          630          567 
TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A8CQ TCGA-AK-3425 
         574          861         1993          617            3         3343 
TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 
        2566         2223         2017          480         1853         2087 
TCGA-AK-3436 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 
        2044         1423         1471         1217         1779         1481 
TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
        1397          874         1143         1168          951          853 
TCGA-AS-3778 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4718 TCGA-B0-4813 TCGA-B0-5097 
          43           26           96          616           18          665 
TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5120 
         911         1092          797          657           59          493 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 
         554          652         1132          449         2408         3431 
TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 
        1487         3076         1420         1835         2583         2741 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 
        1732         1605         1203         3668         2414         3117 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 
        1459         2931         2722         1865         2963          992 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 
        1092           51          374          648          952          358 
TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 
         315          417          656          507          291          175 
TCGA-B4-5834 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 
          38          141           11            7          511          826 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 
         838          762          750          523          777          788 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5164 TCGA-B8-5165 
         700          636          722           36           26          737 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
         522          505          434           15         1046          435 
TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J 
         830          519           53          256          150           66 
TCGA-B8-A7U6 TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
         110         3377         2881         2746         3074         2839 
TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4169 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 
        3037           13          701         1893         1879         1955 
TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 
        1670         2964         1625          845         1888         1133 
TCGA-BP-4335 TCGA-BP-4344 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4756 
         461         1666         1367          372          970          374 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4765 TCGA-BP-4766 
        2208         2372         2361          182         2184         1462 
TCGA-BP-4769 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 
        1876         1885         1843          411         1731         2080 
TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4801 
         354         1854         1489          620         1107         1124 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 
         204         1459          211         2660         2172         1935 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4969 TCGA-BP-4970 
        1785         1834         1871          205         1794          433 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4982 
        1487         1502         1433         1632          454         1014 
TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
        1413          785         1124          118         1413          501 
TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 
         177         1371          932         1266          563         1177 
TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 
         840         1140         1071          193         2412         2257 
TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
         293         2263         1495         1165         1291         1133 
TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5192 
        1132          693          406          822         1011          714 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 
         408          749         1018          603         1355         1063 
TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4639 
         951           29         1820         1416         1924         2308 
TCGA-CJ-4640 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
        1998         1628         1793         2554         1498         2423 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
        1435         2259         2283         2353         1955         2186 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4889 TCGA-CJ-4890 
        1883         1759         2125         1952         1946         2085 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4902 
        1521          750          841         1808         1528         1520 
TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 
        1560         1792         1496         1499         1531         1657 
TCGA-CJ-4916 TCGA-CJ-5671 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5681 TCGA-CJ-5682 
        1373         1943         2430         2575          552         1883 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6031 TCGA-CJ-6032 
        1889         2231         2038         1855         1906         2548 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-5591 
        2799         2489         2609         2226         2378         2271 
TCGA-CW-6088 TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4858 TCGA-CZ-4859 
        3222         3146          774           18         1943         1787 
TCGA-CZ-4862 TCGA-CZ-4864 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5456 
        1843         2830         1929         1789           25         1712 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5463 TCGA-CZ-5464 
        1732         1683         1430          330          662         1740 
TCGA-CZ-5466 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 
         685          386         2439         1997          373          435 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5569 
         693         1905         1329         1398         1470          355 
TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 
        1130          723         1729          551          119          206 
TCGA-EU-5907 TCGA-GK-A6C7 
         127           61 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 7                  3 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              2859               3668 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              1294               1299 
[1] "7.0 - 2859.0 (1294.0)" "3.0 - 3668.0 (1299.0)"
[1] "hr=" "3.4"
D64V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  13Q LOSS MUTATED        23        2        25       19
  13Q LOSS WILD-TYPE     221       54       101       60
D64V3, multiclass
           clus
vv          13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  STAGE I                 23                221
  STAGE II                 2                 54
  STAGE III               25                101
  STAGE IV                19                 60
[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"
                    vv
clus                  T1  T2  T3  T4
  13Q LOSS MUTATED    25   3  34   7
  13Q LOSS WILD-TYPE 225  64 143   4
D64V4, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  T1               25                225
  T2                3                 64
  T3               34                143
  T4                7                  4
[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"
D64V5, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    33   4
  13Q LOSS WILD-TYPE 197  14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     33    4
  13Q LOSS WILD-TYPE  197   14
   clus
vv  13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  0               33                197
  1                4                 14
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  13Q LOSS MUTATED    52  17   0
  13Q LOSS WILD-TYPE 365  61   9
D64V6, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  M0               52                365
  M1               17                 61
  MX                0                  9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V7, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    20  49
  13Q LOSS WILD-TYPE 158 278
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     20   49
  13Q LOSS WILD-TYPE  158  278
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE               20                158
  MALE                 49                278
[1] 2 2
[1] FALSE
D64V8, continuous
D64V9, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  13Q LOSS MUTATED       0                         2    66
  13Q LOSS WILD-TYPE     8                        31   391
D64V10, multiclass
                           clus
vv                          13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  ASIAN                                    0                  8
  BLACK OR AFRICAN AMERICAN                2                 31
  WHITE                                   66                391
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V11, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED     1  47
  13Q LOSS WILD-TYPE  23 283
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      1   47
  13Q LOSS WILD-TYPE   23  283
                        clus
vv                       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 23
  NOT HISPANIC OR LATINO               47                283
[1] 2 2
[1] FALSE

Clustering(65) Variable = 14Q LOSS MUTATION ANALYSIS
D65V1, survival
                    sevent
clus2                  0   1
  14Q LOSS MUTATED   123  15
  14Q LOSS WILD-TYPE 215  11
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               138                226 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                15                 11 
$`14Q LOSS MUTATED`
TCGA-A3-3306 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3324 
        1120         1493         1491         1130         1508         1186 
TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3347 TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3378 
         665         1043         1610          910         2688          630 
TCGA-A3-3382 TCGA-A3-3387 TCGA-AK-3427 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3436 
         574          617         2566         2017          480         2044 
TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3458 TCGA-B0-4819 TCGA-B0-5097 
        1779         1481          874         1168          183          665 
TCGA-B0-5113 TCGA-B0-5400 TCGA-B0-5692 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5701 
         359         1132         1487         1835         2583         1732 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B2-4098 TCGA-B2-4102 TCGA-B2-5633 
        1459         2931         2722           51          952          358 
TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B4-5832 TCGA-B4-5836 TCGA-B4-5838 
         315          417          656            7          141          166 
TCGA-B4-5843 TCGA-B8-4619 TCGA-B8-5158 TCGA-B8-5162 TCGA-B8-5164 TCGA-B8-5550 
          11          523          636           36           26          434 
TCGA-B8-5551 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54G TCGA-B8-A54I TCGA-BP-4163 
          15          435          830           53          150         2839 
TCGA-BP-4167 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4347 TCGA-BP-4761 
        2718         1893         1879         1955         1367          182 
TCGA-BP-4768 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4797 TCGA-BP-4803 TCGA-BP-4959 
         400         1731         2080         1107          204         2660 
TCGA-BP-4962 TCGA-BP-4965 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4973 TCGA-BP-4977 
        1785         1871          433         1487         1384          454 
TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4989 TCGA-BP-4992 TCGA-BP-5000 TCGA-BP-5004 
        1413          785          118          501          563         1126 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5180 TCGA-BP-5183 
         193         2412         2257          932         2263         1291 
TCGA-BP-5185 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5196 TCGA-BP-5198 
        1132          822         1011          967         1018          603 
TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4640 TCGA-CJ-4642 TCGA-CJ-4868 TCGA-CJ-4869 
         951         1924         1998         1628          646         2554 
TCGA-CJ-4871 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4881 
        2423         2259         2283         2353         1955         2014 
TCGA-CJ-4884 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4897 TCGA-CJ-4903 TCGA-CJ-4907 
        1759          750          841         1808         1560         1499 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-5671 TCGA-CJ-5675 TCGA-CJ-5676 
        1531         1657         1373         1943         2430         2575 
TCGA-CJ-5682 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-6090 
        1883         2038         1855         2226         2017         2552 
TCGA-CZ-4854 TCGA-CZ-4858 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5452 
        1404         1943         1928         2830         1868         1789 
TCGA-CZ-5456 TCGA-CZ-5461 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5468 TCGA-CZ-5469 
        1712          330          662         1446           59          946 
TCGA-CZ-5470 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5987 TCGA-CZ-5989 TCGA-DV-5573 
         386         2067         1997          435         1905         1130 

$`14Q LOSS WILD-TYPE`
TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3325 
        1436           16          735         1478         1106          751 
TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3343 TCGA-A3-3349 TCGA-A3-3358 TCGA-A3-3359 
        1137         1485          945         1385         1307         2504 
TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 
        1559          319          873         2270         2274          735 
TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 
        1621         1314         1070          567          861         1993 
TCGA-A3-A8CQ TCGA-AK-3425 TCGA-AK-3428 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 
           3         3343         2223         1853         2192         2087 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3453 
        1745         1423         1471         1280         1217         1397 
TCGA-AK-3456 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 
        1143          951          853          369         1238           43 
TCGA-B0-4699 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4718 TCGA-B0-4813 TCGA-B0-5108 
         110           26           96          616           18          911 
TCGA-B0-5110 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 
        1092          797          657          535           59          493 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5693 
         554          652          449         2408         3431         3076 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5699 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 
        1420         1727         2741         1605         1203         3668 
TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 
        2414         3117         1865         2963          992         1092 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 
         374          648          507          291          175           38 
TCGA-B4-5835 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
          16            7          511          826          838          762 
TCGA-B8-4154 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5159 TCGA-B8-5163 
         750          777          788          700          722          822 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5552 TCGA-B8-A54F 
         737          522          505          194         1046          519 
TCGA-B8-A54H TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4161 
         256           66          110         3377         2881         2746 
TCGA-BP-4162 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4169 TCGA-BP-4177 TCGA-BP-4325 
        3074         3037           13          701         1670         2964 
TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 
        1625          845         1888         1133          645          461 
TCGA-BP-4338 TCGA-BP-4344 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4756 TCGA-BP-4758 
        2859         1666          372          970          374         2208 
TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4774 
        2372         2361         2184         1462         1876         1885 
TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4795 
        1843          411          354         1854         1489          620 
TCGA-BP-4801 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4963 
        1124         1459          211         2172         1935         1834 
TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4972 TCGA-BP-4975 
        1862          205         1746         1794         1502         1433 
TCGA-BP-4976 TCGA-BP-4982 TCGA-BP-4987 TCGA-BP-4991 TCGA-BP-4993 TCGA-BP-4994 
        1632         1014         1124         1413          177         1308 
TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5001 TCGA-BP-5006 TCGA-BP-5007 
        1371          932         1266         1177          840         1140 
TCGA-BP-5008 TCGA-BP-5177 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5184 TCGA-BP-5186 
        1071          293         1495         1165         1133          693 
TCGA-BP-5187 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5199 TCGA-BP-5200 
         406          714          408          749         1355         1063 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4639 TCGA-CJ-4643 TCGA-CJ-4870 
          29         1820         1416         2308         1793         1498 
TCGA-CJ-4872 TCGA-CJ-4878 TCGA-CJ-4882 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4889 
        1435         2186         1883         2125         1952         1946 
TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4899 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4904 
        2085         1521         1528         1450         1520         1792 
TCGA-CJ-4905 TCGA-CJ-5681 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-6031 TCGA-CJ-6032 
        1496          552         1889         2231         1906         2548 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6088 
        2799         2489         2609         2378         2271         3222 
TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-5451 
        3146          774           18         1787         1843         1929 
TCGA-CZ-5453 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5464 
          25         1683         1732         1683         1430         1740 
TCGA-CZ-5466 TCGA-CZ-5982 TCGA-CZ-5986 TCGA-CZ-5988 TCGA-DV-5565 TCGA-DV-5566 
         685         2439          373          693         1329         1398 
TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-EU-5904 
        1470          370          355          723         1729          551 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-GK-A6C7 
         119          206          127           61 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                 7                  3 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              2931               3668 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            1378.5             1252.0 
[1] "7.0 - 2931.0 (1378.5)" "3.0 - 3668.0 (1252.0)"
[1] "hr=" "2.3"
D65V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  14Q LOSS MUTATED        76       26        64       45
  14Q LOSS WILD-TYPE     168       30        62       34
D65V3, multiclass
           clus
vv          14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  STAGE I                 76                168
  STAGE II                26                 30
  STAGE III               64                 62
  STAGE IV                45                 34
[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"
                    vv
clus                  T1  T2  T3  T4
  14Q LOSS MUTATED    82  34  92   3
  14Q LOSS WILD-TYPE 168  33  85   8
D65V4, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  T1               82                168
  T2               34                 33
  T3               92                 85
  T4                3                  8
[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"
D65V5, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    92  14
  14Q LOSS WILD-TYPE 138   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     92   14
  14Q LOSS WILD-TYPE  138    4
   clus
vv  14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  0               92                138
  1               14                  4
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  14Q LOSS MUTATED   162  46   3
  14Q LOSS WILD-TYPE 255  32   6
D65V6, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  M0              162                255
  M1               46                 32
  MX                3                  6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V7, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    63 148
  14Q LOSS WILD-TYPE 115 179
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     63  148
  14Q LOSS WILD-TYPE  115  179
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE               63                115
  MALE                148                179
[1] 2 2
[1] FALSE
D65V8, continuous
D65V9, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  14Q LOSS MUTATED       2                         9   196
  14Q LOSS WILD-TYPE     6                        24   261
D65V10, multiclass
                           clus
vv                          14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  ASIAN                                    2                  6
  BLACK OR AFRICAN AMERICAN                9                 24
  WHITE                                  196                261
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V11, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    12 142
  14Q LOSS WILD-TYPE  12 188
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     12  142
  14Q LOSS WILD-TYPE   12  188
                        clus
vv                       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   12                 12
  NOT HISPANIC OR LATINO              142                188
[1] 2 2
[1] FALSE

Clustering(66) Variable = 15Q LOSS MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                  0   1
  15Q LOSS MUTATED    17   2
  15Q LOSS WILD-TYPE 321  24
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                19                345 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 2                 24 
$`15Q LOSS MUTATED`
TCGA-A3-3319 TCGA-A3-3382 TCGA-B0-5116 TCGA-B4-5832 TCGA-B8-4620 TCGA-B8-5549 
        1130          574          657            7          777          194 
TCGA-BP-4167 TCGA-BP-4768 TCGA-BP-4775 TCGA-BP-4797 TCGA-BP-5169 TCGA-BP-5175 
        2718          400         1843         1107          193          932 
TCGA-BP-5200 TCGA-CJ-4901 TCGA-CJ-4907 TCGA-CZ-5457 TCGA-CZ-5461 TCGA-CZ-5469 
        1063         1450         1499         1683          330          946 
TCGA-CZ-5984 
        2067 

$`15Q LOSS WILD-TYPE`
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 
        1120         1436           16          735         1493         1491 
TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 
        1508         1478         1106         1186          751         1137 
TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3347 TCGA-A3-3349 
        1485          665         1043          945         1610         1385 
TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 
         910         2688         1307         2504         1559          319 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 
         873         2270         2274          735         1621         1314 
TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 
        1070          630          567          861         1993          617 
TCGA-A3-A8CQ TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 
           3         3343         2566         2223         2017          480 
TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 
        1853         2192         2087         2044         1745         1423 
TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 
        1471         1280         1217         1779         1481         1397 
TCGA-AK-3454 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 
         874         1143         1168          951          853          369 
TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4699 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4718 
        1238           43          110           26           96          616 
TCGA-B0-4813 TCGA-B0-4819 TCGA-B0-5097 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 
          18          183          665          911         1092          359 
TCGA-B0-5115 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
         797          535           59          493          554          652 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 
        1132          449         2408         3431         1487         3076 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 
        1420         1727         1835         2583         2741         1732 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 
        1605         1203         3668         2414         3117         1459 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 
        2931         2722         1865         2963          992         1092 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 
          51          374          648          952          358          315 
TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 
         417          656          507          291          175           38 
TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 
          16          141          166           11            7          511 
TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4621 
         826          838          762          750          523          788 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 
         700          636          722           36          822           26 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
         737          522          505          434           15         1046 
TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I 
         435          830          519           53          256          150 
TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 
          66          110         3377         2881         2746         3074 
TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4169 TCGA-BP-4173 TCGA-BP-4174 
        2839         3037           13          701         1893         1879 
TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 
        1955         1670         2964         1625          845         1888 
TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4338 TCGA-BP-4344 TCGA-BP-4347 
        1133          645          461         2859         1666         1367 
TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 
         372          970          374         2208         2372         2361 
TCGA-BP-4761 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4774 TCGA-BP-4776 
         182         2184         1462         1876         1885          411 
TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4795 
        1731         2080          354         1854         1489          620 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 
        1124          204         1459          211         2660         2172 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 
        1935         1785         1834         1862         1871          205 
TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 
        1746         1794          433         1487         1502         1384 
TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4986 
        1433         1632          454         1014         1413          785 
TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 
        1124          118         1413          501          177         1308 
TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
        1371          932         1266          563         1177         1126 
TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5177 
         840         1140         1071         2412         2257          293 
TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 
        2263         1495         1165         1291         1133         1132 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 
         693          406          822         1011          967          714 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5201 
         408          749         1018          603         1355          951 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4639 TCGA-CJ-4640 
          29         1820         1416         1924         2308         1998 
TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
        1628         1793          646         2554         1498         2423 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
        1435         2259         2283         2353         1955         2186 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4889 
        2014         1883         1759         2125         1952         1946 
TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4897 TCGA-CJ-4899 
        2085         1521          750          841         1808         1528 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 
        1520         1560         1792         1496         1531         1657 
TCGA-CJ-4916 TCGA-CJ-5671 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5681 TCGA-CJ-5682 
        1373         1943         2430         2575          552         1883 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6031 TCGA-CJ-6032 
        1889         2231         2038         1855         1906         2548 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 
        2799         2489         2609         2226         2017         2378 
TCGA-CW-5591 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4854 
        2271         3222         2552         3146          774         1404 
TCGA-CZ-4856 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 
          18         1943         1787         1843         1928         2830 
TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5456 TCGA-CZ-5458 
        1868         1929         1789           25         1712         1732 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 
        1683         1430          662         1740         1446          685 
TCGA-CZ-5468 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 
          59          386         2439         1997          373          435 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 
         693         1905         1329         1398         1470          370 
TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5905 
         355         1130          723         1729          551          119 
TCGA-EU-5906 TCGA-EU-5907 TCGA-GK-A6C7 
         206          127           61 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 7                  3 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              2718               3668 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               946               1329 
[1] "7.0 - 2718.0 (946.0)"  "3.0 - 3668.0 (1329.0)"
[1] "hr=" "1.8"
D66V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  15Q LOSS MUTATED         8        2        13       12
  15Q LOSS WILD-TYPE     236       54       113       67
D66V3, multiclass
           clus
vv          15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  STAGE I                  8                236
  STAGE II                 2                 54
  STAGE III               13                113
  STAGE IV                12                 67
[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"
                    vv
clus                  T1  T2  T3  T4
  15Q LOSS MUTATED     9   2  21   3
  15Q LOSS WILD-TYPE 241  65 156   8
D66V4, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  T1                9                241
  T2                2                 65
  T3               21                156
  T4                3                  8
[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"
D66V5, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED    17   1
  15Q LOSS WILD-TYPE 213  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     17    1
  15Q LOSS WILD-TYPE  213   17
   clus
vv  15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  0               17                213
  1                1                 17
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  15Q LOSS MUTATED    24  11   0
  15Q LOSS WILD-TYPE 393  67   9
D66V6, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  M0               24                393
  M1               11                 67
  MX                0                  9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V7, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     7  28
  15Q LOSS WILD-TYPE 171 299
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      7   28
  15Q LOSS WILD-TYPE  171  299
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE                7                171
  MALE                 28                299
[1] 2 2
[1] FALSE
D66V8, continuous
D66V9, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  15Q LOSS MUTATED       1                         0    34
  15Q LOSS WILD-TYPE     7                        33   423
D66V10, multiclass
                           clus
vv                          15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  ASIAN                                    1                  7
  BLACK OR AFRICAN AMERICAN                0                 33
  WHITE                                   34                423
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V11, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     0  21
  15Q LOSS WILD-TYPE  24 309
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      0   21
  15Q LOSS WILD-TYPE   24  309
                        clus
vv                       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 24
  NOT HISPANIC OR LATINO               21                309
[1] 2 2
[1] FALSE

Clustering(67) Variable = 16P LOSS MUTATION ANALYSIS
D67V1, survival
                    sevent
clus2                  0   1
  16P LOSS MUTATED     4   0
  16P LOSS WILD-TYPE 334  26
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 4                360 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 0                 26 
$`16P LOSS MUTATED`
TCGA-A3-3316 TCGA-B8-5551 TCGA-BP-4797 TCGA-CZ-5982 
        1493           15         1107         2439 

$`16P LOSS WILD-TYPE`
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3319 
        1120         1436           16          735         1491         1130 
TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 
        1508         1478         1106         1186          751         1137 
TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3347 TCGA-A3-3349 
        1485          665         1043          945         1610         1385 
TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 
         910         2688         1307         2504         1559          319 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 
         873         2270         2274          735         1621         1314 
TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 
        1070          630          567          574          861         1993 
TCGA-A3-3387 TCGA-A3-A8CQ TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
         617            3         3343         2566         2223         2017 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
         480         1853         2192         2087         2044         1745 
TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 
        1423         1471         1280         1217         1779         1481 
TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
        1397          874         1143         1168          951          853 
TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4699 TCGA-B0-4706 TCGA-B0-4710 
         369         1238           43          110           26           96 
TCGA-B0-4718 TCGA-B0-4813 TCGA-B0-4819 TCGA-B0-5097 TCGA-B0-5108 TCGA-B0-5110 
         616           18          183          665          911         1092 
TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 
         359          797          657          535           59          493 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 
         554          652         1132          449         2408         3431 
TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 
        1487         3076         1420         1727         1835         2583 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
        2741         1732         1605         1203         3668         2414 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 
        3117         1459         2931         2722         1865         2963 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 
         992         1092           51          374          648          952 
TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 
         358          315          417          656          507          291 
TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
         175            7           38           16          141          166 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
          11            7          511          826          838          762 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 
         750          523          777          788          700          636 
TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
         722           36          822           26          737          522 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D 
         505          194          434         1046          435          830 
TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 
         519           53          256          150           66          110 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 
        3377         2881         2746         3074         2839         3037 
TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 
          13         2718          701         1893         1879         1955 
TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 
        1670         2964         1625          845         1888         1133 
TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4338 TCGA-BP-4344 TCGA-BP-4347 TCGA-BP-4349 
         645          461         2859         1666         1367          372 
TCGA-BP-4351 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 
         970          374         2208         2372         2361          182 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4774 TCGA-BP-4775 
        2184         1462          400         1876         1885         1843 
TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4789 
         411         1731         2080          354         1854         1489 
TCGA-BP-4795 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 
         620         1124          204         1459          211         2660 
TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 
        2172         1935         1785         1834         1862         1871 
TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
         205         1746         1794          433         1487         1502 
TCGA-BP-4973 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4982 TCGA-BP-4983 
        1384         1433         1632          454         1014         1413 
TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 
         785         1124          118         1413          501          177 
TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 
        1308         1371          932         1266          563         1177 
TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5169 TCGA-BP-5170 
        1126          840         1140         1071          193         2412 
TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 
        2257          932          293         2263         1495         1165 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 
        1291         1133         1132          693          406          822 
TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
        1011          967          714          408          749         1018 
TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 
         603         1355         1063          951           29         1820 
TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4642 TCGA-CJ-4643 
        1416         1924         2308         1998         1628         1793 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 
         646         2554         1498         2423         1435         2259 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 
        2283         2353         1955         2186         2014         1883 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 
        1759         2125         1952         1946         2085         1521 
TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4901 TCGA-CJ-4902 
         750          841         1808         1528         1450         1520 
TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 
        1560         1792         1496         1499         1531         1657 
TCGA-CJ-4916 TCGA-CJ-5671 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5681 TCGA-CJ-5682 
        1373         1943         2430         2575          552         1883 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6031 TCGA-CJ-6032 
        1889         2231         2038         1855         1906         2548 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 
        2799         2489         2609         2226         2017         2378 
TCGA-CW-5591 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4854 
        2271         3222         2552         3146          774         1404 
TCGA-CZ-4856 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 
          18         1943         1787         1843         1928         2830 
TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5456 TCGA-CZ-5457 
        1868         1929         1789           25         1712         1683 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5463 TCGA-CZ-5464 
        1732         1683         1430          330          662         1740 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5984 
        1446          685           59          946          386         2067 
TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 
        1997          373          435          693         1905         1329 
TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 
        1398         1470          370          355         1130          723 
TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-GK-A6C7 
        1729          551          119          206          127           61 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                15                  3 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              2439               3668 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              1300               1299 
[1] "15.0 - 2439.0 (1300.0)" "3.0 - 3668.0 (1299.0)" 
[1] "hr="     "3300000"
D67V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  16P LOSS MUTATED         2        2         3        2
  16P LOSS WILD-TYPE     242       54       123       77
D67V3, multiclass
           clus
vv          16P LOSS MUTATED 16P LOSS WILD-TYPE
  STAGE I                  2                242
  STAGE II                 2                 54
  STAGE III                3                123
  STAGE IV                 2                 77
[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"
                    vv
clus                  T1  T2  T3  T4
  16P LOSS MUTATED     2   2   3   2
  16P LOSS WILD-TYPE 248  65 174   9
D67V4, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  T1                2                248
  T2                2                 65
  T3                3                174
  T4                2                  9
[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"
D67V5, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     5   1
  16P LOSS WILD-TYPE 225  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      5    1
  16P LOSS WILD-TYPE  225   17
   clus
vv  16P LOSS MUTATED 16P LOSS WILD-TYPE
  0                5                225
  1                1                 17
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  16P LOSS MUTATED     8   1   0
  16P LOSS WILD-TYPE 409  77   9
D67V6, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  M0                8                409
  M1                1                 77
  MX                0                  9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V7, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     3   6
  16P LOSS WILD-TYPE 175 321
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      3    6
  16P LOSS WILD-TYPE  175  321
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE                3                175
  MALE                  6                321
[1] 2 2
[1] FALSE
D67V8, continuous
[1] "Remove cluster labels:" "16P LOSS MUTATED"      
clus
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 1                 36 
        TCGA-A3-A8CQ         TCGA-AK-3426         TCGA-AK-3430 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B0-4838         TCGA-B2-5639         TCGA-B4-5377 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B4-5378         TCGA-B4-5832         TCGA-B4-5834 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B4-5835         TCGA-B4-5836         TCGA-B4-5838 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B4-5843         TCGA-B4-5844         TCGA-CZ-4854 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CZ-4856         TCGA-CZ-4858         TCGA-CZ-4860 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CZ-4861         TCGA-CZ-4862         TCGA-CZ-5456 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CZ-5457         TCGA-CZ-5465         TCGA-CZ-5469 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DV-5565         TCGA-DV-5566         TCGA-DV-5567 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DV-5568         TCGA-DV-5569         TCGA-DV-5573 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DV-5574         TCGA-DV-5575         TCGA-DV-5576 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EU-5904         TCGA-EU-5905         TCGA-EU-5907 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
D67V9, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16P LOSS MUTATED       0                         1     8
  16P LOSS WILD-TYPE     8                        32   449
D67V10, multiclass
                           clus
vv                          16P LOSS MUTATED 16P LOSS WILD-TYPE
  ASIAN                                    0                  8
  BLACK OR AFRICAN AMERICAN                1                 32
  WHITE                                    8                449
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V11, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     0   4
  16P LOSS WILD-TYPE  24 326
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      0    4
  16P LOSS WILD-TYPE   24  326
                        clus
vv                       16P LOSS MUTATED 16P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 24
  NOT HISPANIC OR LATINO                4                326
[1] 2 2
[1] FALSE

Clustering(68) Variable = 16Q LOSS MUTATION ANALYSIS
D68V1, survival
                    sevent
clus2                  0   1
  16Q LOSS MUTATED     7   0
  16Q LOSS WILD-TYPE 331  26
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 7                357 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 0                 26 
$`16Q LOSS MUTATED`
TCGA-A3-3306 TCGA-A3-3316 TCGA-B0-5097 TCGA-B0-5402 TCGA-B8-5551 TCGA-BP-4797 
        1120         1493          665          449           15         1107 
TCGA-CZ-5982 
        2439 

$`16Q LOSS WILD-TYPE`
TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 
        1436           16          735         1491         1130         1508 
TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 
        1478         1106         1186          751         1137         1485 
TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 
         665         1043          945         1610         1385          910 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
        2688         1307         2504         1559          319          873 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 
        2270         2274          735         1621         1314         1070 
TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 
         630          567          574          861         1993          617 
TCGA-A3-A8CQ TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 
           3         3343         2566         2223         2017          480 
TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 
        1853         2192         2087         2044         1745         1423 
TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 
        1471         1280         1217         1779         1481         1397 
TCGA-AK-3454 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 
         874         1143         1168          951          853          369 
TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4699 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4718 
        1238           43          110           26           96          616 
TCGA-B0-4813 TCGA-B0-4819 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 
          18          183          911         1092          359          797 
TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
         657          535           59          493          554          652 
TCGA-B0-5400 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 
        1132         2408         3431         1487         3076         1420 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
        1727         1835         2583         2741         1732         1605 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
        1203         3668         2414         3117         1459         2931 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
        2722         1865         2963          992         1092           51 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 
         374          648          952          358          315          417 
TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 
         656          507          291          175            7           38 
TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 
          16          141          166           11            7          511 
TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 
         826          838          762          750          523          777 
TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 
         788          700          636          722           36          822 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 
          26          737          522          505          194          434 
TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H 
        1046          435          830          519           53          256 
TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4161 
         150           66          110         3377         2881         2746 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 
        3074         2839         3037           13         2718          701 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 
        1893         1879         1955         1670         2964         1625 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4338 
         845         1888         1133          645          461         2859 
TCGA-BP-4344 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4756 TCGA-BP-4758 
        1666         1367          372          970          374         2208 
TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 
        2372         2361          182         2184         1462          400 
TCGA-BP-4769 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 
        1876         1885         1843          411         1731         2080 
TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4795 TCGA-BP-4801 TCGA-BP-4803 
         354         1854         1489          620         1124          204 
TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
        1459          211         2660         2172         1935         1785 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 
        1834         1862         1871          205         1746         1794 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4975 TCGA-BP-4976 
         433         1487         1502         1384         1433         1632 
TCGA-BP-4977 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4989 
         454         1014         1413          785         1124          118 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 
        1413          501          177         1308         1371          932 
TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 
        1266          563         1177         1126          840         1140 
TCGA-BP-5008 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5177 
        1071          193         2412         2257          932          293 
TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 
        2263         1495         1165         1291         1133         1132 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 
         693          406          822         1011          967          714 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 
         408          749         1018          603         1355         1063 
TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4639 
         951           29         1820         1416         1924         2308 
TCGA-CJ-4640 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
        1998         1628         1793          646         2554         1498 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 
        2423         1435         2259         2283         2353         1955 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 
        2186         2014         1883         1759         2125         1952 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4897 
        1946         2085         1521          750          841         1808 
TCGA-CJ-4899 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 
        1528         1450         1520         1560         1792         1496 
TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-5671 TCGA-CJ-5675 
        1499         1531         1657         1373         1943         2430 
TCGA-CJ-5676 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 
        2575          552         1883         1889         2231         2038 
TCGA-CJ-6027 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 
        1855         1906         2548         2799         2489         2609 
TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6088 TCGA-CW-6090 
        2226         2017         2378         2271         3222         2552 
TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4858 TCGA-CZ-4859 
        3146          774         1404           18         1943         1787 
TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 
        1843         1928         2830         1868         1929         1789 
TCGA-CZ-5453 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
          25         1712         1683         1732         1683         1430 
TCGA-CZ-5461 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5468 
         330          662         1740         1446          685           59 
TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 
         946          386         2067         1997          373          435 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 
         693         1905         1329         1398         1470          370 
TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5905 
         355         1130          723         1729          551          119 
TCGA-EU-5906 TCGA-EU-5907 TCGA-GK-A6C7 
         206          127           61 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                15                  3 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              2439               3668 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              1107               1308 
[1] "15.0 - 2439.0 (1107.0)" "3.0 - 3668.0 (1308.0)" 
[1] "hr="     "9100000"
D68V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  16Q LOSS MUTATED         4        2         3        4
  16Q LOSS WILD-TYPE     240       54       123       75
D68V3, multiclass
           clus
vv          16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  STAGE I                  4                240
  STAGE II                 2                 54
  STAGE III                3                123
  STAGE IV                 4                 75
[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"
                    vv
clus                  T1  T2  T3  T4
  16Q LOSS MUTATED     4   2   4   3
  16Q LOSS WILD-TYPE 246  65 173   8
D68V4, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  T1                4                246
  T2                2                 65
  T3                4                173
  T4                3                  8
[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"
D68V5, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED     7   1
  16Q LOSS WILD-TYPE 223  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      7    1
  16Q LOSS WILD-TYPE  223   17
   clus
vv  16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  0                7                223
  1                1                 17
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  16Q LOSS MUTATED    11   2   0
  16Q LOSS WILD-TYPE 406  76   9
D68V6, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  M0               11                406
  M1                2                 76
  MX                0                  9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V7, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED     4   9
  16Q LOSS WILD-TYPE 174 318
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      4    9
  16Q LOSS WILD-TYPE  174  318
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE                4                174
  MALE                  9                318
[1] 2 2
[1] FALSE
D68V8, continuous
[1] "Remove cluster labels:" "16Q LOSS MUTATED"      
clus
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 1                 36 
        TCGA-A3-A8CQ         TCGA-AK-3426         TCGA-AK-3430 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B0-4838         TCGA-B2-5639         TCGA-B4-5377 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B4-5378         TCGA-B4-5832         TCGA-B4-5834 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B4-5835         TCGA-B4-5836         TCGA-B4-5838 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B4-5843         TCGA-B4-5844         TCGA-CZ-4854 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CZ-4856         TCGA-CZ-4858         TCGA-CZ-4860 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CZ-4861         TCGA-CZ-4862         TCGA-CZ-5456 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CZ-5457         TCGA-CZ-5465         TCGA-CZ-5469 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DV-5565         TCGA-DV-5566         TCGA-DV-5567 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DV-5568         TCGA-DV-5569         TCGA-DV-5573 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DV-5574         TCGA-DV-5575         TCGA-DV-5576 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EU-5904         TCGA-EU-5905         TCGA-EU-5907 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
D68V9, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16Q LOSS MUTATED       0                         1    12
  16Q LOSS WILD-TYPE     8                        32   445
D68V10, multiclass
                           clus
vv                          16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  ASIAN                                    0                  8
  BLACK OR AFRICAN AMERICAN                1                 32
  WHITE                                   12                445
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V11, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED     0   8
  16Q LOSS WILD-TYPE  24 322
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      0    8
  16Q LOSS WILD-TYPE   24  322
                        clus
vv                       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 24
  NOT HISPANIC OR LATINO                8                322
[1] 2 2
[1] FALSE

Clustering(69) Variable = 17P LOSS MUTATION ANALYSIS
D69V1, survival
                    sevent
clus2                  0   1
  17P LOSS MUTATED    28   5
  17P LOSS WILD-TYPE 310  21
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                33                331 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 5                 21 
$`17P LOSS MUTATED`
TCGA-A3-3316 TCGA-A3-3319 TCGA-A3-3374 TCGA-A3-3382 TCGA-AK-3433 TCGA-AK-3436 
        1493         1130         1314          574         2192         2044 
TCGA-AK-3440 TCGA-AK-3447 TCGA-AK-3456 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4699 
        1745         1217         1143          369         1238          110 
TCGA-B0-4813 TCGA-B0-5117 TCGA-B0-5702 TCGA-B2-3923 TCGA-B4-5835 TCGA-BP-4166 
          18          535         1605          992           16           13 
TCGA-BP-4334 TCGA-BP-4351 TCGA-BP-4797 TCGA-BP-4994 TCGA-BP-5196 TCGA-BP-5198 
         645          970         1107         1308         1018          603 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-5676 TCGA-CW-5588 TCGA-CZ-4858 TCGA-CZ-5460 
        2423         1435         2575         2017         1943         1430 
TCGA-CZ-5465 TCGA-CZ-5468 TCGA-DV-5565 
        1446           59         1329 

$`17P LOSS WILD-TYPE`
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3320 
        1120         1436           16          735         1491         1508 
TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 
        1478         1106         1186          751         1137         1485 
TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 
         665         1043          945         1610         1385          910 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
        2688         1307         2504         1559          319          873 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 
        2270         2274          735         1621         1070          630 
TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A8CQ TCGA-AK-3425 
         567          861         1993          617            3         3343 
TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 
        2566         2223         2017          480         1853         2087 
TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 
        1423         1471         1280         1779         1481         1397 
TCGA-AK-3454 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4706 
         874         1168          951          853           43           26 
TCGA-B0-4710 TCGA-B0-4718 TCGA-B0-4819 TCGA-B0-5097 TCGA-B0-5108 TCGA-B0-5110 
          96          616          183          665          911         1092 
TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
         359          797          657           59          493          554 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 
         652         1132          449         2408         3431         1487 
TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 
        3076         1420         1727         1835         2583         2741 
TCGA-B0-5701 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 
        1732         1203         3668         2414         3117         1459 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3924 TCGA-B2-4098 
        2931         2722         1865         2963         1092           51 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 
         374          648          952          358          315          417 
TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 
         656          507          291          175            7           38 
TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 
         141          166           11            7          511          826 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 
         838          762          750          523          777          788 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 
         700          636          722           36          822           26 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 
         737          522          505          194          434           15 
TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H 
        1046          435          830          519           53          256 
TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4161 
         150           66          110         3377         2881         2746 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4173 
        3074         2839         3037         2718          701         1893 
TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 
        1879         1955         1670         2964         1625          845 
TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4335 TCGA-BP-4338 TCGA-BP-4344 TCGA-BP-4347 
        1888         1133          461         2859         1666         1367 
TCGA-BP-4349 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 
         372          374         2208         2372         2361          182 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4774 TCGA-BP-4775 
        2184         1462          400         1876         1885         1843 
TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4789 
         411         1731         2080          354         1854         1489 
TCGA-BP-4795 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 
         620         1124          204         1459          211         2660 
TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 
        2172         1935         1785         1834         1862         1871 
TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
         205         1746         1794          433         1487         1502 
TCGA-BP-4973 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4982 TCGA-BP-4983 
        1384         1433         1632          454         1014         1413 
TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 
         785         1124          118         1413          501          177 
TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
        1371          932         1266          563         1177         1126 
TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 
         840         1140         1071          193         2412         2257 
TCGA-BP-5175 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 
         932          293         2263         1495         1165         1291 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 
        1133         1132          693          406          822         1011 
TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5199 TCGA-BP-5200 
         967          714          408          749         1355         1063 
TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4639 
         951           29         1820         1416         1924         2308 
TCGA-CJ-4640 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
        1998         1628         1793          646         2554         1498 
TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 
        2259         2283         2353         1955         2186         2014 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4889 TCGA-CJ-4890 
        1883         1759         2125         1952         1946         2085 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4901 
        1521          750          841         1808         1528         1450 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 
        1520         1560         1792         1496         1499         1531 
TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-5671 TCGA-CJ-5675 TCGA-CJ-5681 TCGA-CJ-5682 
        1657         1373         1943         2430          552         1883 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6031 TCGA-CJ-6032 
        1889         2231         2038         1855         1906         2548 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-5591 
        2799         2489         2609         2226         2378         2271 
TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 
        3222         2552         3146          774         1404           18 
TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 
        1787         1843         1928         2830         1868         1929 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 
        1789           25         1712         1683         1732         1683 
TCGA-CZ-5461 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5469 TCGA-CZ-5470 
         330          662         1740          685          946          386 
TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 
        2439         2067         1997          373          435          693 
TCGA-CZ-5989 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 
        1905         1398         1470          370          355         1130 
TCGA-DV-5574 TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
         723         1729          551          119          206          127 
TCGA-GK-A6C7 
          61 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                13                  3 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              2575               3668 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              1217               1355 
[1] "13.0 - 2575.0 (1217.0)" "3.0 - 3668.0 (1355.0)" 
[1] "hr=" "2.7"
D69V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  17P LOSS MUTATED        16        6        11       11
  17P LOSS WILD-TYPE     228       50       115       68
D69V3, multiclass
           clus
vv          17P LOSS MUTATED 17P LOSS WILD-TYPE
  STAGE I                 16                228
  STAGE II                 6                 50
  STAGE III               11                115
  STAGE IV                11                 68
[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"
                    vv
clus                  T1  T2  T3  T4
  17P LOSS MUTATED    16   7  19   2
  17P LOSS WILD-TYPE 234  60 158   9
D69V4, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  T1               16                234
  T2                7                 60
  T3               19                158
  T4                2                  9
[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"
D69V5, binary
                    cls
clus                   0   1
  17P LOSS MUTATED    18   0
  17P LOSS WILD-TYPE 212  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     18    0
  17P LOSS WILD-TYPE  212   18
   clus
vv  17P LOSS MUTATED 17P LOSS WILD-TYPE
  0               18                212
  1                0                 18
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  17P LOSS MUTATED    32  12   0
  17P LOSS WILD-TYPE 385  66   9
D69V6, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  M0               32                385
  M1               12                 66
  MX                0                  9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V7, binary
                    cls
clus                   0   1
  17P LOSS MUTATED    11  33
  17P LOSS WILD-TYPE 167 294
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     11   33
  17P LOSS WILD-TYPE  167  294
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE               11                167
  MALE                 33                294
[1] 2 2
[1] FALSE
D69V8, continuous
D69V9, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17P LOSS MUTATED       0                         3    40
  17P LOSS WILD-TYPE     8                        30   417
D69V10, multiclass
                           clus
vv                          17P LOSS MUTATED 17P LOSS WILD-TYPE
  ASIAN                                    0                  8
  BLACK OR AFRICAN AMERICAN                3                 30
  WHITE                                   40                417
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V11, binary
                    cls
clus                   0   1
  17P LOSS MUTATED     1  29
  17P LOSS WILD-TYPE  23 301
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      1   29
  17P LOSS WILD-TYPE   23  301
                        clus
vv                       17P LOSS MUTATED 17P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 23
  NOT HISPANIC OR LATINO               29                301
[1] 2 2
[1] FALSE

Clustering(70) Variable = 17Q LOSS MUTATION ANALYSIS
D70V1, survival
                    sevent
clus2                  0   1
  17Q LOSS MUTATED    21   2
  17Q LOSS WILD-TYPE 317  24
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                23                341 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 2                 24 
$`17Q LOSS MUTATED`
TCGA-A3-3316 TCGA-A3-3319 TCGA-A3-3374 TCGA-AK-3433 TCGA-AK-3436 TCGA-AK-3440 
        1493         1130         1314         2192         2044         1745 
TCGA-AK-3447 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4699 TCGA-B0-5117 TCGA-B2-3923 
        1217          369         1238          110          535          992 
TCGA-BP-4166 TCGA-BP-4334 TCGA-BP-4351 TCGA-BP-4797 TCGA-BP-4994 TCGA-BP-5196 
          13          645          970         1107         1308         1018 
TCGA-CJ-4871 TCGA-CJ-5676 TCGA-CW-5588 TCGA-CZ-5460 TCGA-CZ-5465 
        2423         2575         2017         1430         1446 

$`17Q LOSS WILD-TYPE`
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3320 
        1120         1436           16          735         1491         1508 
TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 
        1478         1106         1186          751         1137         1485 
TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 
         665         1043          945         1610         1385          910 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
        2688         1307         2504         1559          319          873 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 
        2270         2274          735         1621         1070          630 
TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A8CQ 
         567          574          861         1993          617            3 
TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 
        3343         2566         2223         2017          480         1853 
TCGA-AK-3434 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 
        2087         1423         1471         1280         1779         1481 
TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
        1397          874         1143         1168          951          853 
TCGA-AS-3778 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4718 TCGA-B0-4813 TCGA-B0-4819 
          43           26           96          616           18          183 
TCGA-B0-5097 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 
         665          911         1092          359          797          657 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
          59          493          554          652         1132          449 
TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5696 
        2408         3431         1487         3076         1420         1727 
TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
        1835         2583         2741         1732         1605         1203 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
        3668         2414         3117         1459         2931         2722 
TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 
        1865         2963         1092           51          374          648 
TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR 
         952          358          315          417          656          507 
TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
         291          175            7           38           16          141 
TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
         166           11            7          511          826          838 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 
         762          750          523          777          788          700 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
         636          722           36          822           26          737 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
         522          505          194          434           15         1046 
TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I 
         435          830          519           53          256          150 
TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 
          66          110         3377         2881         2746         3074 
TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4173 TCGA-BP-4174 
        2839         3037         2718          701         1893         1879 
TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 
        1955         1670         2964         1625          845         1888 
TCGA-BP-4332 TCGA-BP-4335 TCGA-BP-4338 TCGA-BP-4344 TCGA-BP-4347 TCGA-BP-4349 
        1133          461         2859         1666         1367          372 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4765 
         374         2208         2372         2361          182         2184 
TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 
        1462          400         1876         1885         1843          411 
TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4795 
        1731         2080          354         1854         1489          620 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 
        1124          204         1459          211         2660         2172 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 
        1935         1785         1834         1862         1871          205 
TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 
        1746         1794          433         1487         1502         1384 
TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4986 
        1433         1632          454         1014         1413          785 
TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 
        1124          118         1413          501          177         1371 
TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 
         932         1266          563         1177         1126          840 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5175 
        1140         1071          193         2412         2257          932 
TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
         293         2263         1495         1165         1291         1133 
TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 
        1132          693          406          822         1011          967 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 
         714          408          749          603         1355         1063 
TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4639 
         951           29         1820         1416         1924         2308 
TCGA-CJ-4640 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
        1998         1628         1793          646         2554         1498 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
        1435         2259         2283         2353         1955         2186 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4889 
        2014         1883         1759         2125         1952         1946 
TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4897 TCGA-CJ-4899 
        2085         1521          750          841         1808         1528 
TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 
        1450         1520         1560         1792         1496         1499 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-5671 TCGA-CJ-5675 TCGA-CJ-5681 
        1531         1657         1373         1943         2430          552 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6031 
        1883         1889         2231         2038         1855         1906 
TCGA-CJ-6032 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 
        2548         2799         2489         2609         2226         2378 
TCGA-CW-5591 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4854 
        2271         3222         2552         3146          774         1404 
TCGA-CZ-4856 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 
          18         1943         1787         1843         1928         2830 
TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5456 TCGA-CZ-5457 
        1868         1929         1789           25         1712         1683 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5461 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5466 
        1732         1683          330          662         1740          685 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
          59          946          386         2439         2067         1997 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
         373          435          693         1905         1329         1398 
TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 
        1470          370          355         1130          723         1729 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-GK-A6C7 
         551          119          206          127           61 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                13                  3 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              2575               3668 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              1238               1307 
[1] "13.0 - 2575.0 (1238.0)" "3.0 - 3668.0 (1307.0)" 
[1] "hr=" "1.2"
D70V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  17Q LOSS MUTATED        10        4         7        7
  17Q LOSS WILD-TYPE     234       52       119       72
D70V3, multiclass
           clus
vv          17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  STAGE I                 10                234
  STAGE II                 4                 52
  STAGE III                7                119
  STAGE IV                 7                 72
[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"
                    vv
clus                  T1  T2  T3  T4
  17Q LOSS MUTATED    10   5  12   1
  17Q LOSS WILD-TYPE 240  62 165  10
D70V4, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  T1               10                240
  T2                5                 62
  T3               12                165
  T4                1                 10
[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"
D70V5, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    10   0
  17Q LOSS WILD-TYPE 220  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     10    0
  17Q LOSS WILD-TYPE  220   18
   clus
vv  17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  0               10                220
  1                0                 18
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  17Q LOSS MUTATED    21   7   0
  17Q LOSS WILD-TYPE 396  71   9
D70V6, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  M0               21                396
  M1                7                 71
  MX                0                  9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V7, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     7  21
  17Q LOSS WILD-TYPE 171 306
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      7   21
  17Q LOSS WILD-TYPE  171  306
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE                7                171
  MALE                 21                306
[1] 2 2
[1] FALSE
D70V8, continuous
[1] "Remove cluster labels:" "17Q LOSS MUTATED"      
clus
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 1                 36 
        TCGA-A3-A8CQ         TCGA-AK-3426         TCGA-AK-3430 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-B0-4838         TCGA-B2-5639         TCGA-B4-5377 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-B4-5378         TCGA-B4-5832         TCGA-B4-5834 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-B4-5835         TCGA-B4-5836         TCGA-B4-5838 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-B4-5843         TCGA-B4-5844         TCGA-CZ-4854 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CZ-4856         TCGA-CZ-4858         TCGA-CZ-4860 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CZ-4861         TCGA-CZ-4862         TCGA-CZ-5456 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CZ-5457         TCGA-CZ-5469         TCGA-CZ-5982 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DV-5565         TCGA-DV-5566         TCGA-DV-5567 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DV-5568         TCGA-DV-5569         TCGA-DV-5573 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DV-5574         TCGA-DV-5575         TCGA-DV-5576 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EU-5904         TCGA-EU-5905         TCGA-EU-5907 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
D70V9, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17Q LOSS MUTATED       0                         2    25
  17Q LOSS WILD-TYPE     8                        31   432
D70V10, multiclass
                           clus
vv                          17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  ASIAN                                    0                  8
  BLACK OR AFRICAN AMERICAN                2                 31
  WHITE                                   25                432
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V11, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     1  18
  17Q LOSS WILD-TYPE  23 312
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      1   18
  17Q LOSS WILD-TYPE   23  312
                        clus
vv                       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 23
  NOT HISPANIC OR LATINO               18                312
[1] 2 2
[1] FALSE

Clustering(71) Variable = 18P LOSS MUTATION ANALYSIS
D71V1, survival
                    sevent
clus2                  0   1
  18P LOSS MUTATED    50   7
  18P LOSS WILD-TYPE 288  19
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                57                307 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 7                 19 
$`18P LOSS MUTATED`
TCGA-A3-3319 TCGA-A3-3347 TCGA-A3-3357 TCGA-A3-3372 TCGA-A3-3387 TCGA-AK-3425 
        1130         1610         2688          735          617         3343 
TCGA-AK-3430 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3465 TCGA-B0-4699 TCGA-B0-4819 
         480         2044         1745          369          110          183 
TCGA-B0-5097 TCGA-B2-4098 TCGA-B2-5641 TCGA-B4-5832 TCGA-B4-5835 TCGA-B8-4620 
         665           51          656            7           16          777 
TCGA-B8-4621 TCGA-B8-5163 TCGA-B8-5549 TCGA-B8-5550 TCGA-BP-4166 TCGA-BP-4338 
         788          822          194          434           13         2859 
TCGA-BP-4756 TCGA-BP-4761 TCGA-BP-4781 TCGA-BP-4797 TCGA-BP-4803 TCGA-BP-4962 
         374          182         2080         1107          204         1785 
TCGA-BP-4977 TCGA-BP-4994 TCGA-BP-5000 TCGA-BP-5169 TCGA-BP-5175 TCGA-BP-5181 
         454         1308          563          193          932         1495 
TCGA-BP-5191 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5201 TCGA-CJ-4636 
         967         1018          603         1063          951         1924 
TCGA-CJ-4873 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4901 TCGA-CJ-4907 TCGA-CJ-6027 
        2259         2014         1883         1450         1499         1855 
TCGA-CW-5588 TCGA-CZ-4858 TCGA-CZ-4863 TCGA-CZ-4866 TCGA-CZ-5456 TCGA-CZ-5468 
        2017         1943         1928         1868         1712           59 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5988 
        2067         1997          693 

$`18P LOSS WILD-TYPE`
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 
        1120         1436           16          735         1493         1491 
TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 
        1508         1478         1106         1186          751         1137 
TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3349 TCGA-A3-3351 
        1485          665         1043          945         1385          910 
TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 
        1307         2504         1559          319          873         2270 
TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 
        2274         1621         1314         1070          630          567 
TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-A8CQ TCGA-AK-3427 TCGA-AK-3428 
         574          861         1993            3         2566         2223 
TCGA-AK-3429 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3443 TCGA-AK-3444 
        2017         1853         2192         2087         1423         1471 
TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 
        1280         1217         1779         1481         1397          874 
TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3777 TCGA-AS-3778 
        1143         1168          951          853         1238           43 
TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4718 TCGA-B0-4813 TCGA-B0-5108 TCGA-B0-5110 
          26           96          616           18          911         1092 
TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 
         359          797          657          535           59          493 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 
         554          652         1132          449         2408         3431 
TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 
        1487         3076         1420         1727         1835         2583 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
        2741         1732         1605         1203         3668         2414 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 
        3117         1459         2931         2722         1865         2963 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 
         992         1092          374          648          952          358 
TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 
         315          417          507          291          175           38 
TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 
         141          166           11            7          511          826 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4622 TCGA-B8-5158 
         838          762          750          523          700          636 
TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
         722           36           26          737          522          505 
TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G 
          15         1046          435          830          519           53 
TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4158 TCGA-BP-4160 
         256          150           66          110         3377         2881 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4167 TCGA-BP-4169 
        2746         3074         2839         3037         2718          701 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 
        1893         1879         1955         1670         2964         1625 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4344 
         845         1888         1133          645          461         1666 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 
        1367          372          970         2208         2372         2361 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4774 TCGA-BP-4775 
        2184         1462          400         1876         1885         1843 
TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4795 
         411         1731          354         1854         1489          620 
TCGA-BP-4801 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 
        1124         1459          211         2660         2172         1935 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 
        1834         1862         1871          205         1746         1794 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4975 TCGA-BP-4976 
         433         1487         1502         1384         1433         1632 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 
        1014         1413          785         1124          118         1413 
TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5001 
         501          177         1371          932         1266         1177 
TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5170 TCGA-BP-5174 
        1126          840         1140         1071         2412         2257 
TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 
         293         2263         1165         1291         1133         1132 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 
         693          406          822         1011          714          408 
TCGA-BP-5195 TCGA-BP-5199 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4639 
         749         1355           29         1820         1416         2308 
TCGA-CJ-4640 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
        1998         1628         1793          646         2554         1498 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
        2423         1435         2283         2353         1955         2186 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 
        1759         2125         1952         1946         2085         1521 
TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4902 TCGA-CJ-4903 
         750          841         1808         1528         1520         1560 
TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-5671 
        1792         1496         1531         1657         1373         1943 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
        2430         2575          552         1883         1889         2231 
TCGA-CJ-5686 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 
        2038         1906         2548         2799         2489         2609 
TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 
        2226         2378         2271         3222         2552         3146 
TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-4864 
         774         1404           18         1787         1843         2830 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 
        1929         1789           25         1683         1732         1683 
TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 
        1430          330          662         1740         1446          685 
TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5989 
         946          386         2439          373          435         1905 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 
        1329         1398         1470          370          355         1130 
TCGA-DV-5574 TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
         723         1729          551          119          206          127 
TCGA-GK-A6C7 
          61 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 7                  3 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              3343               3668 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               967               1367 
[1] "7.0 - 3343.0 (967.0)"  "3.0 - 3668.0 (1367.0)"
[1] "hr=" "2.2"
D71V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  18P LOSS MUTATED        29        7        33       22
  18P LOSS WILD-TYPE     215       49        93       57
D71V3, multiclass
           clus
vv          18P LOSS MUTATED 18P LOSS WILD-TYPE
  STAGE I                 29                215
  STAGE II                 7                 49
  STAGE III               33                 93
  STAGE IV                22                 57
[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"
                    vv
clus                  T1  T2  T3  T4
  18P LOSS MUTATED    31   9  46   5
  18P LOSS WILD-TYPE 219  58 131   6
D71V4, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  T1               31                219
  T2                9                 58
  T3               46                131
  T4                5                  6
[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"
D71V5, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    42   3
  18P LOSS WILD-TYPE 188  15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     42    3
  18P LOSS WILD-TYPE  188   15
   clus
vv  18P LOSS MUTATED 18P LOSS WILD-TYPE
  0               42                188
  1                3                 15
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  18P LOSS MUTATED    71  20   0
  18P LOSS WILD-TYPE 346  58   9
D71V6, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  M0               71                346
  M1               20                 58
  MX                0                  9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V7, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    26  65
  18P LOSS WILD-TYPE 152 262
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     26   65
  18P LOSS WILD-TYPE  152  262
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE               26                152
  MALE                 65                262
[1] 2 2
[1] FALSE
D71V8, continuous
D71V9, continuous
[1] "Remove cluster labels:" "18P LOSS MUTATED"      
clus
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 1                  7 
        TCGA-A3-A8CQ         TCGA-B2-A4SR         TCGA-B8-5158 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-B8-5164         TCGA-B8-A54F         TCGA-B8-A54G 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G6-A5PC 
"18P LOSS WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18P LOSS MUTATED       2                         4    85
  18P LOSS WILD-TYPE     6                        29   372
D71V10, multiclass
                           clus
vv                          18P LOSS MUTATED 18P LOSS WILD-TYPE
  ASIAN                                    2                  6
  BLACK OR AFRICAN AMERICAN                4                 29
  WHITE                                   85                372
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V11, binary
                    cls
clus                   0   1
  18P LOSS MUTATED     1  60
  18P LOSS WILD-TYPE  23 270
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      1   60
  18P LOSS WILD-TYPE   23  270
                        clus
vv                       18P LOSS MUTATED 18P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 23
  NOT HISPANIC OR LATINO               60                270
[1] 2 2
[1] FALSE

Clustering(72) Variable = 18Q LOSS MUTATION ANALYSIS
D72V1, survival
                    sevent
clus2                  0   1
  18Q LOSS MUTATED    53   9
  18Q LOSS WILD-TYPE 285  17
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                62                302 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 9                 17 
$`18Q LOSS MUTATED`
TCGA-A3-3313 TCGA-A3-3319 TCGA-A3-3347 TCGA-A3-3357 TCGA-A3-3372 TCGA-A3-3387 
         735         1130         1610         2688          735          617 
TCGA-AK-3425 TCGA-AK-3430 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3465 TCGA-B0-4699 
        3343          480         2044         1745          369          110 
TCGA-B0-4819 TCGA-B0-5097 TCGA-B0-5121 TCGA-B2-4098 TCGA-B2-5641 TCGA-B4-5832 
         183          665          554           51          656            7 
TCGA-B4-5835 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-5163 TCGA-B8-5549 TCGA-B8-5550 
          16          777          788          822          194          434 
TCGA-BP-4166 TCGA-BP-4338 TCGA-BP-4756 TCGA-BP-4761 TCGA-BP-4781 TCGA-BP-4797 
          13         2859          374          182         2080         1107 
TCGA-BP-4803 TCGA-BP-4962 TCGA-BP-4977 TCGA-BP-4994 TCGA-BP-5000 TCGA-BP-5169 
         204         1785          454         1308          563          193 
TCGA-BP-5175 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5191 TCGA-BP-5196 TCGA-BP-5198 
         932         1495         1165          967         1018          603 
TCGA-BP-5200 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4881 
        1063          951         1924         1435         2259         2014 
TCGA-CJ-4901 TCGA-CJ-4907 TCGA-CJ-6027 TCGA-CJ-6032 TCGA-CW-5588 TCGA-CZ-4854 
        1450         1499         1855         2548         2017         1404 
TCGA-CZ-4858 TCGA-CZ-4863 TCGA-CZ-4866 TCGA-CZ-5456 TCGA-CZ-5468 TCGA-CZ-5984 
        1943         1928         1868         1712           59         2067 
TCGA-CZ-5985 TCGA-CZ-5988 
        1997          693 

$`18Q LOSS WILD-TYPE`
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3320 
        1120         1436           16         1493         1491         1508 
TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 
        1478         1106         1186          751         1137         1485 
TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3358 
         665         1043          945         1385          910         1307 
TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 
        2504         1559          319          873         2270         2274 
TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 
        1621         1314         1070          630          567          574 
TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-A8CQ TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
         861         1993            3         2566         2223         2017 
TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 
        1853         2192         2087         1423         1471         1280 
TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3456 
        1217         1779         1481         1397          874         1143 
TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4706 
        1168          951          853         1238           43           26 
TCGA-B0-4710 TCGA-B0-4718 TCGA-B0-4813 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 
          96          616           18          911         1092          359 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5399 
         797          657          535           59          493          652 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 
        1132          449         2408         3431         1487         3076 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 
        1420         1727         1835         2583         2741         1732 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 
        1605         1203         3668         2414         3117         1459 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 
        2931         2722         1865         2963          992         1092 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 
         374          648          952          358          315          417 
TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5836 TCGA-B4-5838 
         507          291          175           38          141          166 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
          11            7          511          826          838          762 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 
         750          523          700          636          722           36 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5551 TCGA-B8-5552 
          26          737          522          505           15         1046 
TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I 
         435          830          519           53          256          150 
TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 
          66          110         3377         2881         2746         3074 
TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4173 TCGA-BP-4174 
        2839         3037         2718          701         1893         1879 
TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 
        1955         1670         2964         1625          845         1888 
TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4344 TCGA-BP-4347 TCGA-BP-4349 
        1133          645          461         1666         1367          372 
TCGA-BP-4351 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4765 TCGA-BP-4766 
         970         2208         2372         2361         2184         1462 
TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 
         400         1876         1885         1843          411         1731 
TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4795 TCGA-BP-4801 TCGA-BP-4804 
         354         1854         1489          620         1124         1459 
TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4963 TCGA-BP-4964 
         211         2660         2172         1935         1834         1862 
TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 
        1871          205         1746         1794          433         1487 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4982 TCGA-BP-4983 
        1502         1384         1433         1632         1014         1413 
TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 
         785         1124          118         1413          501          177 
TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 
        1371          932         1266         1177         1126          840 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5177 TCGA-BP-5180 
        1140         1071         2412         2257          293         2263 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 
        1291         1133         1132          693          406          822 
TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5199 TCGA-BP-5202 
        1011          714          408          749         1355           29 
TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4642 TCGA-CJ-4643 
        1820         1416         2308         1998         1628         1793 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4874 TCGA-CJ-4875 
         646         2554         1498         2423         2283         2353 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 
        1955         2186         1883         1759         2125         1952 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4897 
        1946         2085         1521          750          841         1808 
TCGA-CJ-4899 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4908 
        1528         1520         1560         1792         1496         1531 
TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-5671 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5681 
        1657         1373         1943         2430         2575          552 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6031 TCGA-CW-5581 
        1883         1889         2231         2038         1906         2799 
TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6088 
        2489         2609         2226         2378         2271         3222 
TCGA-CW-6090 TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4859 TCGA-CZ-4862 
        2552         3146          774           18         1787         1843 
TCGA-CZ-4864 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5457 TCGA-CZ-5458 
        2830         1929         1789           25         1683         1732 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 
        1683         1430          330          662         1740         1446 
TCGA-CZ-5466 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5986 TCGA-CZ-5987 
         685          946          386         2439          373          435 
TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 
        1905         1329         1398         1470          370          355 
TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 
        1130          723         1729          551          119          206 
TCGA-EU-5907 TCGA-GK-A6C7 
         127           61 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 7                  3 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              3343               3668 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             992.5             1369.0 
[1] "7.0 - 3343.0 (992.5)"  "3.0 - 3668.0 (1369.0)"
[1] "hr=" "2.9"
D72V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  18Q LOSS MUTATED        33        8        30       22
  18Q LOSS WILD-TYPE     211       48        96       57
D72V3, multiclass
           clus
vv          18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  STAGE I                 33                211
  STAGE II                 8                 48
  STAGE III               30                 96
  STAGE IV                22                 57
[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"
                    vv
clus                  T1  T2  T3  T4
  18Q LOSS MUTATED    35  10  43   5
  18Q LOSS WILD-TYPE 215  57 134   6
D72V4, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  T1               35                215
  T2               10                 57
  T3               43                134
  T4                5                  6
[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"
D72V5, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED    45   3
  18Q LOSS WILD-TYPE 185  15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     45    3
  18Q LOSS WILD-TYPE  185   15
   clus
vv  18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  0               45                185
  1                3                 15
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  18Q LOSS MUTATED    73  20   0
  18Q LOSS WILD-TYPE 344  58   9
D72V6, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  M0               73                344
  M1               20                 58
  MX                0                  9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V7, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED    26  67
  18Q LOSS WILD-TYPE 152 260
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     26   67
  18Q LOSS WILD-TYPE  152  260
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE               26                152
  MALE                 67                260
[1] 2 2
[1] FALSE
D72V8, continuous
D72V9, continuous
[1] "Remove cluster labels:" "18Q LOSS MUTATED"      
clus
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 1                  7 
        TCGA-A3-A8CQ         TCGA-B2-A4SR         TCGA-B8-5158 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-B8-5164         TCGA-B8-A54F         TCGA-B8-A54G 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G6-A5PC 
"18Q LOSS WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18Q LOSS MUTATED       2                         4    87
  18Q LOSS WILD-TYPE     6                        29   370
D72V10, multiclass
                           clus
vv                          18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  ASIAN                                    2                  6
  BLACK OR AFRICAN AMERICAN                4                 29
  WHITE                                   87                370
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V11, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED     2  61
  18Q LOSS WILD-TYPE  22 269
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      2   61
  18Q LOSS WILD-TYPE   22  269
                        clus
vv                       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                 22
  NOT HISPANIC OR LATINO               61                269
[1] 2 2
[1] FALSE

Clustering(73) Variable = 19P LOSS MUTATION ANALYSIS
D73V1, survival
                    sevent
clus2                  0   1
  19P LOSS MUTATED     2   0
  19P LOSS WILD-TYPE 336  26
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 2                362 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 0                 26 
$`19P LOSS MUTATED`
TCGA-A3-3319 TCGA-AK-3425 
        1130         3343 

$`19P LOSS WILD-TYPE`
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 
        1120         1436           16          735         1493         1491 
TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 
        1508         1478         1106         1186          751         1137 
TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3347 TCGA-A3-3349 
        1485          665         1043          945         1610         1385 
TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 
         910         2688         1307         2504         1559          319 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 
         873         2270         2274          735         1621         1314 
TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 
        1070          630          567          574          861         1993 
TCGA-A3-3387 TCGA-A3-A8CQ TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 
         617            3         2566         2223         2017          480 
TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 
        1853         2192         2087         2044         1745         1423 
TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 
        1471         1280         1217         1779         1481         1397 
TCGA-AK-3454 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 
         874         1143         1168          951          853          369 
TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4699 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4718 
        1238           43          110           26           96          616 
TCGA-B0-4813 TCGA-B0-4819 TCGA-B0-5097 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 
          18          183          665          911         1092          359 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
         797          657          535           59          493          554 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 
         652         1132          449         2408         3431         1487 
TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 
        3076         1420         1727         1835         2583         2741 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 
        1732         1605         1203         3668         2414         3117 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 
        1459         2931         2722         1865         2963          992 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 
        1092           51          374          648          952          358 
TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 
         315          417          656          507          291          175 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 
           7           38           16          141          166           11 
TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
           7          511          826          838          762          750 
TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 
         523          777          788          700          636          722 
TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
          36          822           26          737          522          505 
TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D 
         194          434           15         1046          435          830 
TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 
         519           53          256          150           66          110 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 
        3377         2881         2746         3074         2839         3037 
TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 
          13         2718          701         1893         1879         1955 
TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 
        1670         2964         1625          845         1888         1133 
TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4338 TCGA-BP-4344 TCGA-BP-4347 TCGA-BP-4349 
         645          461         2859         1666         1367          372 
TCGA-BP-4351 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 
         970          374         2208         2372         2361          182 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4774 TCGA-BP-4775 
        2184         1462          400         1876         1885         1843 
TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4789 
         411         1731         2080          354         1854         1489 
TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 
         620         1107         1124          204         1459          211 
TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 
        2660         2172         1935         1785         1834         1862 
TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 
        1871          205         1746         1794          433         1487 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4982 
        1502         1384         1433         1632          454         1014 
TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
        1413          785         1124          118         1413          501 
TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 
         177         1308         1371          932         1266          563 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5169 
        1177         1126          840         1140         1071          193 
TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5181 
        2412         2257          932          293         2263         1495 
TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 
        1165         1291         1133         1132          693          406 
TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
         822         1011          967          714          408          749 
TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 
        1018          603         1355         1063          951           29 
TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4642 
        1820         1416         1924         2308         1998         1628 
TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 
        1793          646         2554         1498         2423         1435 
TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 
        2259         2283         2353         1955         2186         2014 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4889 TCGA-CJ-4890 
        1883         1759         2125         1952         1946         2085 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4901 
        1521          750          841         1808         1528         1450 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 
        1520         1560         1792         1496         1499         1531 
TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-5671 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5681 
        1657         1373         1943         2430         2575          552 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6031 
        1883         1889         2231         2038         1855         1906 
TCGA-CJ-6032 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 
        2548         2799         2489         2609         2226         2017 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CZ-4853 
        2378         2271         3222         2552         3146          774 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-4863 
        1404           18         1943         1787         1843         1928 
TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5456 
        2830         1868         1929         1789           25         1712 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5463 
        1683         1732         1683         1430          330          662 
TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 
        1740         1446          685           59          946          386 
TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 
        2439         2067         1997          373          435          693 
TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 
        1905         1329         1398         1470          370          355 
TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 
        1130          723         1729          551          119          206 
TCGA-EU-5907 TCGA-GK-A6C7 
         127           61 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              1130                  3 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              3343               3668 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
            2236.5             1299.0 
[1] "1130.0 - 3343.0 (2236.5)" "3.0 - 3668.0 (1299.0)"   
[1] "Remove cluster labels:" "19P LOSS MUTATED"      
D73V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  19P LOSS MUTATED         2        0         5        4
  19P LOSS WILD-TYPE     242       56       121       75
D73V3, multiclass
           clus
vv          19P LOSS MUTATED 19P LOSS WILD-TYPE
  STAGE I                  2                242
  STAGE II                 0                 56
  STAGE III                5                121
  STAGE IV                 4                 75
[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"
                    vv
clus                  T1  T2  T3  T4
  19P LOSS MUTATED     2   1   5   3
  19P LOSS WILD-TYPE 248  66 172   8
D73V4, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  T1                2                248
  T2                1                 66
  T3                5                172
  T4                3                  8
[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"
D73V5, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     6   0
  19P LOSS WILD-TYPE 224  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      6    0
  19P LOSS WILD-TYPE  224   18
   clus
vv  19P LOSS MUTATED 19P LOSS WILD-TYPE
  0                6                224
  1                0                 18
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  19P LOSS MUTATED     8   3   0
  19P LOSS WILD-TYPE 409  75   9
D73V6, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  M0                8                409
  M1                3                 75
  MX                0                  9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V7, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     3   8
  19P LOSS WILD-TYPE 175 319
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      3    8
  19P LOSS WILD-TYPE  175  319
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE                3                175
  MALE                  8                319
[1] 2 2
[1] FALSE
D73V8, continuous
[1] "Remove cluster labels:" "19P LOSS MUTATED"      
clus
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 1                 36 
        TCGA-A3-A8CQ         TCGA-AK-3426         TCGA-AK-3430 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B0-4838         TCGA-B2-5639         TCGA-B4-5377 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B4-5378         TCGA-B4-5832         TCGA-B4-5834 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B4-5835         TCGA-B4-5836         TCGA-B4-5838 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B4-5843         TCGA-B4-5844         TCGA-CZ-4854 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CZ-4856         TCGA-CZ-4858         TCGA-CZ-4861 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CZ-4862         TCGA-CZ-5456         TCGA-CZ-5457 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CZ-5465         TCGA-CZ-5469         TCGA-CZ-5982 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DV-5565         TCGA-DV-5566         TCGA-DV-5567 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DV-5568         TCGA-DV-5569         TCGA-DV-5573 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DV-5574         TCGA-DV-5575         TCGA-DV-5576 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EU-5904         TCGA-EU-5905         TCGA-EU-5907 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
D73V9, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19P LOSS MUTATED       1                         0    10
  19P LOSS WILD-TYPE     7                        33   447
D73V10, multiclass
                           clus
vv                          19P LOSS MUTATED 19P LOSS WILD-TYPE
  ASIAN                                    1                  7
  BLACK OR AFRICAN AMERICAN                0                 33
  WHITE                                   10                447
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V11, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     0   6
  19P LOSS WILD-TYPE  24 324
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      0    6
  19P LOSS WILD-TYPE   24  324
                        clus
vv                       19P LOSS MUTATED 19P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 24
  NOT HISPANIC OR LATINO                6                324
[1] 2 2
[1] FALSE

Clustering(74) Variable = 19Q LOSS MUTATION ANALYSIS
D74V1, survival
                    sevent
clus2                  0   1
  19Q LOSS MUTATED     1   0
  19Q LOSS WILD-TYPE 337  26
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 1                363 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 0                 26 
$`19Q LOSS MUTATED`
TCGA-A3-3319 
        1130 

$`19Q LOSS WILD-TYPE`
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 
        1120         1436           16          735         1493         1491 
TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 
        1508         1478         1106         1186          751         1137 
TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3347 TCGA-A3-3349 
        1485          665         1043          945         1610         1385 
TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 
         910         2688         1307         2504         1559          319 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 
         873         2270         2274          735         1621         1314 
TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 
        1070          630          567          574          861         1993 
TCGA-A3-3387 TCGA-A3-A8CQ TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
         617            3         3343         2566         2223         2017 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
         480         1853         2192         2087         2044         1745 
TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 
        1423         1471         1280         1217         1779         1481 
TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
        1397          874         1143         1168          951          853 
TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4699 TCGA-B0-4706 TCGA-B0-4710 
         369         1238           43          110           26           96 
TCGA-B0-4718 TCGA-B0-4813 TCGA-B0-4819 TCGA-B0-5097 TCGA-B0-5108 TCGA-B0-5110 
         616           18          183          665          911         1092 
TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 
         359          797          657          535           59          493 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 
         554          652         1132          449         2408         3431 
TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 
        1487         3076         1420         1727         1835         2583 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
        2741         1732         1605         1203         3668         2414 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 
        3117         1459         2931         2722         1865         2963 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 
         992         1092           51          374          648          952 
TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 
         358          315          417          656          507          291 
TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
         175            7           38           16          141          166 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
          11            7          511          826          838          762 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 
         750          523          777          788          700          636 
TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
         722           36          822           26          737          522 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
         505          194          434           15         1046          435 
TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J 
         830          519           53          256          150           66 
TCGA-B8-A7U6 TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
         110         3377         2881         2746         3074         2839 
TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4173 TCGA-BP-4174 
        3037           13         2718          701         1893         1879 
TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 
        1955         1670         2964         1625          845         1888 
TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4338 TCGA-BP-4344 TCGA-BP-4347 
        1133          645          461         2859         1666         1367 
TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 
         372          970          374         2208         2372         2361 
TCGA-BP-4761 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4774 
         182         2184         1462          400         1876         1885 
TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 
        1843          411         1731         2080          354         1854 
TCGA-BP-4789 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 
        1489          620         1107         1124          204         1459 
TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
         211         2660         2172         1935         1785         1834 
TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 
        1862         1871          205         1746         1794          433 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 
        1487         1502         1384         1433         1632          454 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 
        1014         1413          785         1124          118         1413 
TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 
         501          177         1308         1371          932         1266 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 
         563         1177         1126          840         1140         1071 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5177 TCGA-BP-5180 
         193         2412         2257          932          293         2263 
TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
        1495         1165         1291         1133         1132          693 
TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 
         406          822         1011          967          714          408 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 
         749         1018          603         1355         1063          951 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4639 TCGA-CJ-4640 
          29         1820         1416         1924         2308         1998 
TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
        1628         1793          646         2554         1498         2423 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
        1435         2259         2283         2353         1955         2186 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4889 
        2014         1883         1759         2125         1952         1946 
TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4897 TCGA-CJ-4899 
        2085         1521          750          841         1808         1528 
TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 
        1450         1520         1560         1792         1496         1499 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-5671 TCGA-CJ-5675 TCGA-CJ-5676 
        1531         1657         1373         1943         2430         2575 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 
         552         1883         1889         2231         2038         1855 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5587 
        1906         2548         2799         2489         2609         2226 
TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 
        2017         2378         2271         3222         2552         3146 
TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4862 
         774         1404           18         1943         1787         1843 
TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 
        1928         2830         1868         1929         1789           25 
TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 
        1712         1683         1732         1683         1430          330 
TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5469 
         662         1740         1446          685           59          946 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 
         386         2439         2067         1997          373          435 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 
         693         1905         1329         1398         1470          370 
TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5905 
         355         1130          723         1729          551          119 
TCGA-EU-5906 TCGA-EU-5907 TCGA-GK-A6C7 
         206          127           61 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              1130                  3 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              1130               3668 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              1130               1307 
[1] "1130.0 - 1130.0 (1130.0)" "3.0 - 3668.0 (1307.0)"   
[1] "Remove cluster labels:" "19Q LOSS MUTATED"      
D74V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  19Q LOSS MUTATED         1        0         1        2
  19Q LOSS WILD-TYPE     243       56       125       77
D74V3, multiclass
           clus
vv          19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  STAGE I                  1                243
  STAGE II                 0                 56
  STAGE III                1                125
  STAGE IV                 2                 77
[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"
                    vv
clus                  T1  T2  T3  T4
  19Q LOSS MUTATED     1   0   1   2
  19Q LOSS WILD-TYPE 249  67 176   9
D74V4, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  T1                1                249
  T2                0                 67
  T3                1                176
  T4                2                  9
[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"
D74V5, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED     1   0
  19Q LOSS WILD-TYPE 229  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      1    0
  19Q LOSS WILD-TYPE  229   18
   clus
vv  19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  0                1                229
  1                0                 18
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  19Q LOSS MUTATED     2   2   0
  19Q LOSS WILD-TYPE 415  76   9
D74V6, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  M0                2                415
  M1                2                 76
  MX                0                  9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V7, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED     1   3
  19Q LOSS WILD-TYPE 177 324
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      1    3
  19Q LOSS WILD-TYPE  177  324
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE                1                177
  MALE                  3                324
[1] 2 2
[1] FALSE
D74V8, continuous
[1] "Remove cluster labels:" "19Q LOSS MUTATED"      
clus
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 1                 36 
        TCGA-A3-A8CQ         TCGA-AK-3426         TCGA-AK-3430 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-B0-4838         TCGA-B2-5639         TCGA-B4-5377 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-B4-5378         TCGA-B4-5832         TCGA-B4-5834 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-B4-5835         TCGA-B4-5836         TCGA-B4-5838 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-B4-5843         TCGA-B4-5844         TCGA-CZ-4854 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CZ-4856         TCGA-CZ-4858         TCGA-CZ-4861 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CZ-4862         TCGA-CZ-5456         TCGA-CZ-5457 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CZ-5465         TCGA-CZ-5469         TCGA-CZ-5982 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DV-5565         TCGA-DV-5566         TCGA-DV-5567 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DV-5568         TCGA-DV-5569         TCGA-DV-5573 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DV-5574         TCGA-DV-5575         TCGA-DV-5576 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EU-5904         TCGA-EU-5905         TCGA-EU-5907 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
D74V9, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19Q LOSS MUTATED       0                         0     4
  19Q LOSS WILD-TYPE     8                        33   453
D74V10, multiclass
                           clus
vv                          19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  ASIAN                                    0                  8
  BLACK OR AFRICAN AMERICAN                0                 33
  WHITE                                    4                453
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V11, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED     0   1
  19Q LOSS WILD-TYPE  24 329
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      0    1
  19Q LOSS WILD-TYPE   24  329
                        clus
vv                       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 24
  NOT HISPANIC OR LATINO                1                329
[1] 2 2
[1] FALSE

Clustering(75) Variable = 20P LOSS MUTATION ANALYSIS
D75V1, survival
                    sevent
clus2                  0   1
  20P LOSS MUTATED     5   0
  20P LOSS WILD-TYPE 333  26
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 5                359 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 0                 26 
$`20P LOSS MUTATED`
TCGA-A3-3319 TCGA-BP-4962 TCGA-BP-5000 TCGA-BP-5182 TCGA-BP-5184 
        1130         1785          563         1165         1133 

$`20P LOSS WILD-TYPE`
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 
        1120         1436           16          735         1493         1491 
TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 
        1508         1478         1106         1186          751         1137 
TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3347 TCGA-A3-3349 
        1485          665         1043          945         1610         1385 
TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 
         910         2688         1307         2504         1559          319 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 
         873         2270         2274          735         1621         1314 
TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 
        1070          630          567          574          861         1993 
TCGA-A3-3387 TCGA-A3-A8CQ TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
         617            3         3343         2566         2223         2017 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
         480         1853         2192         2087         2044         1745 
TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 
        1423         1471         1280         1217         1779         1481 
TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
        1397          874         1143         1168          951          853 
TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4699 TCGA-B0-4706 TCGA-B0-4710 
         369         1238           43          110           26           96 
TCGA-B0-4718 TCGA-B0-4813 TCGA-B0-4819 TCGA-B0-5097 TCGA-B0-5108 TCGA-B0-5110 
         616           18          183          665          911         1092 
TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 
         359          797          657          535           59          493 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 
         554          652         1132          449         2408         3431 
TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 
        1487         3076         1420         1727         1835         2583 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
        2741         1732         1605         1203         3668         2414 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 
        3117         1459         2931         2722         1865         2963 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 
         992         1092           51          374          648          952 
TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 
         358          315          417          656          507          291 
TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
         175            7           38           16          141          166 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
          11            7          511          826          838          762 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 
         750          523          777          788          700          636 
TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
         722           36          822           26          737          522 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
         505          194          434           15         1046          435 
TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J 
         830          519           53          256          150           66 
TCGA-B8-A7U6 TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
         110         3377         2881         2746         3074         2839 
TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4173 TCGA-BP-4174 
        3037           13         2718          701         1893         1879 
TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 
        1955         1670         2964         1625          845         1888 
TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4338 TCGA-BP-4344 TCGA-BP-4347 
        1133          645          461         2859         1666         1367 
TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 
         372          970          374         2208         2372         2361 
TCGA-BP-4761 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4774 
         182         2184         1462          400         1876         1885 
TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 
        1843          411         1731         2080          354         1854 
TCGA-BP-4789 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 
        1489          620         1107         1124          204         1459 
TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4963 TCGA-BP-4964 
         211         2660         2172         1935         1834         1862 
TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 
        1871          205         1746         1794          433         1487 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4982 
        1502         1384         1433         1632          454         1014 
TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
        1413          785         1124          118         1413          501 
TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5001 
         177         1308         1371          932         1266         1177 
TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5169 TCGA-BP-5170 
        1126          840         1140         1071          193         2412 
TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5183 
        2257          932          293         2263         1495         1291 
TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 
        1132          693          406          822         1011          967 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 
         714          408          749         1018          603         1355 
TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 
        1063          951           29         1820         1416         1924 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 
        2308         1998         1628         1793          646         2554 
TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 
        1498         2423         1435         2259         2283         2353 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
        1955         2186         2014         1883         1759         2125 
TCGA-CJ-4886 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 
        1952         1946         2085         1521          750          841 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 
        1808         1528         1450         1520         1560         1792 
TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-5671 
        1496         1499         1531         1657         1373         1943 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
        2430         2575          552         1883         1889         2231 
TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CW-5581 TCGA-CW-5583 
        2038         1855         1906         2548         2799         2489 
TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6088 
        2609         2226         2017         2378         2271         3222 
TCGA-CW-6090 TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4858 
        2552         3146          774         1404           18         1943 
TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 
        1787         1843         1928         2830         1868         1929 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 
        1789           25         1712         1683         1732         1683 
TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 
        1430          330          662         1740         1446          685 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
          59          946          386         2439         2067         1997 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
         373          435          693         1905         1329         1398 
TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 
        1470          370          355         1130          723         1729 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-GK-A6C7 
         551          119          206          127           61 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
               563                  3 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
              1785               3668 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
              1133               1308 
[1] "563.0 - 1785.0 (1133.0)" "3.0 - 3668.0 (1308.0)"  
[1] "hr="     "9100000"
D75V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  20P LOSS MUTATED         4        1         1        2
  20P LOSS WILD-TYPE     240       55       125       77
D75V3, multiclass
           clus
vv          20P LOSS MUTATED 20P LOSS WILD-TYPE
  STAGE I                  4                240
  STAGE II                 1                 55
  STAGE III                1                125
  STAGE IV                 2                 77
[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"
                    vv
clus                  T1  T2  T3  T4
  20P LOSS MUTATED     4   2   2   0
  20P LOSS WILD-TYPE 246  65 175  11
D75V4, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  T1                4                246
  T2                2                 65
  T3                2                175
  T4                0                 11
[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"
D75V5, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     3   0
  20P LOSS WILD-TYPE 227  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      3    0
  20P LOSS WILD-TYPE  227   18
   clus
vv  20P LOSS MUTATED 20P LOSS WILD-TYPE
  0                3                227
  1                0                 18
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  20P LOSS MUTATED     6   2   0
  20P LOSS WILD-TYPE 411  76   9
D75V6, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  M0                6                411
  M1                2                 76
  MX                0                  9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V7, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     3   5
  20P LOSS WILD-TYPE 175 322
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      3    5
  20P LOSS WILD-TYPE  175  322
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  FEMALE                3                175
  MALE                  5                322
[1] 2 2
[1] FALSE
D75V8, continuous
D75V9, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20P LOSS MUTATED       1                         0     7
  20P LOSS WILD-TYPE     7                        33   450
D75V10, multiclass
                           clus
vv                          20P LOSS MUTATED 20P LOSS WILD-TYPE
  ASIAN                                    1                  7
  BLACK OR AFRICAN AMERICAN                0                 33
  WHITE                                    7                450
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V11, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     1   3
  20P LOSS WILD-TYPE  23 327
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      1    3
  20P LOSS WILD-TYPE   23  327
                        clus
vv                       20P LOSS MUTATED 20P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 23
  NOT HISPANIC OR LATINO                3                327
[1] 2 2
[1] FALSE

Clustering(76) Variable = 20Q LOSS MUTATION ANALYSIS
D76V1, survival
                    sevent
clus2                  0   1
  20Q LOSS MUTATED     2   0
  20Q LOSS WILD-TYPE 336  26
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 2                362 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 0                 26 
$`20Q LOSS MUTATED`
TCGA-BP-4962 TCGA-BP-5000 
        1785          563 

$`20Q LOSS WILD-TYPE`
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 
        1120         1436           16          735         1493         1491 
TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 
        1130         1508         1478         1106         1186          751 
TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3347 
        1137         1485          665         1043          945         1610 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 
        1385          910         2688         1307         2504         1559 
TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 
         319          873         2270         2274          735         1621 
TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 
        1314         1070          630          567          574          861 
TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A8CQ TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 
        1993          617            3         3343         2566         2223 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 
        2017          480         1853         2192         2087         2044 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 
        1745         1423         1471         1280         1217         1779 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
        1481         1397          874         1143         1168          951 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4699 TCGA-B0-4706 
         853          369         1238           43          110           26 
TCGA-B0-4710 TCGA-B0-4718 TCGA-B0-4813 TCGA-B0-4819 TCGA-B0-5097 TCGA-B0-5108 
          96          616           18          183          665          911 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 
        1092          359          797          657          535           59 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 
         493          554          652         1132          449         2408 
TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 
        3431         1487         3076         1420         1727         1835 
TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 
        2583         2741         1732         1605         1203         3668 
TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
        2414         3117         1459         2931         2722         1865 
TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 
        2963          992         1092           51          374          648 
TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR 
         952          358          315          417          656          507 
TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
         291          175            7           38           16          141 
TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
         166           11            7          511          826          838 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 
         762          750          523          777          788          700 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
         636          722           36          822           26          737 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
         522          505          194          434           15         1046 
TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I 
         435          830          519           53          256          150 
TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 
          66          110         3377         2881         2746         3074 
TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4173 
        2839         3037           13         2718          701         1893 
TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 
        1879         1955         1670         2964         1625          845 
TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4338 TCGA-BP-4344 
        1888         1133          645          461         2859         1666 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 
        1367          372          970          374         2208         2372 
TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 
        2361          182         2184         1462          400         1876 
TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 
        1885         1843          411         1731         2080          354 
TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4801 TCGA-BP-4803 
        1854         1489          620         1107         1124          204 
TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4963 
        1459          211         2660         2172         1935         1834 
TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 
        1862         1871          205         1746         1794          433 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 
        1487         1502         1384         1433         1632          454 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 
        1014         1413          785         1124          118         1413 
TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 
         501          177         1308         1371          932         1266 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5169 
        1177         1126          840         1140         1071          193 
TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5181 
        2412         2257          932          293         2263         1495 
TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 
        1165         1291         1133         1132          693          406 
TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
         822         1011          967          714          408          749 
TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 
        1018          603         1355         1063          951           29 
TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4642 
        1820         1416         1924         2308         1998         1628 
TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 
        1793          646         2554         1498         2423         1435 
TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 
        2259         2283         2353         1955         2186         2014 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4889 TCGA-CJ-4890 
        1883         1759         2125         1952         1946         2085 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4901 
        1521          750          841         1808         1528         1450 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 
        1520         1560         1792         1496         1499         1531 
TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-5671 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5681 
        1657         1373         1943         2430         2575          552 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6031 
        1883         1889         2231         2038         1855         1906 
TCGA-CJ-6032 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 
        2548         2799         2489         2609         2226         2017 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CZ-4853 
        2378         2271         3222         2552         3146          774 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-4863 
        1404           18         1943         1787         1843         1928 
TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5456 
        2830         1868         1929         1789           25         1712 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5463 
        1683         1732         1683         1430          330          662 
TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 
        1740         1446          685           59          946          386 
TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 
        2439         2067         1997          373          435          693 
TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 
        1905         1329         1398         1470          370          355 
TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 
        1130          723         1729          551          119          206 
TCGA-EU-5907 TCGA-GK-A6C7 
         127           61 

  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
               563                  3 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
              1785               3668 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
              1174               1299 
[1] "563.0 - 1785.0 (1174.0)" "3.0 - 3668.0 (1299.0)"  
[1] "Remove cluster labels:" "20Q LOSS MUTATED"      
D76V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  20Q LOSS MUTATED         1        1         0        1
  20Q LOSS WILD-TYPE     243       55       126       78
D76V3, multiclass
           clus
vv          20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  STAGE I                  1                243
  STAGE II                 1                 55
  STAGE III                0                126
  STAGE IV                 1                 78
[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"
                    vv
clus                  T1  T2  T3  T4
  20Q LOSS MUTATED     1   2   0   0
  20Q LOSS WILD-TYPE 249  65 177  11
D76V4, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  T1                1                249
  T2                2                 65
  T3                0                177
  T4                0                 11
[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"
D76V5, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     0   0
  20Q LOSS WILD-TYPE 230  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      0    0
  20Q LOSS WILD-TYPE  230   18
                    vv
clus                  M0  M1  MX
  20Q LOSS MUTATED     2   1   0
  20Q LOSS WILD-TYPE 415  77   9
D76V6, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  M0                2                415
  M1                1                 77
  MX                0                  9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V7, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     1   2
  20Q LOSS WILD-TYPE 177 325
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      1    2
  20Q LOSS WILD-TYPE  177  325
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  FEMALE                1                177
  MALE                  2                325
[1] 2 2
[1] FALSE
D76V8, continuous
D76V9, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20Q LOSS MUTATED       0                         0     3
  20Q LOSS WILD-TYPE     8                        33   454
D76V10, multiclass
                           clus
vv                          20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  ASIAN                                    0                  8
  BLACK OR AFRICAN AMERICAN                0                 33
  WHITE                                    3                454
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V11, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     1   0
  20Q LOSS WILD-TYPE  23 330
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      1    0
  20Q LOSS WILD-TYPE   23  330
                        clus
vv                       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 23
  NOT HISPANIC OR LATINO                0                330
[1] 2 2
[1] FALSE

Clustering(77) Variable = 21Q LOSS MUTATION ANALYSIS
D77V1, survival
                    sevent
clus2                  0   1
  21Q LOSS MUTATED    35   3
  21Q LOSS WILD-TYPE 303  23
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                38                326 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 3                 23 
$`21Q LOSS MUTATED`
TCGA-A3-3317 TCGA-A3-3374 TCGA-AK-3427 TCGA-AK-3430 TCGA-AK-3433 TCGA-AK-3440 
        1491         1314         2566          480         2192         1745 
TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4699 TCGA-B0-4710 TCGA-B0-5117 TCGA-B0-5402 
         369         1238          110           96          535          449 
TCGA-B0-5695 TCGA-B0-5697 TCGA-B4-5838 TCGA-B8-4619 TCGA-B8-5553 TCGA-BP-4173 
        1420         1835          166          523          435         1893 
TCGA-BP-4325 TCGA-BP-4334 TCGA-BP-4768 TCGA-BP-4803 TCGA-BP-4960 TCGA-BP-4983 
        2964          645          400          204         2172         1413 
TCGA-BP-4994 TCGA-BP-5169 TCGA-BP-5198 TCGA-CJ-4881 TCGA-CJ-4897 TCGA-CJ-4901 
        1308          193          603         2014         1808         1450 
TCGA-CJ-4903 TCGA-CJ-4907 TCGA-CJ-5686 TCGA-CW-5588 TCGA-CZ-5457 TCGA-CZ-5458 
        1560         1499         2038         2017         1683         1732 
TCGA-CZ-5465 TCGA-CZ-5466 
        1446          685 

$`21Q LOSS WILD-TYPE`
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3319 
        1120         1436           16          735         1493         1130 
TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 
        1508         1478         1106         1186          751         1137 
TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3347 TCGA-A3-3349 
        1485          665         1043          945         1610         1385 
TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 
         910         2688         1307         2504         1559          319 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 
         873         2270         2274          735         1621         1070 
TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 
         630          567          574          861         1993          617 
TCGA-A3-A8CQ TCGA-AK-3425 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3431 TCGA-AK-3434 
           3         3343         2223         2017         1853         2087 
TCGA-AK-3436 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 
        2044         1423         1471         1280         1217         1779 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
        1481         1397          874         1143         1168          951 
TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4706 TCGA-B0-4718 TCGA-B0-4813 TCGA-B0-4819 
         853           43           26          616           18          183 
TCGA-B0-5097 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 
         665          911         1092          359          797          657 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5690 
          59          493          554          652         1132         2408 
TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5696 TCGA-B0-5698 TCGA-B0-5699 
        3431         1487         3076         1727         2583         2741 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 
        1732         1605         1203         3668         2414         3117 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 
        1459         2931         2722         1865         2963          992 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 
        1092           51          374          648          952          358 
TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 
         315          417          656          507          291          175 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 
           7           38           16          141           11            7 
TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4620 
         511          826          838          762          750          777 
TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 
         788          700          636          722           36          822 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 
          26          737          522          505          194          434 
TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H 
          15         1046          830          519           53          256 
TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4161 
         150           66          110         3377         2881         2746 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 
        3074         2839         3037           13         2718          701 
TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 
        1879         1955         1670         1625          845         1888 
TCGA-BP-4332 TCGA-BP-4335 TCGA-BP-4338 TCGA-BP-4344 TCGA-BP-4347 TCGA-BP-4349 
        1133          461         2859         1666         1367          372 
TCGA-BP-4351 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 
         970          374         2208         2372         2361          182 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 
        2184         1462         1876         1885         1843          411 
TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4795 
        1731         2080          354         1854         1489          620 
TCGA-BP-4797 TCGA-BP-4801 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4961 
        1107         1124         1459          211         2660         1935 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 
        1785         1834         1862         1871          205         1746 
TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4975 
        1794          433         1487         1502         1384         1433 
TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4982 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4989 
        1632          454         1014          785         1124          118 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 
        1413          501          177         1371          932         1266 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 
         563         1177         1126          840         1140         1071 
TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5181 
        2412         2257          932          293         2263         1495 
TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 
        1165         1291         1133         1132          693          406 
TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
         822         1011          967          714          408          749 
TCGA-BP-5196 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 
        1018         1355         1063          951           29         1820 
TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4642 TCGA-CJ-4643 
        1416         1924         2308         1998         1628         1793 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 
         646         2554         1498         2423         1435         2259 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4882 TCGA-CJ-4884 
        2283         2353         1955         2186         1883         1759 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 
        2125         1952         1946         2085         1521          750 
TCGA-CJ-4894 TCGA-CJ-4899 TCGA-CJ-4902 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4908 
         841         1528         1520         1792         1496         1531 
TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-5671 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5681 
        1657         1373         1943         2430         2575          552 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-6027 TCGA-CJ-6031 TCGA-CJ-6032 
        1883         1889         2231         1855         1906         2548 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-5591 
        2799         2489         2609         2226         2378         2271 
TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 
        3222         2552         3146          774         1404           18 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 
        1943         1787         1843         1928         2830         1868 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5456 TCGA-CZ-5459 TCGA-CZ-5460 
        1929         1789           25         1712         1683         1430 
TCGA-CZ-5461 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 
         330          662         1740           59          946          386 
TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 
        2439         2067         1997          373          435          693 
TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 
        1905         1329         1398         1470          370          355 
TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 
        1130          723         1729          551          119          206 
TCGA-EU-5907 TCGA-GK-A6C7 
         127           61 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                96                  3 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              2964               3668 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            1416.5             1241.5 
[1] "96.0 - 2964.0 (1416.5)" "3.0 - 3668.0 (1241.5)" 
[1] "hr=" "1.2"
D77V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  21Q LOSS MUTATED        20        4        18       11
  21Q LOSS WILD-TYPE     224       52       108       68
D77V3, multiclass
           clus
vv          21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  STAGE I                 20                224
  STAGE II                 4                 52
  STAGE III               18                108
  STAGE IV                11                 68
[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"
                    vv
clus                  T1  T2  T3  T4
  21Q LOSS MUTATED    20   5  23   5
  21Q LOSS WILD-TYPE 230  62 154   6
D77V4, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  T1               20                230
  T2                5                 62
  T3               23                154
  T4                5                  6
[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"
D77V5, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    21   4
  21Q LOSS WILD-TYPE 209  14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     21    4
  21Q LOSS WILD-TYPE  209   14
   clus
vv  21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  0               21                209
  1                4                 14
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  21Q LOSS MUTATED    45   8   0
  21Q LOSS WILD-TYPE 372  70   9
D77V6, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  M0               45                372
  M1                8                 70
  MX                0                  9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V7, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    17  36
  21Q LOSS WILD-TYPE 161 291
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     17   36
  21Q LOSS WILD-TYPE  161  291
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE               17                161
  MALE                 36                291
[1] 2 2
[1] FALSE
D77V8, continuous
D77V9, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  21Q LOSS MUTATED       1                         2    47
  21Q LOSS WILD-TYPE     7                        31   410
D77V10, multiclass
                           clus
vv                          21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  ASIAN                                    1                  7
  BLACK OR AFRICAN AMERICAN                2                 31
  WHITE                                   47                410
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V11, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED     2  34
  21Q LOSS WILD-TYPE  22 296
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      2   34
  21Q LOSS WILD-TYPE   22  296
                        clus
vv                       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                 22
  NOT HISPANIC OR LATINO               34                296
[1] 2 2
[1] FALSE

Clustering(78) Variable = 22Q LOSS MUTATION ANALYSIS
D78V1, survival
                    sevent
clus2                  0   1
  22Q LOSS MUTATED    17   5
  22Q LOSS WILD-TYPE 321  21
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                22                342 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 5                 21 
$`22Q LOSS MUTATED`
TCGA-A3-3347 TCGA-AK-3453 TCGA-AK-3456 TCGA-B0-5116 TCGA-B0-5701 TCGA-B2-4098 
        1610         1397         1143          657         1732           51 
TCGA-BP-4768 TCGA-BP-4960 TCGA-BP-4967 TCGA-BP-4986 TCGA-BP-4992 TCGA-BP-5175 
         400         2172          205          785          501          932 
TCGA-BP-5196 TCGA-CJ-4640 TCGA-CJ-4897 TCGA-CJ-4901 TCGA-CZ-4866 TCGA-CZ-5457 
        1018         1998         1808         1450         1868         1683 
TCGA-CZ-5461 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-DV-5566 
         330           59          946         1398 

$`22Q LOSS WILD-TYPE`
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 
        1120         1436           16          735         1493         1491 
TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 
        1130         1508         1478         1106         1186          751 
TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3349 
        1137         1485          665         1043          945         1385 
TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 
         910         2688         1307         2504         1559          319 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 
         873         2270         2274          735         1621         1314 
TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 
        1070          630          567          574          861         1993 
TCGA-A3-3387 TCGA-A3-A8CQ TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
         617            3         3343         2566         2223         2017 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
         480         1853         2192         2087         2044         1745 
TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 
        1423         1471         1280         1217         1779         1481 
TCGA-AK-3454 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 
         874         1168          951          853          369         1238 
TCGA-AS-3778 TCGA-B0-4699 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4718 TCGA-B0-4813 
          43          110           26           96          616           18 
TCGA-B0-4819 TCGA-B0-5097 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 
         183          665          911         1092          359          797 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
         535           59          493          554          652         1132 
TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 
         449         2408         3431         1487         3076         1420 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5702 TCGA-B0-5703 
        1727         1835         2583         2741         1605         1203 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
        3668         2414         3117         1459         2931         2722 
TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4099 TCGA-B2-4101 
        1865         2963          992         1092          374          648 
TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR 
         952          358          315          417          656          507 
TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
         291          175            7           38           16          141 
TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
         166           11            7          511          826          838 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 
         762          750          523          777          788          700 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
         636          722           36          822           26          737 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
         522          505          194          434           15         1046 
TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I 
         435          830          519           53          256          150 
TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 
          66          110         3377         2881         2746         3074 
TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4173 
        2839         3037           13         2718          701         1893 
TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 
        1879         1955         1670         2964         1625          845 
TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4338 TCGA-BP-4344 
        1888         1133          645          461         2859         1666 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 
        1367          372          970          374         2208         2372 
TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4774 
        2361          182         2184         1462         1876         1885 
TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 
        1843          411         1731         2080          354         1854 
TCGA-BP-4789 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 
        1489          620         1107         1124          204         1459 
TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 
         211         2660         1935         1785         1834         1862 
TCGA-BP-4965 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
        1871         1746         1794          433         1487         1502 
TCGA-BP-4973 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4982 TCGA-BP-4983 
        1384         1433         1632          454         1014         1413 
TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 
        1124          118         1413          177         1308         1371 
TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 
         932         1266          563         1177         1126          840 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5177 
        1140         1071          193         2412         2257          293 
TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 
        2263         1495         1165         1291         1133         1132 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 
         693          406          822         1011          967          714 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 
         408          749          603         1355         1063          951 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4639 TCGA-CJ-4642 
          29         1820         1416         1924         2308         1628 
TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 
        1793          646         2554         1498         2423         1435 
TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 
        2259         2283         2353         1955         2186         2014 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4889 TCGA-CJ-4890 
        1883         1759         2125         1952         1946         2085 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4899 TCGA-CJ-4902 TCGA-CJ-4903 
        1521          750          841         1528         1520         1560 
TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4916 
        1792         1496         1499         1531         1657         1373 
TCGA-CJ-5671 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
        1943         2430         2575          552         1883         1889 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CW-5581 
        2231         2038         1855         1906         2548         2799 
TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 
        2489         2609         2226         2017         2378         2271 
TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 
        3222         2552         3146          774         1404           18 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-5451 
        1943         1787         1843         1928         2830         1929 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5456 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
        1789           25         1712         1732         1683         1430 
TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5470 TCGA-CZ-5982 
         662         1740         1446          685          386         2439 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
        2067         1997          373          435          693         1905 
TCGA-DV-5565 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 
        1329         1470          370          355         1130          723 
TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-GK-A6C7 
        1729          551          119          206          127           61 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                51                  3 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              2172               3668 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            1080.5             1307.5 
[1] "51.0 - 2172.0 (1080.5)" "3.0 - 3668.0 (1307.5)" 
[1] "hr=" "4.2"
D78V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  22Q LOSS MUTATED        10        4        14       10
  22Q LOSS WILD-TYPE     234       52       112       69
D78V3, multiclass
           clus
vv          22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  STAGE I                 10                234
  STAGE II                 4                 52
  STAGE III               14                112
  STAGE IV                10                 69
[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"
                    vv
clus                  T1  T2  T3  T4
  22Q LOSS MUTATED    13   6  19   0
  22Q LOSS WILD-TYPE 237  61 158  11
D78V4, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  T1               13                237
  T2                6                 61
  T3               19                158
  T4                0                 11
[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"
D78V5, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    16   1
  22Q LOSS WILD-TYPE 214  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     16    1
  22Q LOSS WILD-TYPE  214   17
   clus
vv  22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  0               16                214
  1                1                 17
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  22Q LOSS MUTATED    28  10   0
  22Q LOSS WILD-TYPE 389  68   9
D78V6, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  M0               28                389
  M1               10                 68
  MX                0                  9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V7, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    12  26
  22Q LOSS WILD-TYPE 166 301
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     12   26
  22Q LOSS WILD-TYPE  166  301
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE               12                166
  MALE                 26                301
[1] 2 2
[1] FALSE
D78V8, continuous
D78V9, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  22Q LOSS MUTATED       0                         3    35
  22Q LOSS WILD-TYPE     8                        30   422
D78V10, multiclass
                           clus
vv                          22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  ASIAN                                    0                  8
  BLACK OR AFRICAN AMERICAN                3                 30
  WHITE                                   35                422
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V11, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED     5  23
  22Q LOSS WILD-TYPE  19 307
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      5   23
  22Q LOSS WILD-TYPE   19  307
                        clus
vv                       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    5                 19
  NOT HISPANIC OR LATINO               23                307
[1] 2 2
[1] FALSE

Clustering(79) Variable = XQ LOSS MUTATION ANALYSIS
D79V1, survival
                   sevent
clus2                 0   1
  XQ LOSS MUTATED    28   5
  XQ LOSS WILD-TYPE 310  21
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               33               331 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                5                21 
$`XQ LOSS MUTATED`
TCGA-A3-3306 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3382 TCGA-AK-3440 TCGA-AK-3445 
        1120         1491         1130          574         1745         1280 
TCGA-AK-3447 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4699 TCGA-B0-4813 TCGA-B0-5117 
        1217          369         1238          110           18          535 
TCGA-B0-5402 TCGA-B0-5705 TCGA-B2-3923 TCGA-B8-5159 TCGA-B8-5549 TCGA-B8-A54D 
         449         3668          992          722          194          830 
TCGA-BP-4334 TCGA-BP-4756 TCGA-BP-4761 TCGA-BP-4959 TCGA-BP-5004 TCGA-BP-5180 
         645          374          182         2660         1126         2263 
TCGA-BP-5196 TCGA-CJ-4642 TCGA-CJ-4894 TCGA-CJ-6027 TCGA-CW-6090 TCGA-CZ-5465 
        1018         1628          841         1855         2552         1446 
TCGA-CZ-5985 TCGA-CZ-5987 TCGA-EU-5907 
        1997          435          127 

$`XQ LOSS WILD-TYPE`
TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3320 TCGA-A3-3322 
        1436           16          735         1493         1508         1478 
TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 
        1106         1186          751         1137         1485          665 
TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 
        1043          945         1610         1385          910         2688 
TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 
        1307         2504         1559          319          873         2270 
TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 
        2274          735         1621         1314         1070          630 
TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A8CQ TCGA-AK-3425 
         567          861         1993          617            3         3343 
TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 
        2566         2223         2017          480         1853         2192 
TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3450 TCGA-AK-3451 
        2087         2044         1423         1471         1779         1481 
TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
        1397          874         1143         1168          951          853 
TCGA-AS-3778 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4718 TCGA-B0-4819 TCGA-B0-5097 
          43           26           96          616          183          665 
TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 
         911         1092          359          797          657           59 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5690 TCGA-B0-5691 
         493          554          652         1132         2408         3431 
TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 
        1487         3076         1420         1727         1835         2583 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5706 TCGA-B0-5709 
        2741         1732         1605         1203         2414         3117 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3924 
        1459         2931         2722         1865         2963         1092 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 
          51          374          648          952          358          315 
TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 
         417          656          507          291          175            7 
TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 
          38           16          141          166           11            7 
TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 
         511          826          838          762          750          523 
TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5162 TCGA-B8-5163 
         777          788          700          636           36          822 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5550 TCGA-B8-5551 
          26          737          522          505          434           15 
TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I 
        1046          435          519           53          256          150 
TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 
          66          110         3377         2881         2746         3074 
TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4173 
        2839         3037           13         2718          701         1893 
TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 
        1879         1955         1670         2964         1625          845 
TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4335 TCGA-BP-4338 TCGA-BP-4344 TCGA-BP-4347 
        1888         1133          461         2859         1666         1367 
TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4765 
         372          970         2208         2372         2361         2184 
TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 
        1462          400         1876         1885         1843          411 
TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4795 
        1731         2080          354         1854         1489          620 
TCGA-BP-4797 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 
        1107         1124          204         1459          211         2172 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 
        1935         1785         1834         1862         1871          205 
TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 
        1746         1794          433         1487         1502         1384 
TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4986 
        1433         1632          454         1014         1413          785 
TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 
        1124          118         1413          501          177         1308 
TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5006 
        1371          932         1266          563         1177          840 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5175 
        1140         1071          193         2412         2257          932 
TCGA-BP-5177 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 
         293         1495         1165         1291         1133         1132 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 
         693          406          822         1011          967          714 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 
         408          749          603         1355         1063          951 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4639 TCGA-CJ-4640 
          29         1820         1416         1924         2308         1998 
TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 
        1793          646         2554         1498         2423         1435 
TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 
        2259         2283         2353         1955         2186         2014 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4889 TCGA-CJ-4890 
        1883         1759         2125         1952         1946         2085 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4901 TCGA-CJ-4902 
        1521          750         1808         1528         1450         1520 
TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 
        1560         1792         1496         1499         1531         1657 
TCGA-CJ-4916 TCGA-CJ-5671 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5681 TCGA-CJ-5682 
        1373         1943         2430         2575          552         1883 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CW-5581 
        1889         2231         2038         1906         2548         2799 
TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 
        2489         2609         2226         2017         2378         2271 
TCGA-CW-6088 TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4858 
        3222         3146          774         1404           18         1943 
TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 
        1787         1843         1928         2830         1868         1929 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 
        1789           25         1712         1683         1732         1683 
TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5468 
        1430          330          662         1740          685           59 
TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5986 TCGA-CZ-5988 
         946          386         2439         2067          373          693 
TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 
        1905         1329         1398         1470          370          355 
TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 
        1130          723         1729          551          119          206 
TCGA-GK-A6C7 
          61 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               18                 3 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             3668              3431 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             1018              1371 
[1] "18.0 - 3668.0 (1018.0)" "3.0 - 3431.0 (1371.0)" 
[1] "hr=" "2.7"
D79V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  XQ LOSS MUTATED        20        6        10        9
  XQ LOSS WILD-TYPE     224       50       116       70
D79V3, multiclass
           clus
vv          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  STAGE I                20               224
  STAGE II                6                50
  STAGE III              10               116
  STAGE IV                9                70
[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"
                   vv
clus                 T1  T2  T3  T4
  XQ LOSS MUTATED    20   6  16   3
  XQ LOSS WILD-TYPE 230  61 161   8
D79V4, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  T1              20               230
  T2               6                61
  T3              16               161
  T4               3                 8
[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"
D79V5, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    14   2
  XQ LOSS WILD-TYPE 216  16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     14    2
  XQ LOSS WILD-TYPE  216   16
   clus
vv  XQ LOSS MUTATED XQ LOSS WILD-TYPE
  0              14               216
  1               2                16
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  XQ LOSS MUTATED    37   7   1
  XQ LOSS WILD-TYPE 380  71   8
D79V6, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  M0              37               380
  M1               7                71
  MX               1                 8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V7, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    11  34
  XQ LOSS WILD-TYPE 167 293
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     11   34
  XQ LOSS WILD-TYPE  167  293
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE              11               167
  MALE                34               293
[1] 2 2
[1] FALSE
D79V8, continuous
[1] "Remove cluster labels:" "XQ LOSS MUTATED"       
clus
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                2                35 
       TCGA-A3-A8CQ        TCGA-AK-3426        TCGA-AK-3430        TCGA-B0-4838 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-B2-5639        TCGA-B4-5377        TCGA-B4-5378        TCGA-B4-5832 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-B4-5834        TCGA-B4-5835        TCGA-B4-5836        TCGA-B4-5838 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-B4-5843        TCGA-B4-5844        TCGA-CZ-4854        TCGA-CZ-4856 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CZ-4858        TCGA-CZ-4860        TCGA-CZ-4861        TCGA-CZ-4862 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CZ-5456        TCGA-CZ-5457        TCGA-CZ-5469        TCGA-CZ-5982 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DV-5565        TCGA-DV-5566        TCGA-DV-5567        TCGA-DV-5568 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DV-5569        TCGA-DV-5573        TCGA-DV-5574        TCGA-DV-5575 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DV-5576        TCGA-EU-5904        TCGA-EU-5905 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
D79V9, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XQ LOSS MUTATED       1                         3    39
  XQ LOSS WILD-TYPE     7                        30   418
D79V10, multiclass
                           clus
vv                          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  ASIAN                                   1                 7
  BLACK OR AFRICAN AMERICAN               3                30
  WHITE                                  39               418
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V11, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     0  30
  XQ LOSS WILD-TYPE  24 300
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      0   30
  XQ LOSS WILD-TYPE   24  300
                        clus
vv                       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                24
  NOT HISPANIC OR LATINO              30               300
[1] 2 2
[1] FALSE
